Contacts of the strand formed by residues 26 - 31 (chain B) in PDB entry 5VGR
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 PRO 26 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B GLY* 1.3 84.9 - - - +
27B VAL* 1.3 62.1 + - - +
28B GLN 4.2 0.9 + - - -
107B SER* 3.4 31.0 - - - +
108B TRP* 4.0 25.1 - - + +
110B GLY 6.4 0.2 - - - -
120B GLN* 3.7 27.0 - - + +
121B ILE 3.5 6.3 - - - +
122B TRP* 3.5 14.1 - - + -
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Residues in contact with VAL 27 (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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25B GLY 3.8 0.7 - - - +
26B PRO* 1.3 78.9 - - - +
28B GLN* 1.3 66.1 + - - +
29B VAL* 3.3 6.4 + - + +
45B ALA* 4.0 27.1 - - + +
49B ILE* 3.6 25.4 - - + -
120B GLN* 3.3 4.4 - - - -
121B ILE* 2.7 35.4 + - + +
123B SER* 3.6 30.3 - - - -
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Residues in contact with GLN 28 (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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26B PRO 4.2 1.2 + - - -
27B VAL* 1.3 77.1 - - - +
29B VAL* 1.3 60.3 + - - +
30B VAL 3.3 18.3 + - - +
31B LEU* 3.4 36.0 - - + +
42B ASP* 3.8 19.2 - - - +
45B ALA* 4.2 1.6 - - - +
116B THR* 5.3 11.0 - - - +
117B THR 5.1 1.4 + - - -
118B GLY* 4.0 7.1 - - - -
119B ILE 3.6 17.2 + - - +
120B GLN* 3.7 27.7 + - + +
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Residues in contact with VAL 29 (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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27B VAL* 3.4 22.7 - - + +
28B GLN* 1.3 75.7 - - - +
30B VAL* 1.3 76.5 + - + +
31B LEU* 4.3 1.6 - - - -
41B LEU* 3.4 8.5 - - - +
42B ASP* 2.9 29.8 + - - -
46B LEU* 4.1 30.3 - - + +
119B ILE* 3.0 27.4 + - + +
121B ILE* 3.7 26.9 - - + +
325B PHE* 4.6 13.0 - - + -
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Residues in contact with VAL 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B GLN* 3.3 10.4 + - - -
29B VAL* 1.3 94.7 - - + +
31B LEU* 1.3 63.6 + - - +
39B PHE* 3.8 15.0 - - + -
40B GLU 3.3 11.4 - - - +
41B LEU* 5.0 6.5 - - + -
118B GLY* 3.4 4.2 - - - -
119B ILE* 3.2 46.4 + - + +
158B THR* 6.2 0.7 - - + -
159B ILE* 3.5 23.8 - - + -
162B LEU* 4.6 20.2 - - + -
325B PHE* 4.8 10.8 - - + -
329B ILE* 5.0 0.7 - - + -
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Residues in contact with LEU 31 (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 GLN* 3.4 34.3 - - + +
29B VAL 4.3 1.8 - - - -
30B VAL* 1.3 75.4 - - - +
32B VAL* 1.3 65.3 + - - +
39B PHE* 3.2 12.6 - - - -
40B GLU* 2.8 41.8 + - + +
42B ASP* 4.0 36.8 - - + +
116B THR* 6.3 1.8 - - - -
117B THR 4.8 2.5 - - - -
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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