Contacts of the helix formed by residues 15 - 31 (chain A) in PDB entry 4N9W
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 GLY 15 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A VAL 3.5 2.4 + - - -
14A PRO* 1.3 76.4 - - - +
16A GLY* 1.3 60.7 + - - -
17A VAL 3.4 2.7 - - - -
18A GLN* 3.3 18.3 + - - +
19A SER* 3.0 32.4 + - - -
401A GDP 3.6 23.0 + - - -
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Residues in contact with GLY 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLY* 1.3 68.5 - - - -
17A VAL* 1.3 65.4 + - - +
18A GLN* 4.1 0.2 + - - -
19A SER* 4.0 2.6 - - - -
20A HIS* 3.0 26.0 + - - +
118A HIS* 5.4 2.0 - - - -
168A ASN* 5.1 4.4 + - - -
278A ILE* 4.7 8.7 - - - -
401A GDP 3.0 37.5 + - - -
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Residues in contact with VAL 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A CYS* 4.2 4.5 - - - -
8A PRO* 4.1 26.7 - - + -
9A TYR* 4.0 15.9 - - + -
15A GLY 3.4 0.4 - - - -
16A GLY* 1.3 74.3 - - - +
18A GLN* 1.3 70.7 + - - +
20A HIS* 3.3 6.8 + - - +
21A VAL* 3.0 24.4 + - + +
94A HIS* 4.1 17.7 - - + -
95A GLU* 3.9 14.8 - - + +
118A HIS* 3.7 33.0 - - + +
119A THR* 6.0 1.6 - - + -
401A GDP 4.9 0.6 + - - -
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Residues in contact with GLN 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A CYS* 4.0 7.4 - - - -
9A TYR* 3.6 36.9 - - - +
10A SER 3.2 22.1 + - - +
11A PHE* 3.4 34.6 - - + -
13A VAL* 3.1 31.7 + - - +
14A PRO* 4.1 1.0 + - + -
15A GLY* 3.3 27.6 - - - +
16A GLY 4.1 0.2 + - - -
17A VAL* 1.3 77.1 + - - +
19A SER* 1.3 62.5 + - - +
21A VAL* 3.4 0.3 + - - +
22A LEU* 3.1 20.7 + - - +
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Residues in contact with SER 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PRO* 5.8 0.7 - - - +
15A GLY 3.0 19.7 + - - -
16A GLY* 4.1 3.4 - - - -
18A GLN* 1.3 74.4 - - - +
20A HIS* 1.3 67.3 + - - +
22A LEU* 4.7 4.7 - - - +
23A GLN* 3.0 50.1 + - - +
253A ASP* 5.6 3.1 + - - -
256A LYS* 5.5 1.6 + - - -
278A ILE* 6.3 0.2 - - - -
401A GDP 4.0 23.2 + - - -
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Residues in contact with HIS 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLY 3.0 19.2 + - - +
17A VAL 3.4 4.3 - - - +
19A SER* 1.3 77.2 - - - +
21A VAL* 1.3 58.0 + - + +
24A LEU* 2.9 44.2 + - + +
92A HIS* 5.1 0.4 - - - -
94A HIS* 3.4 33.3 - + - -
116A THR* 4.8 6.3 + - + +
118A HIS* 3.7 18.0 - + + -
167A PRO 5.3 1.3 - - - -
168A ASN* 3.1 38.3 + - + +
169A GLY 5.9 0.7 - - - -
349A TRP* 3.6 33.9 - + - -
356A ILE* 4.5 10.6 - - + +
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Residues in contact with VAL 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A MET* 4.0 21.1 - - + +
7A CYS* 4.2 22.9 - - + +
11A PHE* 4.7 2.2 - - + -
17A VAL* 3.0 18.9 + - + +
18A GLN 3.9 3.4 - - - +
20A HIS* 1.3 78.5 - - + +
22A LEU* 1.3 57.4 + - - +
24A LEU* 3.9 3.6 - - - +
25A ALA* 2.9 28.4 + - - +
37A VAL* 3.9 29.2 - - + -
94A HIS* 3.6 39.7 - - + +
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Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE* 3.5 44.0 - - + -
18A GLN 3.1 13.0 + - - +
19A SER* 4.3 3.8 - - - +
21A VAL* 1.3 73.6 - - - +
23A GLN* 1.3 68.5 + - + +
25A ALA* 3.3 4.6 + - - +
26A GLU* 3.0 29.9 + - + +
37A VAL* 5.0 4.0 - - + -
47A LEU* 4.0 13.9 - - + -
48A PRO* 4.4 15.0 - - + -
50A TYR* 3.9 9.7 + - + +
51A VAL* 4.0 23.6 - - + -
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Residues in contact with GLN 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A SER* 3.0 38.4 + - - +
22A LEU* 1.3 79.7 - - + +
24A LEU* 1.3 63.5 + - - +
26A GLU* 3.1 8.6 + - + +
27A VAL* 2.9 29.2 + - + +
169A GLY 4.3 5.2 - - - +
170A VAL* 4.3 2.4 - - - +
171A ASP* 4.3 8.5 + - - +
175A PHE* 6.4 0.2 - - - -
253A ASP* 5.1 8.7 + - - +
256A LYS* 5.7 3.6 - - - +
282A GLU* 5.3 6.3 + - - -
349A TRP* 2.7 44.2 + - + +
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Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A MET* 3.8 16.6 - - + -
20A HIS* 2.9 29.5 + - + +
21A VAL* 3.9 3.6 - - - +
23A GLN* 1.3 76.1 - - - +
25A ALA* 1.3 64.1 + - - +
27A VAL* 3.3 4.1 + - + +
28A LEU* 3.0 36.3 + - + +
92A HIS* 4.1 14.1 - - + -
94A HIS* 4.7 1.1 - - + -
349A TRP* 4.0 20.4 - - + -
353A SER* 4.5 11.7 - - - -
356A ILE* 3.8 34.8 - - + -
360A TYR* 3.7 20.4 - - - +
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Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A MET* 4.3 5.3 - - - +
21A VAL 2.9 18.3 + - - +
22A LEU* 3.6 5.8 - - - +
24A LEU* 1.3 78.7 - - - +
26A GLU* 1.3 61.8 + - - +
28A LEU* 3.4 1.9 + - - +
29A ARG* 3.0 28.8 + - - +
35A VAL* 3.8 28.0 - - + +
37A VAL* 4.0 7.2 - - + -
50A TYR* 3.7 23.6 - - + +
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Residues in contact with GLU 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU* 3.0 21.9 + - + +
23A GLN* 3.1 10.1 + - - +
25A ALA* 1.3 75.9 - - - +
27A VAL* 1.3 64.2 + - + +
29A ARG* 3.4 8.7 + - - +
30A ASP* 3.0 34.8 + - - +
48A PRO* 4.5 6.2 - - - +
50A TYR* 2.5 33.4 + - - +
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Residues in contact with VAL 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLN* 2.9 19.3 + - + +
24A LEU* 3.6 9.0 - - + +
26A GLU* 1.3 76.5 - - + +
28A LEU* 1.3 65.2 + - + +
30A ASP* 3.4 9.9 + - - +
31A ALA* 3.3 20.9 + - + +
349A TRP* 3.7 36.6 - - + +
353A SER* 3.8 32.1 - - - +
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Residues in contact with LEU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ILE* 4.1 11.0 - - + -
5A MET* 3.2 34.1 - - + -
24A LEU* 3.0 32.3 + - + +
27A VAL* 1.3 80.3 - - + +
29A ARG* 1.3 61.6 + - - +
31A ALA* 3.1 8.8 + - + -
32A GLY 3.4 0.2 + - - -
33A HIS* 3.1 35.8 + - + -
35A VAL* 3.7 15.9 - - + -
353A SER* 5.8 5.4 - - - +
357A MET* 3.5 32.8 - - + -
360A TYR* 4.1 15.5 - - + -
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Residues in contact with ARG 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ALA 3.0 19.2 + - - +
26A GLU* 3.8 8.3 + - - +
28A LEU* 1.3 75.1 - - - +
30A ASP* 1.3 60.8 + - - +
32A GLY* 3.0 19.6 + - - -
33A HIS 3.4 18.7 + - - +
34A GLU* 5.6 0.6 - - - +
35A VAL* 4.0 19.6 + - + +
49A ASP* 5.2 6.3 + - - -
50A TYR* 3.5 45.9 - - - +
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Residues in contact with ASP 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLU* 3.0 25.5 + - - +
27A VAL* 3.7 8.8 - - - +
28A LEU 3.3 0.2 - - - -
29A ARG* 1.3 77.6 - - - +
31A ALA* 1.3 57.2 + - - +
32A GLY 3.3 1.2 + - - -
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Residues in contact with ALA 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A VAL* 3.3 10.8 + - + +
28A LEU* 3.1 10.7 + - + +
29A ARG 3.1 1.0 - - - -
30A ASP* 1.3 76.1 - - - +
32A GLY* 1.3 59.0 + - - +
33A HIS* 3.5 22.2 + - + +
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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
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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