Contacts of the strand formed by residues 42 - 49 (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 CYS 42 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33B LEU* 2.8 44.6 + - + -
40B HIS* 3.0 15.4 + - - -
41B PHE* 1.3 97.1 - - + +
43B GLY* 1.3 57.7 + - - +
57B HIS* 5.3 0.7 - - - -
58B CYS* 2.2 50.7 - - - -
193C GLY 4.0 5.4 - - - -
195C SER* 3.5 16.4 - - - -
358C V36 5.0 1.6 - - - -
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Residues in contact with GLY 43 (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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30B GLN* 3.8 10.5 - - - -
31B VAL 3.5 11.7 - - - -
33B LEU* 3.6 7.0 - - - +
40B HIS* 4.1 5.1 - - - -
42B CYS* 1.3 75.8 - - - +
44B GLY* 1.3 57.5 + - - -
54B THR* 3.0 20.6 + - - -
140B GLY* 6.4 0.2 - - - -
193C GLY 4.2 3.2 + - - -
194C ASP 4.8 2.0 - - - -
195C SER 2.8 10.9 + - - -
196C GLY* 3.2 12.6 - - - -
197C GLY* 4.0 4.0 - - - -
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Residues in contact with GLY 44 (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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29B TRP 3.6 0.9 - - - +
30B GLN* 3.6 7.3 + - - +
31B VAL* 3.1 39.7 + - - +
33B LEU* 5.2 0.4 - - - -
43B GLY* 1.3 74.0 - - - -
45B SER* 1.3 65.0 + - - -
52B VAL* 4.3 3.4 - - - -
53B VAL 3.2 13.0 - - - -
54B THR* 4.3 1.8 - - - -
196C GLY 3.4 7.8 + - - -
197C GLY* 3.9 3.4 - - - -
198C PRO* 4.2 1.7 - - - +
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Residues in contact with SER 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B TRP* 3.2 10.6 - - - -
31B VAL* 5.0 0.2 - - - -
44B GLY* 1.3 76.6 + - - -
46B LEU* 1.3 61.4 + - - +
47B ILE 3.6 0.2 + - - -
52B VAL* 3.4 5.2 - - - +
53B VAL* 2.8 53.6 + - - +
121B VAL* 4.1 18.8 - - - -
196C GLY 4.5 0.5 + - - -
197C GLY 4.5 0.5 - - - -
198C PRO* 3.2 34.3 - - - +
209C LEU* 4.1 4.3 - - - +
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Residues in contact with LEU 46 (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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28B PRO 4.4 5.8 - - - +
29B TRP* 2.9 11.0 + - - +
31B VAL* 3.8 22.9 - - + -
45B SER* 1.3 72.4 - - - +
47B ILE* 1.3 60.2 + - - +
48B ASN 3.5 21.1 - - - +
51B TRP 3.7 3.4 - - - +
52B VAL* 3.8 20.4 - - + +
66B VAL* 5.7 0.2 - - + -
68B ALA* 4.4 5.8 - - + -
83B LEU* 5.5 1.6 - - + -
108B LEU* 4.2 14.8 - - + -
112B ALA* 4.2 10.1 - - + -
114B PHE* 4.2 4.9 - - + -
118B VAL* 3.6 31.4 - - + -
119B SER 3.8 18.6 - - - +
120B ALA* 3.5 1.2 - - - -
121B VAL* 3.1 26.9 + - - +
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Residues in contact with ILE 47 (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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45B SER 3.6 0.4 + - - +
46B LEU* 1.3 76.1 - - - +
48B ASN* 1.3 65.7 + - - +
51B TRP* 3.1 23.9 + - + +
53B VAL* 3.8 25.8 - - + -
105B LEU* 3.9 26.2 - - + -
120B ALA* 3.5 15.8 - - - +
121B VAL* 4.2 16.0 - - + +
123B LEU* 4.0 31.2 - - + -
238C VAL* 4.0 12.3 - - + -
242C LEU* 3.9 25.4 - - + -
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Residues in contact with ASN 48 (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* 3.5 14.0 - - - +
47B ILE* 1.3 78.3 - - - +
49B GLU* 1.3 73.8 + - - +
50B ASN* 2.9 34.8 + - - +
51B TRP* 3.0 44.3 - - - +
114B PHE* 3.5 13.2 - - - -
120B ALA* 3.9 2.9 - - - +
242C LEU* 3.7 17.5 - - - +
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Residues in contact with GLU 49 (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 ASN* 1.3 81.8 - - - +
50B ASN* 1.3 70.8 + - - +
51B TRP 3.8 0.2 - - - -
108B LEU* 3.3 8.9 - - - +
111B ALA* 3.3 7.8 - - + -
112B ALA* 2.7 51.3 + - - +
114B PHE* 3.4 38.3 + - + +
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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