Contacts of the strand formed by residues 101 - 110 (chain B) in PDB entry 1VGC
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 ASN 101 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91B ASN* 4.0 5.7 - - - +
93B LYS* 3.2 40.2 + - + +
94B TYR* 3.4 15.4 - - - +
95B ASN* 5.5 0.6 - - - +
100B ASN* 1.3 97.6 + - - +
102B ASP* 1.3 59.0 - - - +
103B ILE* 3.0 16.8 + - - +
179C ALA* 3.3 23.9 + - - +
180C MET* 5.7 0.4 - - - +
233C ALA 5.4 0.2 - - - +
234C LEU* 3.5 24.8 - - + +
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Residues in contact with ASP 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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54B THR 4.2 0.3 - - - +
55B ALA* 3.6 13.7 - - - +
56B ALA* 2.8 28.7 + - - +
57B HIS* 2.7 39.7 + - - -
94B TYR* 3.7 8.6 - - + -
99B ILE* 3.5 20.6 - - + +
100B ASN 3.3 0.2 - - - -
101B ASN* 1.3 70.8 - - - +
103B ILE* 1.3 59.7 + - - +
212C ILE* 4.2 3.3 - - - +
214C SER* 2.8 27.9 + - - +
229C ALA* 3.6 24.9 - - + +
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Residues in contact with ILE 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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53B VAL* 4.6 9.6 - - + -
54B THR 3.5 6.3 - - - +
56B ALA* 3.6 7.7 - - - +
91B ASN* 3.3 50.4 + - + +
101B ASN 3.0 8.2 + - - +
102B ASP* 1.3 75.9 - - - +
104B THR* 1.3 69.6 + - - +
212C ILE* 3.6 23.6 - - + -
231C VAL* 5.7 4.5 - - + -
234C LEU* 3.7 31.2 - - + -
237C TRP* 3.9 11.1 - - + -
238C VAL* 3.7 30.3 - - + -
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Residues in contact with THR 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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53B VAL* 3.7 2.6 - - - -
54B THR* 2.9 38.3 + - + +
55B ALA 4.1 6.1 - - - -
56B ALA* 3.3 25.4 + - - +
60B VAL* 5.3 2.7 - - + -
88B VAL* 3.6 29.5 - - + +
89B PHE 3.2 6.5 - - - +
90B LYS* 3.3 20.8 - - - +
103B ILE* 1.3 73.1 + - - +
105B LEU* 1.3 69.5 + - - +
106B LEU* 3.7 12.8 - - + -
237C TRP* 4.4 0.4 - - - -
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Residues in contact with LEU 105 (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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47B ILE* 3.9 17.3 - - + -
51B TRP* 3.8 17.9 - - + -
52B VAL 3.5 7.0 - - - +
53B VAL* 3.4 31.0 - - + -
88B VAL* 3.7 0.3 - - - -
89B PHE* 2.7 45.3 + - + +
104B THR* 1.3 76.0 - - - +
106B LEU* 1.3 60.4 + - - +
107B LYS 4.1 0.2 - - - -
237C TRP* 3.9 20.1 - - + -
238C VAL* 4.0 11.7 - - + -
241C THR* 3.7 31.6 - - + -
242C LEU* 3.7 16.6 - - + -
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Residues in contact with LEU 106 (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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33B LEU* 3.9 28.3 - - + -
50B ASN 3.7 0.2 - - - +
51B TRP* 3.2 8.7 - - - -
52B VAL* 2.8 52.2 + - + +
54B THR* 4.0 14.1 - - + -
60B VAL* 3.7 23.6 - - + -
66B VAL* 4.0 8.1 - - + -
85B ILE* 4.0 23.3 - - + -
87B LYS 3.6 2.7 - - - +
88B VAL* 4.1 14.4 - - + -
104B THR* 3.7 20.6 - - + -
105B LEU* 1.3 77.1 - - - +
107B LYS* 1.3 62.6 + - - +
108B LEU* 3.7 2.5 + - + +
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Residues in contact with LYS 107 (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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50B ASN* 3.5 31.9 + - - +
51B TRP* 3.7 38.9 - - + +
85B ILE* 3.7 2.6 - - - -
86B ALA* 2.8 32.6 + - + -
87B LYS* 3.0 17.0 + - + +
89B PHE* 4.0 12.3 - - + -
106B LEU* 1.3 71.7 - - - +
108B LEU* 1.3 68.7 + - - +
245C ASN* 3.6 21.5 + - + +
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Residues in contact with LEU 108 (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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46B LEU* 4.2 15.0 - - + -
49B GLU 3.3 25.6 - - - +
50B ASN* 2.9 29.6 + - - +
51B TRP 4.3 0.4 - - - +
52B VAL* 4.1 11.7 - - + -
66B VAL* 4.0 32.1 - - + -
83B LEU* 4.1 16.2 - - + -
84B LYS 3.5 10.8 - - - +
85B ILE* 4.5 3.6 - - + +
86B ALA* 4.2 1.5 - - - +
106B LEU 4.7 2.5 - - - +
107B LYS* 1.3 88.4 + - - +
109B SER* 1.3 63.6 + - - +
110B THR 3.2 21.5 + - - +
112B ALA 4.1 4.7 - - - +
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Residues in contact with SER 109 (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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84B LYS* 2.8 40.8 + - - +
85B ILE 4.3 1.6 - - - -
86B ALA* 3.6 27.7 - - - +
108B LEU* 1.3 73.8 - - - +
110B THR* 1.3 61.6 + - - +
111B ALA 4.3 0.5 + - - -
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Residues in contact with THR 110 (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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82B LYS 4.9 1.6 - - - +
83B LEU* 3.8 21.4 - - + +
84B LYS* 3.6 31.4 - - + +
108B LEU* 3.2 19.0 - - - +
109B SER* 1.3 84.3 - - - +
111B ALA* 1.3 70.7 + - - +
112B ALA 3.6 1.2 + - - -
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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
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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