Contacts of the helix formed by residues 70 - 84 (chain G) in PDB entry 3V5I
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 70 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36G ILE* 2.9 13.6 + - - +
37G ASP* 4.4 6.3 - - - -
38G ASP* 4.3 4.3 + - - -
69G GLY* 1.3 70.8 - - - +
71G VAL* 1.3 59.0 + - - +
72G THR* 3.5 9.7 + - - -
73G ALA* 3.1 30.3 + - - +
74G GLY* 2.9 26.0 + - - -
99G MET* 4.0 3.1 - - - +
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Residues in contact with VAL 71 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G GLY 3.3 4.6 + - - +
70G SER* 1.3 71.5 + - - +
72G THR* 1.3 62.4 + - + +
74G GLY* 3.1 2.8 + - - -
75G PHE* 2.9 51.9 + - + -
99G MET* 3.6 28.6 - - + +
125G PRO* 4.4 16.4 - - + -
126G LEU 6.1 0.7 - - - +
146G THR* 3.7 22.2 - - + -
150G LEU* 4.3 11.4 - - + -
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Residues in contact with THR 72 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ASN* 4.8 2.4 + - - -
94A GLY* 3.4 18.3 - - - +
95A MET* 3.8 37.9 - - + +
119A GLU* 4.0 21.1 - - - +
38G ASP* 4.6 5.2 + - - -
70G SER* 3.5 7.7 + - - -
71G VAL* 1.3 81.3 - - + +
73G ALA* 1.3 64.7 + - - +
75G PHE* 3.0 9.7 + - + +
76G ALA 3.0 18.7 + - - -
142G HIS* 6.0 1.6 - - + -
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Residues in contact with ALA 73 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ASN* 4.6 2.2 - - - +
36G ILE* 3.8 7.9 - - + -
37G ASP 3.6 22.0 - - - +
38G ASP* 3.6 18.2 - - - +
41G ALA* 3.4 18.6 - - + +
70G SER* 3.1 25.6 + - - +
72G THR* 1.3 79.9 + - - +
74G GLY* 1.3 62.5 + - - +
76G ALA* 3.3 11.2 + - - +
77G ILE* 3.3 10.9 + - - +
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Residues in contact with GLY 74 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G ILE* 3.8 8.4 - - - +
70G SER 2.9 10.5 + - - -
71G VAL 3.1 4.5 + - - -
73G ALA* 1.3 77.2 - - - +
75G PHE* 1.3 56.9 + - - +
77G ILE* 3.1 8.4 + - - +
78G TYR* 2.8 27.6 + - - +
99G MET* 3.7 26.2 - - - -
102G PHE* 5.8 0.2 - - - -
103G LEU* 3.6 10.0 - - - +
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Residues in contact with PHE 75 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLY* 4.5 7.8 + - - +
117A ASN* 3.7 27.6 - - + +
118A ALA* 5.8 0.2 - - - -
119A GLU* 6.5 0.2 - - - -
71G VAL* 2.9 42.2 + - + -
72G THR* 3.0 11.8 + - + +
74G GLY* 1.3 72.9 - - - +
76G ALA* 1.3 60.4 + - - +
78G TYR* 4.0 14.6 - + + -
79G ASP* 2.8 35.1 + - - +
99G MET* 5.3 0.7 - - - -
102G PHE* 3.7 16.8 - + - -
146G THR* 5.2 1.1 - - + -
149G LYS* 3.5 37.7 - - + -
150G LEU* 3.6 25.6 - - + -
153G ILE* 3.7 23.1 - - + -
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Residues in contact with ALA 76 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ASN* 4.2 14.8 - - - +
93A ILE* 4.1 16.6 - - + +
94A GLY* 3.8 23.7 - - - +
41G ALA* 4.5 3.6 - - + -
45G VAL* 3.9 11.7 - - + -
72G THR 3.0 10.1 + - - +
73G ALA 3.5 9.6 - - - +
74G GLY 3.3 0.4 - - - -
75G PHE* 1.3 76.4 - - - +
77G ILE* 1.3 60.7 + - - +
79G ASP* 4.2 1.4 - - - +
80G THR* 2.8 30.7 + - - -
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Residues in contact with ILE 77 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G LEU* 5.1 3.6 - - + -
36G ILE* 4.4 12.8 - - + -
40G VAL* 5.0 1.1 - - + -
41G ALA* 3.9 30.5 - - + +
44G ILE* 3.9 38.4 - - + -
45G VAL* 4.2 6.1 - - + -
48G LEU* 4.5 1.1 - - + +
62G LEU* 5.0 3.4 - - + -
73G ALA 3.3 10.7 + - - +
74G GLY 3.1 7.5 + - - +
76G ALA* 1.3 74.9 - - - +
78G TYR* 1.3 67.0 + - - +
80G THR* 3.1 3.8 + - - -
81G ILE* 2.9 41.1 + - + +
103G LEU* 4.0 27.8 - - + -
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Residues in contact with TYR 78 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ASN* 3.7 14.1 - - - -
74G GLY 2.8 18.5 + - - +
75G PHE* 3.8 16.4 - + + +
77G ILE* 1.3 73.5 - - - +
79G ASP* 1.3 82.3 + - - +
81G ILE* 3.2 7.7 + - - +
82G GLN* 3.1 41.6 + - + +
102G PHE* 3.6 20.2 - + + -
103G LEU* 3.8 11.2 - - + +
106G ALA* 3.4 29.8 - - + -
153G ILE* 3.2 28.7 - - + +
156G GLU* 5.2 2.1 + - - -
157G ARG* 3.2 26.8 + - - -
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Residues in contact with ASP 79 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ILE* 5.8 0.4 - - + -
94A GLY 5.6 2.0 + - - +
115A LEU* 3.3 32.6 - - + +
116A PRO* 3.9 8.6 - - + +
117A ASN* 2.7 54.1 + - - +
118A ALA* 3.5 4.2 + - - -
75G PHE 2.8 22.7 + - - +
76G ALA* 4.3 2.0 - - - +
78G TYR* 1.3 88.0 - - - +
80G THR* 1.3 55.9 + - - +
82G GLN* 3.3 6.1 + - - +
83G HIS* 2.9 30.3 + - - +
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Residues in contact with THR 80 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ILE* 4.5 5.7 - - - +
115A LEU* 4.4 8.0 - - - +
45G VAL* 3.6 28.1 - - + +
48G LEU* 3.8 30.1 - - + -
49G LEU* 4.4 9.9 - - + -
76G ALA 2.8 22.9 + - - -
77G ILE 3.1 4.1 + - - -
79G ASP* 1.3 74.3 - - - +
81G ILE* 1.3 67.1 + - - +
83G HIS* 3.2 14.5 + - + +
84G ILE* 3.2 24.0 + - + +
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Residues in contact with ILE 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48G LEU* 3.8 17.0 - - + -
62G LEU* 4.1 20.0 - - + -
77G ILE* 2.9 34.3 + - + +
78G TYR* 3.4 11.0 - - - +
80G THR* 1.3 78.1 - - - +
82G GLN* 1.3 78.8 + - - +
83G HIS 3.2 0.2 + - - -
84G ILE* 3.4 21.8 + - - +
86G PRO 4.8 1.7 - - - +
88G VAL* 3.9 31.4 - - + +
90G THR* 5.3 1.3 - - + -
103G LEU* 4.9 7.2 - - + +
106G ALA* 3.8 22.9 - - + +
107G GLY* 5.1 1.1 - - - -
108G ALA 5.6 0.7 - - - +
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Residues in contact with GLN 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A PRO* 3.9 31.8 - - + +
193A GLU 4.3 5.2 + - - -
78G TYR* 3.1 52.1 + - + +
79G ASP* 3.3 7.2 + - - +
80G THR 3.3 0.2 - - - -
81G ILE* 1.3 83.1 + - - +
83G HIS* 1.3 60.8 + - - +
84G ILE 3.7 5.3 + - - +
106G ALA* 3.1 25.2 + - - +
108G ALA* 6.4 0.4 - - - +
157G ARG* 3.5 22.7 + - - +
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Residues in contact with HIS 83 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A TYR* 5.3 7.2 - + - -
115A LEU* 4.4 10.9 - - + +
116A PRO* 6.4 0.9 - - + -
190A MET* 3.3 47.2 - - + +
191A VAL 4.8 11.0 - - - -
192A PRO* 4.9 3.4 - - + -
193A GLU* 4.0 32.2 + - + +
49G LEU* 5.4 6.3 - - + +
52G GLN* 4.7 3.8 + - - -
79G ASP 2.9 18.1 + - - +
80G THR* 3.2 9.0 + - - +
82G GLN* 1.3 78.1 - - - +
84G ILE* 1.3 71.2 + - - +
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Residues in contact with ILE 84 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A GLU* 5.7 3.7 - - - -
48G LEU* 4.1 19.3 - - + +
49G LEU* 4.2 19.7 - - + -
52G GLN* 3.4 29.6 - - + +
60G ILE* 3.8 29.4 - - + -
80G THR* 3.2 16.3 + - + +
81G ILE* 3.4 19.9 - - - +
82G GLN 3.9 4.2 - - - +
83G HIS* 1.3 86.1 - - - +
85G LYS* 1.3 64.1 + - - +
86G PRO* 3.9 13.6 - - + +
88G VAL* 3.9 16.2 - - + -
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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
------------------------------------------------------------
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