Contacts of the helix formed by residues 86 - 104 (chain B) in PDB entry 1VI9
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 86 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54B VAL* 5.0 4.9 - - - +
57B PRO* 4.1 4.3 - - - +
84B LEU* 3.2 8.5 - - - +
85B GLY* 1.3 79.9 - - - +
87B ALA* 1.3 61.3 + - - +
88B GLU* 3.2 23.3 + - - +
89B GLN* 3.1 36.7 + - - +
90B GLY 3.7 1.7 + - - -
125B ALA* 4.5 5.8 - - - -
128B VAL* 3.6 11.9 - - - -
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Residues in contact with ALA 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LEU* 5.5 0.7 - - - -
86B SER* 1.3 72.0 - - - +
88B GLU* 1.3 61.2 + - - +
90B GLY* 2.9 18.9 + - - +
91B GLU* 2.7 21.2 - - - +
126B PRO 5.0 2.8 + - - +
127B GLY* 3.3 36.1 - - - +
128B VAL* 3.6 12.0 - - - +
131B PHE* 4.2 12.1 - - + -
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Residues in contact with GLU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PRO* 3.7 19.3 - - + +
86B SER* 3.2 21.5 + - - -
87B ALA* 1.3 80.7 - - - +
89B GLN* 1.3 65.6 + - - +
91B GLU* 3.1 37.9 + - + +
92B HIS* 3.4 12.6 - - + +
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Residues in contact with GLN 89 (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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38B THR* 3.0 38.0 + - - +
54B VAL* 3.6 6.0 - - + +
55B MSE 2.8 25.6 + - - +
57B PRO* 3.9 19.3 - - + -
60B LEU* 3.9 21.1 - - + +
84B LEU* 3.6 4.7 - - + -
85B GLY* 2.7 29.2 + - - -
86B SER* 3.1 21.1 + - - +
88B GLU* 1.3 78.6 - - - +
90B GLY* 1.3 63.3 + - - +
92B HIS* 3.1 4.4 + - - +
93B ILE* 2.9 31.1 + - + +
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Residues in contact with GLY 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LEU* 3.8 16.2 - - - +
86B SER 3.7 1.6 + - - -
87B ALA 2.9 12.5 + - - -
89B GLN* 1.3 79.1 - - - +
91B GLU* 1.4 61.6 + - - -
93B ILE* 3.0 16.1 + - - +
94B LEU* 3.0 10.6 + - - +
131B PHE* 3.3 31.0 - - - -
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Residues in contact with GLU 91 (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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87B ALA* 2.7 25.3 - - - +
88B GLU* 3.1 33.3 - - + +
90B GLY* 1.4 74.1 - - - +
92B HIS* 1.3 69.0 + - + +
94B LEU* 3.3 8.1 + - - +
95B GLY* 3.2 16.1 + - - -
98B ARG* 4.8 3.3 + - - -
131B PHE* 3.7 12.6 - - + -
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Residues in contact with HIS 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B PRO* 3.0 26.3 + - + +
58B SER* 3.6 25.6 - - - -
60B LEU* 4.9 5.4 - - + -
61B THR* 2.5 31.0 + - + +
88B GLU* 3.4 15.5 - - + +
89B GLN* 3.1 9.0 + - - +
91B GLU* 1.3 84.7 - - + +
93B ILE* 1.3 58.7 + - - +
95B GLY* 3.0 5.0 + - - +
96B ILE* 2.9 31.2 + - - +
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Residues in contact with ILE 93 (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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8B ILE* 3.7 39.5 - - + -
60B LEU* 4.2 12.6 - - + -
79B VAL* 5.1 0.4 - - + -
81B SER* 4.1 22.0 - - - -
84B LEU* 3.4 35.2 - - + -
89B GLN 2.9 19.7 + - - +
90B GLY* 3.0 9.6 + - - +
92B HIS* 1.3 72.6 - - - +
94B LEU* 1.3 60.3 + - + +
96B ILE* 2.9 10.1 + - + +
97B VAL* 2.8 36.8 + - + +
109B TYR* 4.2 11.2 - - + +
131B PHE* 5.6 1.3 - - + -
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Residues in contact with LEU 94 (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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90B GLY 3.0 14.4 + - - +
91B GLU* 3.7 9.4 - - - +
92B HIS 3.2 0.2 - - - -
93B ILE* 1.3 76.9 - - + +
95B GLY* 1.3 60.8 + - - +
97B VAL* 3.4 5.7 + - + +
98B ARG* 3.1 45.9 + - - +
109B TYR* 3.8 33.2 - - + +
131B PHE* 3.8 16.4 - - + -
135B HIS* 3.6 40.8 - - + +
136B GLY* 4.8 0.2 - - - -
139B ALA* 3.9 15.9 - - + -
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Residues in contact with GLY 95 (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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91B GLU 3.2 8.6 + - - -
92B HIS* 3.0 10.0 + - - -
94B LEU* 1.3 76.0 - - - +
96B ILE* 1.3 63.4 + - - +
98B ARG* 3.4 20.4 + - - +
99B GLN* 3.0 25.0 + - - +
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Residues in contact with ILE 96 (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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6B LEU* 3.8 19.1 - - + -
8B ILE* 4.0 16.8 - - + -
36B LEU* 4.4 1.1 - - + -
60B LEU* 3.6 40.8 - - + +
61B THR* 4.1 8.1 - - + +
64B VAL* 3.6 33.0 - - + -
79B VAL* 4.7 3.6 - - + -
92B HIS 2.9 16.8 + - - +
93B ILE* 2.9 15.2 + - + +
95B GLY* 1.3 76.0 - - - +
97B VAL* 1.3 60.5 + - - +
99B GLN* 3.2 8.4 + - - +
100B VAL* 2.9 34.6 + - + +
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Residues in contact with VAL 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B VAL* 4.0 22.9 - - + -
93B ILE* 2.8 25.2 + - + +
94B LEU* 3.7 8.5 - - + +
96B ILE* 1.3 72.0 - - - +
98B ARG* 1.3 65.4 + - + +
100B VAL* 3.4 0.9 + - - +
101B LYS* 3.0 41.9 + - + +
108B LYS 5.8 0.2 - - - -
109B TYR* 3.6 57.7 - - + -
139B ALA* 5.1 7.2 - - + +
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Residues in contact with ARG 98 (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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91B GLU 4.8 3.0 + - - -
94B LEU* 3.1 34.5 + - - +
95B GLY* 3.6 24.8 - - - +
96B ILE 3.2 0.2 - - - -
97B VAL* 1.3 78.3 - - + +
99B GLN* 1.3 60.8 + - - +
101B LYS* 3.4 5.5 + - - +
102B ALA* 3.0 25.6 + - - +
139B ALA* 6.2 1.6 - - - +
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Residues in contact with GLN 99 (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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61B THR* 5.7 1.0 - - - +
64B VAL* 4.0 10.5 - - + +
65B GLN* 2.8 45.3 + - - +
68B ALA* 3.6 18.6 - - + +
73B LEU* 3.7 15.0 - - + +
95B GLY 3.0 15.4 + - - +
96B ILE* 3.2 9.3 + - - +
98B ARG* 1.3 75.8 - - - +
100B VAL* 1.3 62.7 + - - +
102B ALA* 3.3 7.7 + - + +
103B ALA* 3.2 21.3 + - - +
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Residues in contact with VAL 100 (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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6B LEU* 4.5 4.9 - - + -
64B VAL* 4.8 0.7 - - + -
73B LEU* 4.0 31.2 - - + +
76B CYS* 3.6 34.3 - - + +
79B VAL* 3.9 21.1 - - + -
96B ILE* 2.9 34.0 + - + +
97B VAL 3.9 3.1 - - - +
99B GLN* 1.3 71.3 - - - +
101B LYS* 1.3 52.4 + - + +
103B ALA* 3.0 4.5 + - - +
104B ASN* 2.7 33.3 + - - +
107B ALA* 3.8 18.6 - - + -
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Residues in contact with LYS 101 (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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97B VAL* 3.0 36.9 + - + +
98B ARG* 4.0 4.7 - - - +
100B VAL* 1.3 77.2 - - + +
102B ALA* 1.3 59.0 + - - +
104B ASN 3.4 8.1 - - - +
105B PRO* 2.9 39.1 - - + +
107B ALA* 3.2 32.5 + - + +
108B LYS 4.3 0.7 - - - -
109B TYR 4.1 4.9 - - - +
139B ALA 4.5 9.1 + - - -
141B ASP* 2.8 33.0 + - - -
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Residues in contact with ALA 102 (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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98B ARG 3.0 18.5 + - - +
99B GLN* 3.7 8.1 - - + +
100B VAL 3.2 0.2 - - - -
101B LYS* 1.3 76.7 - - - +
103B ALA* 1.3 57.9 + - - +
105B PRO* 4.6 6.0 - - - +
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Residues in contact with ALA 103 (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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73B LEU* 4.0 13.7 - - + -
74B HIS* 3.6 39.6 - - + +
99B GLN 3.2 11.5 + - - +
100B VAL 3.0 9.1 + - - +
102B ALA* 1.3 80.0 - - - +
104B ASN* 1.3 58.0 + - - +
105B PRO* 3.9 5.2 - - - +
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Residues in contact with ASN 104 (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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73B LEU 4.9 0.7 - - - +
74B HIS* 3.4 23.4 + - - +
76B CYS 3.0 28.5 + - - +
77B ASP* 4.1 12.1 + - - +
100B VAL 2.7 12.7 + - - +
101B LYS* 3.1 7.5 - - - +
103B ALA* 1.3 74.4 - - - +
105B PRO* 1.3 60.0 - - - +
106B GLN* 3.2 26.3 + - - +
107B ALA* 2.8 41.7 + - + +
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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
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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