Contacts of the helix formed by residues 70 - 84 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ILE* 2.9 14.1 + - - +
37B ASP* 4.5 5.8 - - - -
38B ASP* 4.4 3.9 + - - -
69B GLY* 1.3 70.7 - - - -
71B VAL* 1.3 58.5 + - - +
72B THR* 3.4 10.0 + - - -
73B ALA* 3.1 30.5 + - - +
74B GLY* 2.9 26.0 + - - -
99B MET* 4.1 2.8 - - - +
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Residues in contact with VAL 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B GLY 3.4 4.9 + - - +
70B SER* 1.3 72.8 + - - +
72B THR* 1.3 61.6 + - + +
74B GLY* 3.2 2.4 + - - -
75B PHE* 2.9 47.3 + - + -
99B MET* 3.7 27.9 - - + +
125B PRO* 4.4 23.3 - - + -
126B LEU 6.1 0.4 - - - +
146B THR* 3.7 27.1 - - + -
150B LEU* 4.4 3.4 - - + -
119C GLU* 6.0 0.7 - - - +
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Residues in contact with THR 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ASP* 4.6 4.9 + - - -
70B SER* 3.4 8.4 + - - -
71B VAL* 1.3 78.1 - - + +
73B ALA* 1.3 68.6 + - - +
75B PHE* 3.1 8.6 + - + +
76B ALA 3.0 18.7 + - - -
142B HIS* 5.9 1.6 - - + -
65C ASN* 4.8 1.9 + - - -
94C GLY* 3.3 17.5 - - - +
95C MET* 3.8 35.7 - - + +
119C GLU* 3.8 25.4 - - - +
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Residues in contact with ALA 73 (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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36B ILE* 3.9 7.9 - - + -
37B ASP 3.6 24.5 - - - +
38B ASP* 3.5 22.2 - - - +
41B ALA* 3.4 15.6 - - + +
70B SER* 3.1 16.6 + - - +
72B THR* 1.3 81.1 + - - +
74B GLY* 1.3 62.8 + - - +
76B ALA* 3.3 12.8 + - - +
77B ILE* 3.4 10.0 + - - +
65C ASN* 4.5 4.9 - - - +
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Residues in contact with GLY 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ILE* 3.9 9.1 - - - +
70B SER 2.9 14.5 + - - -
71B VAL 3.5 4.5 - - - -
72B THR 3.2 0.2 - - - -
73B ALA* 1.3 75.9 - - - +
75B PHE* 1.3 56.2 + - - +
77B ILE* 3.0 8.6 + - - +
78B TYR* 2.8 24.2 + - - +
99B MET* 3.7 21.5 - - - -
103B LEU* 3.5 13.2 - - - +
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Residues in contact with PHE 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL* 2.9 36.0 + - + -
72B THR* 3.1 11.4 + - + +
74B GLY* 1.3 73.0 - - - +
76B ALA* 1.3 61.5 + - - +
78B TYR* 4.0 13.9 - + + -
79B ASP* 2.8 35.0 + - - +
99B MET* 5.3 1.3 - - - -
102B PHE* 3.7 23.6 - + - -
146B THR* 5.2 0.9 - - + -
149B LYS* 3.6 36.3 - - + -
150B LEU* 3.6 33.7 - - + -
153B ILE* 3.8 16.8 - - + -
94C GLY* 4.6 4.7 - - - +
117C ASN* 3.5 33.9 - - + +
119C GLU* 5.8 1.1 - - - -
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Residues in contact with ALA 76 (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 ALA* 4.5 3.1 - - + -
45B VAL* 3.6 7.1 - - + +
72B THR 3.0 6.8 + - - +
73B ALA 3.4 11.2 - - - +
74B GLY 3.2 0.4 - - - -
75B PHE* 1.3 76.3 - - - +
77B ILE* 1.3 57.2 + - - +
79B ASP* 4.3 2.0 - - - +
80B THR* 2.7 33.6 + - - -
65C ASN* 4.2 11.7 - - - +
93C ILE* 3.9 22.0 - - + +
94C GLY* 3.6 29.0 - - - +
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Residues in contact with ILE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 5.1 3.4 - - + -
36B ILE* 4.4 13.9 - - + -
40B VAL* 5.0 1.1 - - + -
41B ALA* 3.9 31.2 - - + +
44B ILE* 3.9 38.4 - - + -
45B VAL* 4.1 6.1 - - + -
48B LEU* 4.7 1.1 - - + -
62B LEU* 5.0 3.4 - - + -
73B ALA 3.4 10.5 + - - +
74B GLY 3.0 7.0 + - - +
76B ALA* 1.3 75.0 - - - +
78B TYR* 1.3 66.6 + - - +
80B THR* 3.1 3.3 + - - -
81B ILE* 2.8 42.3 + - + +
103B LEU* 4.0 27.1 - - + -
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Residues in contact with TYR 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B GLY 2.8 18.3 + - - +
75B PHE* 3.6 15.0 - + + +
77B ILE* 1.3 74.7 - - - +
79B ASP* 1.3 75.2 + - - +
81B ILE* 3.1 8.3 + - - +
82B GLN* 3.0 43.2 + - + +
102B PHE* 3.6 19.1 - + + -
103B LEU* 3.8 10.9 - - + +
106B ALA* 3.3 34.1 - - + -
153B ILE* 3.2 28.2 - - + +
156B GLU* 5.2 2.1 + - - -
157B ARG* 3.2 26.2 + - - -
117C ASN* 3.6 19.1 - - - -
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Residues in contact with ASP 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B PHE 2.8 18.8 + - - +
76B ALA* 4.3 3.1 - - - +
78B TYR* 1.3 82.8 - - - +
80B THR* 1.3 57.6 + - - +
82B GLN* 3.3 5.5 + - - +
83B HIS* 2.9 30.7 + - - +
94C GLY 5.8 0.6 + - - +
115C LEU* 3.2 24.9 - - + +
116C PRO* 3.2 20.4 - - + +
117C ASN* 2.5 56.9 + - - +
118C ALA* 3.4 4.0 + - - +
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Residues in contact with THR 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B VAL* 3.4 31.4 - - + +
48B LEU* 3.8 28.3 - - + -
49B LEU* 4.5 8.7 - - + -
76B ALA 2.7 22.5 + - - -
77B ILE 3.1 4.9 + - - -
79B ASP* 1.3 73.5 - - - +
81B ILE* 1.3 67.1 + - - +
83B HIS* 3.2 11.1 + - + +
84B ILE* 3.2 23.9 + - + +
93C ILE* 4.4 4.3 - - - +
115C LEU* 3.9 13.1 - - - +
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Residues in contact with ILE 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 3.9 17.3 - - + -
62B LEU* 4.1 20.0 - - + -
77B ILE* 2.8 38.6 + - + +
78B TYR* 3.4 10.5 - - - +
80B THR* 1.3 74.8 - - - +
82B GLN* 1.3 77.7 + - - +
83B HIS 3.3 0.2 + - - -
84B ILE* 3.4 21.5 + - - +
86B PRO 4.8 1.4 - - - +
88B VAL* 3.8 32.7 - - + +
90B THR* 5.3 0.9 - - + -
103B LEU* 4.9 9.9 - - + +
106B ALA* 3.9 20.0 - - + +
107B GLY* 5.1 0.2 - - - -
108B ALA 5.5 1.1 - - - +
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Residues in contact with GLN 82 (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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78B TYR* 3.0 54.1 + - + +
79B ASP* 3.9 7.0 - - - +
81B ILE* 1.3 82.7 + - - +
83B HIS* 1.3 61.2 + - - +
84B ILE 3.6 5.7 + - - +
106B ALA* 3.1 25.3 + - - +
107B GLY 6.0 0.2 - - - -
108B ALA* 6.0 1.6 - - - +
157B ARG* 3.4 22.8 + - - +
116C PRO* 6.3 0.9 - - + -
192C PRO* 3.8 32.4 - - + +
193C GLU 4.1 5.5 + - - -
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Residues in contact with HIS 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LEU* 5.3 7.1 - - + +
52B GLN* 4.7 3.5 + - - -
79B ASP 2.9 17.7 + - - +
80B THR* 3.2 5.5 + - - +
82B GLN* 1.3 79.1 - - - +
84B ILE* 1.3 69.4 + - + +
63C TYR* 5.5 5.2 - + - -
115C LEU* 4.3 13.3 - - + +
116C PRO* 6.2 1.3 - - + -
190C MET* 3.2 52.4 - - + +
191C VAL 4.5 13.0 - - - -
192C PRO* 4.6 3.6 - - + -
193C GLU* 3.8 33.3 + - + +
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Residues in contact with ILE 84 (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 LEU* 4.3 20.2 - - + +
49B LEU* 4.2 19.3 - - + -
52B GLN* 3.4 31.2 - - + +
60B ILE* 3.8 28.9 - - + -
80B THR* 3.2 16.1 + - + +
81B ILE* 3.4 18.4 - - - +
82B GLN 3.8 7.4 - - - +
83B HIS* 1.3 85.8 - - - +
85B LYS* 1.3 64.7 + - - +
86B PRO* 3.8 14.2 - - + +
88B VAL* 3.9 15.0 - - + -
193C GLU* 5.4 3.7 - - - -
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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