Contacts of the helix formed by residues 76 - 92 (chain D) in PDB entry 3G33
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 76 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D GLU* 2.8 21.8 + - + +
75D GLU* 1.3 78.9 + - - +
77D VAL* 1.3 65.3 + - - +
78D PHE 3.5 0.2 - - - -
79D PRO* 3.3 4.0 - - - +
80D LEU* 3.2 19.7 + - - +
114D ARG* 3.1 43.5 + - + +
156D ILE* 3.3 16.6 - - + +
158D HIS* 3.2 39.0 + - + -
159D ASP* 4.5 6.1 - - - +
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Residues in contact with VAL 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D CYS* 4.2 14.6 - - - -
73D CYS* 4.1 7.9 - - + -
74D GLU* 3.0 16.7 + - + +
76D GLU* 1.3 76.7 - - - +
78D PHE* 1.3 56.0 + - - +
80D LEU* 3.0 9.4 + - - +
81D ALA* 2.7 35.1 + - + +
107D MET* 4.1 8.7 - - + +
110D ALA* 3.5 21.7 - - + +
111D SER* 3.8 18.2 - - - +
114D ARG* 4.8 4.7 - - + +
115D GLU* 3.4 37.9 - - + +
119D LEU* 5.6 0.2 - - + -
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Residues in contact with PHE 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D ALA* 3.2 29.6 - - + -
64D MET* 3.6 22.2 - - + -
65D LEU* 3.6 30.7 - - + -
68D CYS* 4.1 20.9 - - + +
74D GLU 4.6 1.0 + - - -
75D GLU 4.3 3.2 + - - +
77D VAL* 1.3 77.3 - - - +
79D PRO* 1.3 76.6 - - + +
81D ALA* 3.0 8.7 + - + +
82D MET* 2.9 41.3 + - + +
187D ALA* 3.5 19.1 - - + -
190D ALA* 3.4 20.6 - - + -
191D THR* 3.6 15.0 - - + -
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Residues in contact with PRO 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D GLU 3.4 15.7 - - - +
76D GLU* 3.3 10.3 - - - +
78D PHE* 1.3 104.4 - - + +
80D LEU* 1.3 56.4 + - - +
82D MET* 3.2 3.9 + - + +
83D ASN* 2.9 26.3 + - - +
156D ILE* 3.9 21.9 - - + +
157D ALA* 6.0 2.0 - - + +
158D HIS* 5.3 8.1 - - + +
186D LEU* 4.8 14.1 - - + +
187D ALA* 5.3 1.3 - - + -
190D ALA* 4.1 21.8 - - + -
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Residues in contact with LEU 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D GLU 3.2 9.9 + - - +
77D VAL* 3.0 9.8 + - - +
79D PRO* 1.3 79.7 - - - +
81D ALA* 1.3 62.9 + - - +
83D ASN* 2.9 19.2 + - + +
84D TYR* 3.0 57.6 + - + +
110D ALA* 3.9 21.3 - - + +
113D LEU* 4.4 5.4 - - + -
114D ARG* 3.2 37.7 - - + +
152D LEU 4.0 5.2 - - - +
154D ALA* 4.3 13.5 - - + +
156D ILE* 3.8 13.6 - - + +
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Residues in contact with ALA 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64D MET* 4.5 11.4 - - - -
77D VAL* 2.7 16.7 + - + +
78D PHE* 3.0 12.5 + - - +
80D LEU* 1.3 71.6 - - - +
82D MET* 1.3 58.6 + - - +
84D TYR* 3.2 3.8 + - - -
85D LEU* 2.9 24.7 + - - +
106D CYS* 3.4 37.4 - - + +
107D MET* 3.8 12.1 - - + +
110D ALA* 3.6 10.0 - - + +
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Residues in contact with MET 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D ARG* 3.4 40.8 - - - +
61D ALA* 4.0 16.4 - - + -
64D MET* 3.5 28.0 - - - +
78D PHE* 2.9 38.3 + - + +
79D PRO* 3.5 9.6 - - + +
81D ALA* 1.3 72.9 - - - +
83D ASN* 1.3 65.0 + - - +
85D LEU* 3.4 23.1 - - + +
86D ASP* 3.0 29.5 + - - +
190D ALA* 3.7 20.9 - - + +
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Residues in contact with ASN 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D TYR* 3.1 26.7 + - - +
40D PRO* 4.2 9.8 - - - +
79D PRO 2.9 12.7 + - - +
80D LEU* 2.9 17.0 + - + +
82D MET* 1.3 77.8 - - - +
84D TYR* 1.3 63.1 + - - +
86D ASP* 3.5 4.9 + - - +
87D ARG* 3.0 63.8 + - - +
154D ALA* 3.4 15.2 - - - +
156D ILE* 4.3 11.9 - - + +
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Residues in contact with TYR 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80D LEU* 3.0 39.7 + - + +
81D ALA* 3.5 5.8 - - - +
83D ASN* 1.3 81.1 - - - +
85D LEU* 1.3 66.2 + - - +
87D ARG* 3.3 7.8 + - - +
88D TYR* 2.9 25.5 + - - +
106D CYS* 3.7 31.0 - - - -
109D LEU* 4.0 13.0 - - + -
110D ALA* 3.4 30.4 - - + -
113D LEU* 3.5 5.7 - - - +
144D VAL* 5.2 1.1 - - + -
148D LEU* 3.9 18.9 - - + +
152D LEU* 2.7 58.2 + - + +
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Residues in contact with LEU 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D ARG* 4.4 18.2 - - + +
60D LEU* 4.1 29.6 - - + -
64D MET* 4.1 7.6 - - + -
81D ALA 2.9 14.0 + - - +
82D MET* 3.4 39.9 - - + +
84D TYR* 1.3 78.3 - - - +
86D ASP* 1.3 59.1 + - - +
88D TYR* 3.1 3.6 + - - +
89D LEU* 2.9 44.9 + - + +
99D LEU* 4.9 1.3 - - + -
102D LEU* 3.6 34.5 - - + -
103D GLY 4.9 0.2 - - - +
106D CYS* 3.6 9.8 - - - -
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Residues in contact with ASP 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D PRO* 3.5 23.3 - - + +
44D TYR* 2.6 41.4 + - + -
57D ARG* 2.7 34.8 + - - +
82D MET 3.0 15.5 + - - +
83D ASN* 4.0 2.2 - - - +
85D LEU* 1.3 79.9 - - - +
87D ARG* 1.3 57.2 + - - +
89D LEU 3.2 2.3 + - - -
90D SER* 2.6 34.0 + - - -
193D TYR* 4.3 0.2 - - - -
196D ALA* 3.8 16.2 - - - +
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Residues in contact with ARG 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ARG 5.1 3.8 + - - -
38D TYR* 3.5 29.0 - - - +
39D VAL 5.3 0.7 - - - -
40D PRO* 4.4 18.6 - - + -
41D ARG 5.9 0.2 - - - +
83D ASN* 3.0 51.2 + - - +
84D TYR* 3.7 10.1 - - - +
86D ASP* 1.3 75.6 - - - +
88D TYR* 1.3 62.8 + - - +
90D SER* 3.4 19.3 + - - -
91D CYS* 3.7 12.3 - - - -
148D LEU* 3.6 33.8 + - + +
151D ASP* 2.6 43.4 + - - +
154D ALA* 3.7 4.0 - - - +
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Residues in contact with TYR 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84D TYR 2.9 17.5 + - - +
85D LEU 3.5 3.6 - - - +
87D ARG* 1.3 78.0 - - - +
89D LEU* 1.3 58.2 + - - +
90D SER 3.1 1.8 - - - -
91D CYS* 3.5 3.1 + - - -
92D VAL* 3.0 56.3 + - + +
94D THR* 4.1 12.6 - - - -
102D LEU* 3.6 39.5 - - + -
140D TRP* 3.7 19.3 - + - -
143D LEU* 3.8 14.7 - - - +
144D VAL* 4.1 31.4 - - + -
147D LYS* 3.8 34.4 - - + +
148D LEU* 3.8 9.6 - - + +
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Residues in contact with LEU 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D TYR* 3.0 57.2 - - + +
47D CYS* 4.8 2.4 - - - +
48D VAL* 3.9 7.5 - - + +
52D ILE* 4.3 20.4 - - + -
57D ARG* 4.9 4.7 - - + -
85D LEU* 2.9 40.3 + - + +
86D ASP 3.7 2.7 - - - +
88D TYR* 1.3 74.1 - - + +
90D SER* 1.3 61.9 + - - +
91D CYS 3.4 0.6 + - - -
92D VAL 3.8 11.8 + - - +
94D THR* 3.2 26.5 - - - +
99D LEU* 5.0 11.4 - - + -
102D LEU* 3.8 17.0 - - + -
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Residues in contact with SER 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D PRO* 4.1 8.5 - - - +
41D ARG* 4.3 13.5 + - - -
42D ALA* 3.8 16.0 + - - +
44D TYR* 3.7 17.3 - - - +
47D CYS* 4.2 17.1 - - - +
86D ASP 2.6 22.4 + - - -
87D ARG* 3.4 12.1 - - - -
88D TYR 3.1 0.4 - - - -
89D LEU* 1.3 79.9 - - - +
91D CYS* 1.3 59.9 + - - +
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Residues in contact with CYS 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D CYS* 6.3 1.3 - - - -
87D ARG 3.7 16.6 - - - -
88D TYR* 3.9 2.7 - - - -
90D SER* 1.3 77.6 - - - +
92D VAL* 1.3 78.6 + - - +
93D PRO* 3.6 9.4 - - - +
147D LYS* 4.4 19.4 + - - -
148D LEU* 5.7 0.4 - - - -
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Residues in contact with VAL 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D CYS* 6.1 0.7 - - - -
48D VAL* 4.5 0.3 - - - +
88D TYR* 3.0 50.2 + - + +
89D LEU* 3.8 12.8 - - - +
91D CYS* 1.3 91.2 - - - +
93D PRO* 1.3 69.4 - - + +
94D THR* 3.1 15.9 + - - +
147D LYS* 3.6 43.5 - - + +
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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
------------------------------------------------------------
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