Contacts of the helix formed by residues 9 - 31 (chain B) in PDB entry 4PBY
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 ASP 9 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B PHE* 1.3 104.7 - - - +
10B ASP* 1.3 63.3 + - - +
11B ALA 3.0 1.0 + - - -
12B VAL* 3.3 21.9 + - + +
13B GLU* 3.6 14.0 + - - +
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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
----------------------------------------------------------
8B PHE 3.0 25.7 + - - -
9B ASP* 1.3 76.7 + - - +
11B ALA* 1.3 66.0 + - - +
13B GLU* 5.0 3.3 - - - +
14B GLU* 5.1 4.2 + - - +
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Residues in contact with ALA 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PHE* 2.8 15.3 + - - +
10B ASP* 1.3 81.4 + - - +
12B VAL* 1.3 61.9 + - - +
13B GLU 3.2 2.5 - - - -
14B GLU* 3.3 33.4 + - - +
15B ARG* 3.5 6.9 + - - +
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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
----------------------------------------------------------
8B PHE* 2.8 60.2 + - + +
9B ASP* 3.3 15.4 + - - +
11B ALA* 1.3 71.9 - - - +
13B GLU* 1.3 66.1 + - - +
15B ARG* 3.5 18.9 + - + +
16B VAL* 3.5 15.4 - - + +
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Residues in contact with GLU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ASP 3.6 10.3 + - - +
10B ASP 5.3 3.6 - - - +
12B VAL* 1.3 76.8 - - - +
14B GLU* 1.3 67.1 + - - +
15B ARG 3.1 0.2 - - - -
16B VAL* 2.9 21.1 + - + +
17B ILE* 3.0 28.8 + - + +
340B ARG* 2.7 32.3 + - - +
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Residues in contact with GLU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ASP 5.1 2.3 + - - +
11B ALA* 3.3 29.3 + - - +
13B GLU* 1.3 80.1 + - - +
15B ARG* 1.3 58.8 + - - +
17B ILE* 3.7 14.5 - - + +
18B ASN* 2.9 38.4 + - - +
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Residues in contact with ARG 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ALA 3.5 5.8 + - - +
12B VAL* 3.5 14.5 + - + +
13B GLU 3.1 0.6 - - - -
14B GLU* 1.3 79.2 - - - +
16B VAL* 1.3 60.9 + - + +
18B ASN* 3.3 11.7 + - - +
19B GLU* 3.1 46.9 + - + +
22B LYS* 5.8 2.0 - - - +
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Residues in contact with VAL 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B VAL* 3.5 20.4 - - + +
13B GLU* 2.9 11.4 + - + +
15B ARG* 1.3 78.0 - - + +
17B ILE* 1.3 56.3 + - - +
19B GLU* 3.2 7.0 + - + +
20B GLU* 2.7 58.7 + - + +
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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
----------------------------------------------------------
13B GLU* 3.0 35.3 + - + +
14B GLU* 3.7 16.8 - - + +
16B VAL* 1.3 76.4 - - - +
18B ASN* 1.3 61.1 + - - +
20B GLU* 3.7 5.2 - - - +
21B TYR* 2.8 32.4 + - - +
340B ARG* 3.4 47.3 - - - +
374B THR* 3.8 38.5 - - + +
685D TYR* 6.1 0.2 - - - -
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Residues in contact with ASN 18 (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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14B GLU* 2.9 29.7 + - - +
15B ARG* 3.3 17.1 + - - +
16B VAL 3.2 0.6 - - - -
17B ILE* 1.3 82.5 - - - +
19B GLU* 1.3 67.8 + - - +
21B TYR* 3.2 8.9 + - - +
22B LYS* 3.2 35.9 + - - +
374B THR* 5.7 1.7 - - - +
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Residues in contact with GLU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ARG* 3.1 32.2 + - + +
16B VAL* 3.2 9.8 + - + +
18B ASN* 1.3 79.6 - - - +
20B GLU* 1.3 64.7 + - + +
22B LYS* 3.3 38.0 + - - +
23B ILE* 3.5 21.5 + - + +
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Residues in contact with GLU 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B VAL* 2.7 41.9 + - + +
17B ILE* 4.1 4.5 - - - +
19B GLU* 1.3 73.2 - - + +
21B TYR* 1.3 62.6 + - - +
22B LYS 3.2 0.2 - - - -
23B ILE* 3.5 9.8 + - + +
24B TRP 3.1 17.0 + - - -
340B ARG* 5.8 2.1 + - - -
341B ARG* 5.1 3.6 + - - -
685D TYR* 3.3 57.5 - - + +
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Residues in contact with TYR 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ILE 2.8 18.4 + - - +
18B ASN* 3.2 7.4 + - - +
20B GLU* 1.3 76.3 - - - +
22B LYS* 1.3 71.3 + - + +
24B TRP* 3.4 30.1 + + - +
25B LYS* 3.0 38.9 + - + +
37B THR* 5.6 5.9 + - - +
371B GLY 5.0 1.8 - - - +
372B GLY 3.5 24.0 - - - -
373B HIS 5.8 0.2 - - - +
374B THR* 3.7 27.1 - - + -
400B GLN* 5.2 2.8 + - - -
685D TYR* 4.9 4.0 - - - -
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Residues in contact with LYS 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B ARG* 5.8 1.6 - - - +
18B ASN* 3.2 24.0 + - - +
19B GLU* 3.6 34.9 + - - +
20B GLU 3.2 0.4 - - - -
21B TYR* 1.3 86.4 - - + +
23B ILE* 1.3 58.5 + - + +
25B LYS* 3.4 7.1 + - - +
26B LYS* 3.0 26.0 + - - +
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Residues in contact with ILE 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B GLU* 3.5 18.9 + - + +
20B GLU* 3.9 9.9 - - + +
21B TYR 3.3 0.4 - - - -
22B LYS* 1.3 76.8 - - + +
24B TRP* 1.3 64.2 + - - +
26B LYS* 3.2 19.3 + - + +
27B ASN* 3.0 32.3 + - - +
685D TYR 3.5 34.5 - - - +
686D LYS* 3.8 11.4 - - - +
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Residues in contact with TRP 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B GLU 3.1 14.1 + - - +
21B TYR* 3.4 46.2 + + - +
23B ILE* 1.3 76.7 - - - +
25B LYS* 1.3 77.9 + - + +
27B ASN* 3.1 5.5 + - - +
28B THR* 3.1 48.5 + - + +
31B LEU* 4.9 4.0 - - + -
32B TYR* 2.8 36.5 + + - -
35B VAL* 4.2 14.6 - - + -
37B THR* 5.2 1.6 - - - -
370B HIS* 4.2 4.7 - + - -
371B GLY* 3.6 26.7 - - - +
372B GLY* 3.3 25.0 - - - +
400B GLN* 3.8 13.5 - - - -
684D PRO* 3.4 25.3 + - + +
685D TYR* 4.2 4.3 - - + -
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Residues in contact with LYS 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PHE* 3.4 42.7 - - + -
21B TYR* 3.0 31.4 + - + +
22B LYS* 3.5 12.1 - - - +
24B TRP* 1.3 92.4 - - + +
26B LYS* 1.3 62.1 + - - +
28B THR* 2.7 30.5 + - + +
98B TYR 4.7 6.0 + - - -
99B ASP* 6.2 0.6 - - - +
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Residues in contact with LYS 26 (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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4A LYS* 5.5 13.7 - - + +
7A ALA* 6.1 4.5 - - + -
8A PHE* 4.6 14.0 - - - +
11A ALA* 5.4 0.5 - - - +
22B LYS 3.0 13.3 + - - +
23B ILE* 3.4 20.2 - - + +
25B LYS* 1.3 76.7 - - - +
27B ASN* 1.3 88.7 + - - +
29B PRO* 3.3 18.0 - - - +
30B PHE* 4.2 12.2 - - + -
686D LYS* 3.9 19.4 + - - -
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Residues in contact with ASN 27 (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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23B ILE* 3.0 18.2 + - - +
24B TRP 3.1 9.5 + - - +
26B LYS* 1.3 94.0 + - - +
28B THR* 1.3 63.0 + - - +
29B PRO* 3.1 5.2 - - - -
30B PHE* 3.1 28.0 + - + +
31B LEU* 3.3 29.9 + - + +
680D ALA* 6.3 2.9 - - - -
683D ARG 4.2 2.4 + - - -
684D PRO 3.1 20.9 + - - +
686D LYS* 3.0 25.3 + - - +
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Residues in contact with THR 28 (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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8A PHE* 3.2 19.1 - - - -
24B TRP* 3.1 53.7 + - + +
25B LYS* 2.7 26.9 + - + +
27B ASN* 1.3 74.8 - - - +
29B PRO* 1.4 65.4 - - - +
32B TYR* 3.1 39.3 + - + -
35B VAL* 4.5 8.1 - - + -
98B TYR* 3.5 14.4 - - - +
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Residues in contact with PRO 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A PHE* 3.9 19.3 - - + -
11A ALA* 3.8 34.3 - - + +
12A VAL* 3.8 24.2 - - + +
15A ARG* 2.8 36.0 + - + +
25B LYS 4.1 0.9 - - - +
26B LYS 3.3 11.7 - - - +
27B ASN 3.1 6.5 - - - -
28B THR* 1.4 97.3 - - - +
30B PHE* 1.3 57.6 + - + +
32B TYR 3.6 0.2 - - - +
98B TYR* 3.4 15.9 + - + -
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Residues in contact with PHE 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ALA* 3.6 32.3 - - + -
14A GLU* 6.1 3.4 - - + -
15A ARG* 4.0 12.5 + - - +
26B LYS* 4.2 14.6 - - + -
27B ASN* 3.1 29.8 + - + +
29B PRO* 1.3 79.1 - - + +
31B LEU* 1.3 66.9 + - + +
405B ALA* 3.7 14.4 - - - +
677D THR* 3.8 19.9 + - + +
680D ALA* 5.8 3.6 - - + -
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Residues in contact with LEU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TRP* 4.9 3.6 - - + -
27B ASN* 3.3 31.8 + - + +
28B THR 3.3 0.2 + - - -
30B PHE* 1.3 82.6 - - + +
32B TYR* 1.3 77.6 + - + +
368B PHE* 3.9 13.5 - - + -
369B ILE 5.4 0.4 - - - +
404B MET* 3.4 4.3 - - - -
405B ALA* 2.6 28.7 + - - +
408B ILE* 3.4 9.0 - - + +
677D THR* 4.5 7.0 - - + +
680D ALA* 3.8 43.5 - - + +
681D ALA* 3.8 10.8 - - + +
683D ARG 5.3 0.2 - - - +
684D PRO* 4.3 19.1 - - + -
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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) + - + + + + + -
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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