Contacts of the helix formed by residues 29 - 45 (chain A) in PDB entry 2GZG
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 SER 29 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A THR* 3.0 15.8 + - - -
28A SER* 1.3 82.4 - - - +
30A GLU* 1.3 64.1 + - - +
31A GLU* 3.4 19.6 + - - +
32A GLU* 2.9 31.8 + - - +
33A LEU 3.3 8.5 + - - -
83B TYR* 3.2 13.2 + - - -
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Residues in contact with GLU 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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29A SER* 1.3 71.5 - - - +
31A GLU* 1.3 70.0 + - - +
33A LEU* 3.1 5.1 + - + +
34A VAL* 2.9 38.3 + - + +
54B ARG* 2.8 36.6 + - - -
83B TYR* 3.4 35.2 - - + -
84B SER 2.9 31.0 + - - +
86B PHE* 6.5 0.4 - - + -
98B VAL* 3.5 16.8 - - + +
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Residues in contact with GLU 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A SER* 3.4 20.1 - - - +
30A GLU* 1.3 78.5 + - - +
32A GLU* 1.3 57.2 + - + +
34A VAL* 3.4 7.2 + - - +
35A LYS* 3.0 29.7 + - - +
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Residues in contact with GLU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A THR* 3.6 15.2 - - + +
28A SER* 3.0 38.0 + - - -
29A SER* 2.9 25.8 + - - +
31A GLU* 1.3 71.8 - - + +
33A LEU* 1.3 62.6 + - - +
35A LYS* 3.4 12.8 + - + +
36A LEU* 3.1 27.0 + - + +
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Residues in contact with LEU 33 (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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22A ILE* 3.8 38.4 - - + +
25A ALA* 3.9 22.4 - - + -
27A THR* 3.7 21.4 - - + +
29A SER 3.3 3.7 + - - +
30A GLU* 3.1 10.8 + - + +
32A GLU* 1.3 76.2 - - - +
34A VAL* 1.3 59.9 + - - +
36A LEU* 3.2 3.6 + - + +
37A VAL* 2.9 33.6 + - + +
54A TYR* 4.1 9.4 - - - +
78B SER* 4.0 8.7 - - - +
83B TYR* 3.9 23.1 - - + -
86B PHE* 3.9 23.6 - - + -
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Residues in contact with VAL 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A GLU* 2.9 34.2 + - + +
31A GLU* 3.7 8.1 - - - +
33A LEU* 1.3 74.8 - - + +
35A LYS* 1.3 57.1 + - - +
37A VAL* 3.3 2.4 + - - +
38A THR* 2.9 37.1 + - - +
86B PHE* 4.0 24.5 - - + -
95B GLY* 4.0 18.4 - - - +
97B LYS* 4.0 23.2 - - + +
98B VAL* 4.5 8.7 - - + -
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Residues in contact with LYS 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LYS* 5.1 11.9 - - - +
31A GLU 3.0 14.2 + - - +
32A GLU* 3.5 14.4 - - + +
34A VAL* 1.3 77.8 - - - +
36A LEU* 1.3 63.5 + - + +
38A THR* 3.4 7.0 + - - -
39A HIS* 3.0 29.1 + - + +
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Residues in contact with LEU 36 (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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18A LEU* 3.9 19.1 - - + +
21A THR* 3.7 30.3 - - + -
22A ILE* 3.7 25.1 - - + +
27A THR* 4.1 17.5 - - + -
32A GLU* 3.1 15.2 + - + +
33A LEU* 3.2 8.0 + - + +
35A LYS* 1.3 84.7 - - + +
37A VAL* 1.3 58.3 + - - +
39A HIS* 3.2 10.7 + - + +
40A PHE* 2.9 29.1 + - - +
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Residues in contact with VAL 37 (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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22A ILE* 3.8 18.8 - - + -
33A LEU* 2.9 22.1 + - + +
34A VAL 3.8 3.8 - - - +
36A LEU* 1.3 72.8 - - - +
38A THR* 1.3 63.7 + - - +
40A PHE* 3.3 8.1 + - - +
41A GLU* 3.0 40.0 + - - +
50A SER* 3.6 22.2 - - - -
53A ILE* 4.7 4.3 - - + -
54A TYR* 3.7 18.8 - - + +
86B PHE* 3.7 29.6 - - + -
97B LYS* 4.2 2.7 - - - -
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Residues in contact with THR 38 (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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34A VAL* 2.9 21.4 + - - +
35A LYS* 3.6 7.6 - - - -
36A LEU 3.3 0.2 - - - -
37A VAL* 1.3 75.7 - - - +
39A HIS* 1.3 62.1 + - - +
41A GLU* 3.2 11.9 + - + +
42A GLU* 3.0 49.2 + - + +
95B GLY* 5.8 1.9 - - - -
97B LYS* 3.8 22.2 + - - +
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Residues in contact with HIS 39 (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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4A LYS* 2.7 36.4 + - + +
10A TYR* 2.8 33.4 - + - -
18A LEU* 3.8 18.6 - - + +
35A LYS* 3.0 16.3 + - + +
36A LEU* 3.2 14.3 + - + +
38A THR* 1.3 73.8 - - - +
40A PHE* 1.3 59.9 + - - +
42A GLU* 3.2 13.0 + - - +
43A MET* 2.8 54.0 + - + +
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Residues in contact with PHE 40 (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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15A PHE* 3.7 31.6 - + - -
18A LEU* 5.0 6.7 - - + +
19A VAL* 3.9 20.0 - - + -
22A ILE* 4.0 13.9 - - + -
36A LEU 2.9 13.6 + - - +
37A VAL* 3.5 10.8 - - - +
39A HIS* 1.3 77.2 + - - +
41A GLU* 1.3 71.1 + - + +
43A MET* 3.7 6.0 - - - +
44A THR* 3.0 45.8 + - + +
49A GLY 3.9 18.6 - - - -
52A LEU* 4.1 8.3 - - + -
53A ILE* 3.6 29.6 - - + -
67A ILE* 3.8 23.8 - - + -
71A VAL* 4.1 7.2 - - + -
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Residues in contact with GLU 41 (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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37A VAL* 3.0 24.5 + - - +
38A THR* 3.2 7.6 + - + +
40A PHE* 1.3 77.8 - - + +
42A GLU* 1.3 64.4 + - + +
44A THR* 3.4 5.8 + - - -
45A GLU* 3.1 23.4 + - - -
46A HIS 4.5 1.7 + - - +
49A GLY* 3.7 15.5 - - - -
50A SER* 3.5 34.0 + - - +
89B LYS* 4.7 9.4 - - - +
92B GLN* 4.5 3.1 - - - +
97B LYS* 3.0 39.8 + - - -
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Residues in contact with GLU 42 (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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38A THR* 3.0 37.9 + - + +
39A HIS* 3.7 12.2 - - - +
41A GLU* 1.3 78.3 - - + +
43A MET* 1.3 73.3 + - + +
45A GLU* 3.7 13.7 - - - +
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Residues in contact with MET 43 (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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4A LYS 3.4 22.9 - - - +
5A HIS* 3.2 24.9 - - - +
6A SER* 3.6 22.2 - - - +
7A ILE* 3.2 32.6 + - + +
10A TYR* 3.8 12.1 - - + -
15A PHE* 4.6 8.7 - - + -
18A LEU* 5.1 0.2 - - + -
39A HIS* 2.8 51.7 + - + +
40A PHE* 3.7 6.3 - - - +
42A GLU* 1.3 82.7 - - + +
44A THR* 1.3 63.3 + - - +
45A GLU* 3.5 3.1 + - - +
75A ARG* 3.3 8.5 + - - -
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Residues in contact with THR 44 (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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7A ILE* 4.4 4.5 - - + -
15A PHE* 3.8 27.8 - - + -
40A PHE* 3.0 46.0 + - + +
41A GLU* 3.4 7.8 + - - -
43A MET* 1.3 75.9 - - - +
45A GLU* 1.3 64.9 + - - +
46A HIS* 3.1 23.2 + - - +
49A GLY* 5.6 0.7 - - - -
71A VAL* 3.9 16.6 - - + -
74A TRP* 3.7 9.4 - - - -
75A ARG* 2.9 22.8 + - - +
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Residues in contact with GLU 45 (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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41A GLU 3.1 12.0 + - - -
42A GLU 3.7 15.5 - - - +
43A MET 3.8 2.7 - - - +
44A THR* 1.3 79.0 + - - +
46A HIS* 1.3 62.6 + - - +
47A PRO* 3.6 2.8 - - - +
74A TRP* 3.4 18.4 - - + -
75A ARG* 2.9 28.7 + - - +
80A LYS* 4.1 21.5 + - - +
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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