Contacts of the helix formed by residues 42 - 56 (chain B) in PDB entry 3G2V
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 GLU 42 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B LEU* 5.1 1.6 - - - +
40B ASP* 3.4 30.0 - - - +
41B PHE* 1.3 80.4 - - - +
43B GLY* 1.3 72.8 + - - +
44B PRO 3.5 0.2 - - - -
45B PRO* 3.1 15.2 - - - +
46B LEU* 3.3 31.7 + - + +
49B ARG* 5.3 1.1 + - - +
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Residues in contact with GLY 43 (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 LEU* 3.4 18.6 - - - +
37B LEU* 3.5 14.6 - - - -
40B ASP* 3.3 9.3 + - - +
41B PHE 3.1 0.6 - - - -
42B GLU* 1.3 86.7 - - - +
44B PRO* 1.3 66.8 - - - +
46B LEU* 3.0 5.0 + - - +
47B ALA* 2.8 26.9 + - - +
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Residues in contact with PRO 44 (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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37B LEU* 3.2 30.3 - - + +
38B ASN* 4.6 1.8 - - - +
40B ASP 3.4 9.0 - - - +
43B GLY* 1.3 88.9 - - - +
45B PRO* 1.4 69.7 - - + +
47B ALA* 3.4 3.5 + - + +
48B THR* 3.2 25.6 + - - -
80B ARG* 3.5 34.5 - - + +
81B PHE* 4.0 20.0 - - + +
84B GLU* 4.0 16.7 - - + +
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Residues in contact with PRO 45 (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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41B PHE 3.9 7.4 - - - +
42B GLU* 3.1 16.2 - - - +
44B PRO* 1.4 96.6 - - + +
46B LEU* 1.3 61.8 + - - +
48B THR* 3.5 6.5 + - + +
49B ARG* 3.2 44.4 + - - +
84B GLU* 3.9 31.4 - - + +
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Residues in contact with LEU 46 (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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58A PRO* 6.3 1.1 - - + -
10B LEU* 3.9 16.8 - - + +
11B GLU* 4.0 28.5 - - - +
42B GLU* 3.3 30.3 + - + +
43B GLY 3.0 8.8 + - - +
45B PRO* 1.3 77.1 - - - +
47B ALA* 1.3 67.1 + - - +
48B THR 3.2 0.2 + - - -
49B ARG* 3.2 27.7 + - + +
50B LEU* 3.0 50.5 + - + +
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Residues in contact with ALA 47 (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 LEU* 3.8 4.7 - - + +
33B PHE* 3.6 19.7 - - + -
37B LEU* 3.6 34.8 - - + -
43B GLY 2.8 15.8 + - - +
44B PRO 3.6 8.7 - - - +
46B LEU* 1.3 71.3 - - - +
48B THR* 1.3 53.3 + - - +
50B LEU* 3.3 3.7 + - - +
51B LEU* 2.8 40.8 + - - +
81B PHE* 4.0 5.8 - - + -
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Residues in contact with THR 48 (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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44B PRO 3.2 13.9 + - - -
45B PRO* 3.8 7.6 - - + +
46B LEU 3.1 0.4 - - - -
47B ALA* 1.3 75.8 - - - +
49B ARG* 1.3 62.2 + - + +
51B LEU* 4.4 5.6 - - - -
52B ALA* 2.9 31.5 + - - +
81B PHE* 3.8 14.2 - - - -
84B GLU* 3.8 22.8 - - - +
85B VAL* 3.8 15.4 - - - +
89B ARG* 5.9 6.5 - - + -
90B PHE* 3.6 31.3 - - + +
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Residues in contact with ARG 49 (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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58A PRO* 4.0 24.3 - - + +
106A ARG* 4.8 23.8 - - - +
42B GLU* 5.3 0.8 + - - +
45B PRO* 3.2 37.8 + - - +
46B LEU* 3.4 37.8 - - + +
48B THR* 1.3 82.0 - - - +
50B LEU* 1.3 62.2 + - + +
52B ALA* 3.5 4.3 + - - +
53B HIS* 3.4 15.2 + - - +
89B ARG* 5.8 9.2 - - - +
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Residues in contact with LEU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A PRO* 4.1 14.4 - - + +
59A GLN* 4.1 4.7 - - + +
10B LEU* 3.7 43.7 - - + +
11B GLU* 3.8 23.3 - - + +
14B ILE* 4.3 11.7 - - + -
33B PHE* 4.5 4.5 - - + -
46B LEU* 3.0 38.9 + - + +
47B ALA 3.8 2.5 - - - +
49B ARG* 1.3 74.9 - - + +
51B LEU* 1.3 63.7 + - - +
53B HIS 3.4 2.3 + - - -
54B LYS* 3.1 27.3 + - - +
148B IOD 3.5 28.4 - - + +
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Residues in contact with LEU 51 (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 ILE* 4.0 11.2 - - + -
33B PHE* 4.0 17.9 - - + -
47B ALA 2.8 22.4 + - - +
48B THR* 3.8 5.8 - - - +
50B LEU* 1.3 78.2 - - - +
52B ALA* 1.3 56.5 + - - +
54B LYS* 3.2 3.7 + - - +
55B ILE* 2.9 43.8 + - + +
66B ALA* 3.5 30.1 - - + +
69B VAL* 3.8 20.4 - - + -
70B LEU* 4.1 17.7 - - + +
81B PHE* 3.8 28.9 - - + -
90B PHE* 4.4 3.6 - - + -
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Residues in contact with ALA 52 (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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48B THR 2.9 18.8 + - - +
49B ARG* 3.8 6.5 - - - +
50B LEU 3.3 0.2 - - - -
51B LEU* 1.3 75.2 - - - +
53B HIS* 1.3 62.6 + - - +
55B ILE* 3.8 5.5 - - - +
56B GLN* 3.1 32.2 + - - +
90B PHE* 4.0 12.9 - - + -
93B GLU* 3.7 37.2 - - + +
94B LEU* 6.2 0.4 - - - -
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Residues in contact with HIS 53 (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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53A HIS* 2.6 87.2 + + - -
54A LYS* 4.7 2.2 - - + -
56A GLN* 3.6 19.5 - - + -
57A SER* 3.5 22.2 + - - -
58A PRO* 3.5 19.5 - - + +
62A GLU* 4.2 6.0 + - - -
49B ARG 3.4 5.7 + - - +
50B LEU 3.4 8.4 + - - +
51B LEU 3.3 0.4 - - - -
52B ALA* 1.3 75.4 - - - +
54B LYS* 1.3 66.6 + - - +
56B GLN* 3.2 14.0 + - - +
148B IOD 3.8 15.8 - - + +
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Residues in contact with LYS 54 (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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53A HIS* 4.8 1.3 - - + -
59A GLN* 4.2 2.8 - - - +
62A GLU* 4.7 13.3 + - - -
14B ILE* 4.0 20.0 - - + -
15B ASN* 2.9 32.2 + - - +
18B THR* 3.4 25.0 + - - +
50B LEU 3.1 15.0 + - - +
51B LEU* 3.9 3.4 - - - +
53B HIS* 1.3 79.6 + - - +
55B ILE* 1.3 64.6 + - - +
57B SER* 3.0 24.9 + - - +
62B GLU* 3.9 22.6 + - + +
63B ALA* 3.4 9.2 + - - -
66B ALA* 3.4 21.5 - - + -
148B IOD 3.9 17.0 - - + -
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Residues in contact with ILE 55 (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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51B LEU* 2.9 31.6 + - + +
52B ALA* 3.8 5.2 - - - +
53B HIS 3.2 0.2 - - - -
54B LYS* 1.3 76.4 - - - +
56B GLN* 1.3 57.3 + - + +
57B SER 3.2 3.9 + - - +
63B ALA* 3.4 17.2 - - - +
66B ALA* 3.8 17.5 - - + +
67B LEU* 3.8 28.5 - - + +
70B LEU* 3.7 33.2 - - + -
90B PHE* 4.1 7.4 - - + -
93B GLU 5.5 0.4 - - - +
94B LEU* 4.0 14.4 - - + -
97B VAL* 4.1 12.8 - - + +
111B VAL* 4.5 5.5 - - - +
115B ILE* 4.0 17.9 - - + -
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Residues in contact with GLN 56 (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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53A HIS* 3.6 16.3 - - + +
56A GLN* 5.5 7.1 - - - +
52B ALA 3.1 18.6 + - - +
53B HIS* 3.2 11.9 + - - +
54B LYS 3.1 1.4 - - - -
55B ILE* 1.3 75.0 - - + +
57B SER* 1.3 64.7 + - - +
58B PRO* 3.5 3.8 - - - +
93B GLU* 2.8 48.0 + - - +
96B LYS* 3.9 8.0 - - - +
97B VAL* 3.7 22.0 - - + -
103B LEU* 4.1 23.9 - - + +
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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
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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