Contacts of the helix formed by residues 5 - 24 (chain B) in PDB entry 1C3B
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 PRO 5 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ALA* 1.4 91.8 - - + +
6B GLN* 1.3 66.8 + - - +
7B GLN* 3.0 11.4 + - + +
8B ILE* 3.1 29.6 + - + +
9B ASN* 3.2 8.5 + - - +
34B TYR* 4.9 10.1 - - + -
39B TYR* 4.0 20.9 - - + +
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Residues in contact with GLN 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ALA 3.4 2.9 + - - -
5B PRO* 1.3 69.8 - - - +
7B GLN* 1.3 53.9 + - - +
9B ASN* 3.2 9.7 + - - +
10B ASP* 2.8 37.6 + - - +
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Residues in contact with GLN 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PRO* 4.6 8.7 - - + +
6B GLN* 1.3 80.0 - - - +
8B ILE* 1.3 63.7 + - + +
10B ASP* 3.2 5.8 + - - +
11B ILE* 3.2 28.1 + - - +
34B TYR* 4.1 16.5 + - - -
359B ALA 5.2 5.8 + - - -
360B LEU* 4.3 18.5 - - + +
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Residues in contact with ILE 8 (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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4B ALA* 4.6 2.7 - - + -
5B PRO* 3.1 22.5 + - + +
7B GLN* 1.3 74.9 - - + +
9B ASN* 1.3 65.7 + - - +
11B ILE* 3.2 8.7 - - - +
12B VAL* 3.1 34.8 + - + +
32B VAL* 4.3 13.9 - - + -
34B TYR* 3.5 45.1 - - + -
39B TYR* 3.8 20.4 - - + -
41B PHE* 3.7 25.4 - - + -
360B LEU* 4.1 20.0 - - + -
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Residues in contact with ASN 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ALA* 3.6 23.6 + - - +
5B PRO 3.2 8.3 + - - +
6B GLN* 3.2 13.1 + - - +
8B ILE* 1.3 78.5 - - - +
10B ASP* 1.3 63.6 + - - +
12B VAL* 4.0 1.2 - - - +
13B HIS* 3.0 27.8 + - - +
41B PHE* 3.1 30.5 - - - -
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Residues in contact with ASP 10 (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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6B GLN* 2.8 21.2 + - + +
7B GLN* 3.5 7.4 - - - +
8B ILE 3.2 0.2 - - - -
9B ASN* 1.3 72.5 - - - +
11B ILE* 1.3 67.2 + - + +
13B HIS* 4.0 2.3 - - - +
14B ARG* 2.6 73.3 + - - +
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Residues in contact with ILE 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B GLN* 3.2 8.2 + - + +
8B ILE* 3.2 11.7 - - - +
10B ASP* 1.3 78.0 - - - +
12B VAL* 1.3 61.3 + - + +
14B ARG* 3.3 5.1 + - - +
15B THR* 2.6 47.8 + - - +
355B GLN* 4.8 1.3 - - + +
356B ILE* 3.8 17.5 - - + +
359B ALA* 3.4 24.2 - - + -
360B LEU* 3.2 50.5 - - + -
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Residues in contact with VAL 12 (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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8B ILE* 3.1 20.1 + - + +
9B ASN 4.0 2.5 - - - +
11B ILE* 1.3 81.4 - - + +
13B HIS* 1.3 57.9 + - - +
16B ILE* 2.8 39.5 + - + +
30B VAL* 4.9 2.9 - - + -
32B VAL* 3.9 26.9 - - + -
41B PHE* 3.8 28.3 - - + -
43B TRP* 3.7 27.1 - - + -
356B ILE* 4.4 17.0 - - + -
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Residues in contact with HIS 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ASN 3.0 19.4 + - - +
10B ASP* 4.0 3.1 - - - +
12B VAL* 1.3 77.0 - - - +
14B ARG* 1.3 67.0 + - + +
17B THR* 2.7 66.7 + - + +
18B PRO* 3.3 2.6 - - - +
41B PHE* 5.9 0.2 - - - -
43B TRP* 5.0 7.0 - + - -
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Residues in contact with ARG 14 (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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10B ASP* 2.6 56.3 + - - +
11B ILE* 3.8 5.4 - - - +
13B HIS* 1.3 78.8 - - + +
15B THR* 1.3 59.4 + - - +
18B PRO* 2.8 23.5 - - - +
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Residues in contact with THR 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ILE* 2.6 33.5 + - - +
12B VAL 4.0 0.2 - - - -
14B ARG* 1.3 76.6 - - - +
16B ILE* 1.3 67.6 + - + +
18B PRO* 3.2 9.2 - - - +
19B LEU* 3.4 14.4 + - - +
352B ALA* 3.8 28.0 - - + +
355B GLN* 3.7 43.1 + - + +
356B ILE* 4.0 12.9 - - + +
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Residues in contact with ILE 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 VAL* 2.8 35.3 + - + +
15B THR* 1.3 78.2 - - + +
17B THR* 1.3 59.6 - - - +
19B LEU* 3.0 10.8 + - + +
20B ILE* 2.7 49.8 + - + +
28B MET* 3.7 22.2 - - + -
30B VAL* 4.4 8.3 - - + -
43B TRP* 3.5 19.3 - - + -
338B MET* 4.7 7.0 - - + -
352B ALA* 4.2 13.9 - - + -
356B ILE* 3.4 27.4 - - + -
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Residues in contact with THR 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B HIS* 2.7 53.8 + - + +
16B ILE* 1.3 75.3 - - - +
18B PRO* 1.3 66.4 - - - +
20B ILE* 3.2 4.1 + - - +
21B GLU* 3.1 41.7 + - + +
43B TRP* 3.5 23.9 + - + +
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Residues in contact with PRO 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B HIS 3.3 7.6 - - - +
14B ARG* 2.8 31.2 - - - +
15B THR 3.2 9.6 - - - +
17B THR* 1.3 92.7 - - - +
19B LEU* 1.3 55.1 + - - +
21B GLU* 3.0 11.3 + - + +
22B GLN* 2.8 45.7 + - - +
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Residues in contact with LEU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B THR 3.4 13.0 + - - +
16B ILE* 3.0 17.3 + - + +
18B PRO* 1.3 80.2 - - - +
20B ILE* 1.3 61.4 + - - +
22B GLN* 4.3 13.2 - - - +
23B GLN* 2.9 45.0 + - + +
25B ILE* 4.7 4.0 - - + -
28B MET* 4.9 9.6 - - + -
338B MET* 5.6 0.9 - - - -
344B TYR* 4.0 24.7 - - + +
348B ALA* 4.0 25.8 - - + +
349B ARG* 5.2 0.2 - - - -
352B ALA* 4.0 23.8 - - + -
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Residues in contact with ILE 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ILE* 2.7 44.7 + - + +
17B THR* 3.2 6.5 + - - +
19B LEU* 1.3 72.8 - - + +
21B GLU* 1.3 70.8 + - - +
24B LYS* 2.9 23.7 + - - -
25B ILE* 3.0 38.6 + - + +
28B MET* 4.1 19.7 - - + -
43B TRP* 3.4 45.5 - - + +
44B GLY* 6.6 0.2 - - - -
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Residues in contact with GLU 21 (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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17B THR* 3.1 32.8 + - + +
18B PRO* 3.0 11.1 + - + +
20B ILE* 1.3 88.6 - - - +
22B GLN* 1.3 67.4 + - + +
24B LYS* 3.1 19.3 + - - +
43B TRP* 5.8 1.2 - - - -
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Residues in contact with GLN 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B PRO* 2.8 36.7 + - - +
19B LEU* 4.1 15.3 - - - +
21B GLU* 1.3 75.4 - - + +
23B GLN* 1.3 69.1 + - + +
24B LYS* 3.9 8.1 - - - +
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Residues in contact with GLN 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU* 2.9 36.9 + - + +
22B GLN* 1.3 81.6 + - + +
24B LYS* 1.3 74.7 + - - +
25B ILE* 3.6 17.5 - - + -
342B LYS* 2.9 25.0 - - - +
344B TYR* 3.6 31.6 - - + +
345B PRO* 3.6 17.1 - - - +
348B ALA* 4.4 9.6 - - - +
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Residues in contact with LYS 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 ILE 2.9 10.1 + - - -
21B GLU* 3.1 14.3 + - - +
22B GLN 3.9 7.0 - - - +
23B GLN* 1.3 86.9 - - - +
25B ILE* 1.3 62.0 + - - +
26B PRO* 3.4 9.7 - - - +
342B LYS* 3.6 12.6 + - - +
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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
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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) + - + + + + + -
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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