Contacts of the helix formed by residues 8 - 30 (chain B) in PDB entry 5NC5
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 8 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B PHE* 2.8 62.1 + - + +
5B PHE* 3.3 18.0 + - + +
6B ILE 3.3 1.0 - - - -
7B ASP* 1.3 94.2 + - - +
9B PRO* 1.3 67.2 - - - +
10B ILE 3.2 2.5 - - - -
11B PHE* 3.4 10.0 + - + +
12B ALA* 3.1 16.3 + - - +
1121B D12 3.3 38.9 - - + +
893C GLU* 2.8 26.9 - - + +
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Residues in contact with PRO 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PHE 3.6 0.6 - - - -
6B ILE 4.0 7.0 - - - +
7B ASP 3.4 7.9 - - - +
8B ARG* 1.3 91.5 - - - +
10B ILE* 1.3 58.8 + - + +
12B ALA* 3.3 2.9 + - - +
13B TRP* 2.9 36.6 + - + +
491B ALA* 3.9 18.6 - - + +
495B THR* 3.9 29.4 - - + +
1103B D10 4.5 18.8 - - + -
893C GLU* 3.5 7.2 - - + +
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Residues in contact with ILE 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PRO* 1.3 72.5 - - + +
11B PHE* 1.3 58.6 + - - +
13B TRP* 2.9 8.6 + - - +
14B VAL* 2.7 28.2 + - - +
1103B D10 4.6 9.4 - - + -
889C ALA* 3.7 37.7 - - + +
890C ALA 4.7 0.2 - - - +
893C GLU* 2.8 23.9 + - - +
894C SER* 3.4 11.9 - - - +
895C TRP* 3.2 64.2 - - + +
1103C D12 5.1 3.8 - - + -
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Residues in contact with PHE 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PHE* 3.9 21.3 - + - -
5B PHE* 3.6 18.4 - + + -
8B ARG* 3.4 12.2 + - + +
10B ILE* 1.3 77.7 - - - +
12B ALA* 1.3 63.7 + - - +
14B VAL* 3.1 14.2 + - + +
15B ILE* 3.1 30.0 + - + +
1109B DD9 4.7 16.6 - - + -
1114B D10 6.1 0.2 - - + -
1118B D10 5.7 3.1 - - + -
1121B D12 3.8 60.1 - - + -
890C ALA* 3.9 23.3 - - + +
893C GLU* 3.5 16.8 + - - +
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Residues in contact with ALA 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PHE* 3.9 7.3 - - + -
8B ARG 3.1 13.0 + - - +
9B PRO 3.6 7.4 - - - +
10B ILE 3.2 0.2 - - - -
11B PHE* 1.3 74.3 - - - +
13B TRP* 1.3 57.9 + - - +
15B ILE* 3.3 4.9 + - - +
16B ALA* 3.0 27.5 + - - +
487B ILE* 3.5 37.4 - - + +
488B LEU* 3.9 15.0 - - + +
491B ALA* 3.9 11.9 - - + -
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Residues in contact with TRP 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PRO* 2.9 27.6 + - + +
10B ILE* 2.9 7.6 + - - +
12B ALA* 1.3 75.2 - - - +
14B VAL* 1.3 64.2 + - - +
16B ALA* 3.4 15.6 + - + +
17B ILE* 2.9 33.7 + - + +
20B MET* 5.8 4.0 - - + -
370B ILE* 4.1 28.3 - - + -
488B LEU* 4.7 6.5 - - + -
491B ALA* 6.4 0.7 - - + -
492B LEU* 3.6 28.1 - - + +
495B THR* 5.6 3.2 + - - -
496B MET* 5.4 0.4 - - - -
1103B D10 3.5 68.0 - - + +
1110B D10 3.8 37.7 - - + -
895C TRP* 4.1 14.6 - - + -
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Residues in contact with VAL 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ILE 2.7 18.4 + - - +
11B PHE* 3.1 10.1 + - + +
13B TRP* 1.3 73.2 - - - +
15B ILE* 1.3 69.0 + - + +
17B ILE* 2.9 18.8 + - - +
18B ILE* 2.9 30.2 + - + +
1121B D12 4.4 9.0 - - + -
886C LEU* 3.3 41.6 - - + +
889C ALA* 4.1 16.4 - - + -
890C ALA* 4.1 15.3 - - + +
895C TRP* 4.5 8.5 - - + -
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Residues in contact with ILE 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B PHE* 4.0 7.2 - - + -
11B PHE* 3.1 36.7 + - + +
12B ALA* 3.5 7.2 - - - +
14B VAL* 1.3 79.9 - - + +
16B ALA* 1.3 64.6 + - - +
18B ILE* 3.3 10.4 + - + +
19B ILE* 3.1 39.0 + - + +
487B ILE* 4.0 33.7 - - + -
1118B D10 4.4 30.3 - - + -
1121B D12 6.3 0.2 - - + -
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Residues in contact with ALA 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ALA 3.0 16.5 + - - +
13B TRP* 3.6 16.4 - - + +
15B ILE* 1.3 78.1 - - - +
17B ILE* 1.3 57.9 + - - +
19B ILE* 3.6 3.6 - - - +
20B MET* 3.0 37.3 + - - +
374B VAL* 4.3 18.7 - - + +
488B LEU* 4.1 28.3 - - + -
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Residues in contact with ILE 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B TRP* 2.9 38.0 + - + +
14B VAL* 2.9 12.0 + - - +
16B ALA* 1.3 72.0 - - - +
18B ILE* 1.3 69.6 + - - +
20B MET* 3.2 10.6 + - - +
21B LEU* 2.9 33.3 + - + +
1103B D10 4.2 32.8 - - + -
882C ILE* 6.0 0.4 - - + -
886C LEU* 3.7 29.4 - - + -
895C TRP* 3.9 22.7 - - + -
1103C D12 5.3 3.1 - - + -
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Residues in contact with ILE 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B VAL* 2.9 32.7 + - + +
15B ILE* 3.4 13.2 - - + +
17B ILE* 1.3 73.1 - - - +
19B ILE* 1.3 59.7 + - + +
21B LEU* 2.5 37.6 + - - +
22B ALA* 2.8 17.3 + - + -
1107B DD9 4.6 21.0 - - + +
1118B D10 4.8 26.7 - - + -
1121B D12 4.7 12.8 - - + -
886C LEU* 4.1 15.0 - - + -
1107C D12 5.4 13.9 - - + -
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Residues in contact with ILE 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ILE* 3.1 32.7 + - + +
16B ALA* 3.6 5.2 - - - +
18B ILE* 1.3 80.9 - - + +
20B MET* 1.3 59.8 + - - +
22B ALA* 3.8 7.7 - - - +
23B GLY* 2.8 24.3 + - - -
374B VAL* 3.4 27.6 - - + +
378B GLY* 3.3 29.3 + - - -
480B LEU* 4.2 16.8 - - + -
483B LEU* 6.5 0.9 - - + -
484B VAL* 5.3 5.4 - - + -
1118B D10 3.8 30.3 - - + -
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Residues in contact with MET 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B TRP* 5.8 4.3 - - + -
16B ALA* 3.0 25.7 + - - +
17B ILE* 3.7 8.1 - - - +
18B ILE 3.0 1.0 + - - -
19B ILE* 1.3 71.4 - - - +
21B LEU* 1.3 60.3 + - + +
24B GLY* 2.7 30.8 + - - -
370B ILE* 5.4 2.2 - - + +
373B PRO* 5.4 6.1 - - + -
374B VAL* 4.0 33.2 - - + +
377B LEU* 3.7 30.8 - - + +
1103B D10 5.0 10.8 - - + -
1110B D10 3.9 27.1 - - + -
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Residues in contact with LEU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ILE* 2.9 31.5 + - + +
18B ILE* 2.5 17.6 + - - +
20B MET* 1.3 70.1 - - + +
22B ALA* 1.3 57.0 + - - +
24B GLY* 3.1 1.6 + - - -
25B LEU* 2.8 31.4 + - - +
1107B DD9 4.1 42.7 - - + +
879C ILE* 4.6 4.3 - - + -
882C ILE* 4.3 25.6 - - + -
886C LEU* 4.7 4.5 - - + -
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Residues in contact with ALA 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ILE* 2.8 17.8 + - + +
19B ILE* 3.9 8.7 - - - +
21B LEU* 1.3 72.5 - - - +
23B GLY* 1.3 65.3 + - - +
25B LEU* 3.3 5.3 + - - +
26B ALA* 3.0 22.5 + - - +
381B ALA* 3.7 19.7 - - + +
1107B DD9 4.3 20.1 - - + +
1118B D10 5.0 11.2 - - + -
1104C D10 5.9 5.6 - - + -
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Residues in contact with GLY 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ILE 2.8 15.5 + - - -
20B MET 3.8 0.7 - - - -
22B ALA* 1.3 77.5 - - - +
24B GLY* 1.3 56.5 + - - +
26B ALA* 3.2 2.3 + - - +
27B ILE* 2.8 39.0 + - - +
377B LEU* 3.4 30.7 - - - -
381B ALA* 3.8 6.7 - - - +
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Residues in contact with GLY 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B MET 2.7 22.3 + - - -
21B LEU* 3.6 1.3 - - - -
23B GLY* 1.3 70.4 - - - +
25B LEU* 1.3 64.9 + - - +
27B ILE* 3.3 19.8 + - - +
28B LEU* 3.4 19.4 + - - +
377B LEU* 4.1 4.8 - - - +
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Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B LEU 2.8 16.5 + - - +
22B ALA* 3.6 5.6 - - - +
24B GLY* 1.3 78.5 - - - +
26B ALA* 1.3 60.8 + - - +
28B LEU* 2.9 29.3 + - + +
29B LYS* 3.2 31.2 + - + +
1107B DD9 3.6 33.4 - - + +
1104C D10 4.3 24.5 - - + -
1107C D12 4.3 20.4 - - + -
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Residues in contact with ALA 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ALA 3.0 13.9 + - - +
23B GLY 3.4 8.3 - - - +
25B LEU* 1.3 78.8 - - - +
27B ILE* 1.3 62.9 + - - +
29B LYS* 4.6 3.6 - - - +
30B LEU* 2.9 33.8 + - + +
380B PHE* 3.3 35.0 - - + +
381B ALA* 3.8 4.3 - - - +
384B ALA* 3.9 12.6 - - + -
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Residues in contact with ILE 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLY 2.8 28.7 + - - +
24B GLY* 3.4 12.3 - - - +
25B LEU 3.2 0.2 - - - -
26B ALA* 1.3 75.7 - - - +
28B LEU* 1.3 70.5 + - + +
30B LEU* 4.4 7.9 + - + +
377B LEU* 3.7 17.3 - - + -
380B PHE* 3.3 38.4 - - + -
1117B D10 3.2 56.3 - - + +
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Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLY 3.4 14.1 - - - +
25B LEU* 2.9 26.7 + - + +
27B ILE* 1.3 90.7 - - + +
29B LYS* 1.3 71.8 + - + +
30B LEU 3.6 0.9 - - - +
1117B D10 3.9 15.9 - - + +
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Residues in contact with LYS 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 3.2 34.4 + - + +
26B ALA* 4.5 2.9 - - - +
28B LEU* 1.3 84.2 - - - +
30B LEU* 1.3 67.3 + - - +
31B PRO* 3.4 7.1 - - - +
384B ALA* 6.2 0.9 - - + -
1107C D12 5.6 9.8 - - - +
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Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ALA 2.9 17.9 + - - +
27B ILE* 4.4 2.9 + - - +
28B LEU 3.6 2.2 - - - +
29B LYS* 1.3 77.9 - - - +
31B PRO* 1.3 70.1 - - + +
32B VAL* 3.7 10.0 + - - +
298B ASN* 4.5 4.2 + - - +
380B PHE* 4.2 29.4 - - + +
383B LEU* 4.7 7.0 - - + -
384B ALA* 3.0 45.8 - - + +
388B PHE 3.8 13.2 - - - +
389B SER 4.7 0.7 - - - -
390B ILE* 3.6 43.7 - - + +
1117B D10 4.4 6.9 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il