Contacts of the strand formed by residues 555 - 559 (chain B) in PDB entry 1VDV
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 ALA 555 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161B ARG* 5.7 0.9 - - - +
553B PRO 3.9 1.5 + - - +
554B PRO* 1.3 76.6 - - - +
556B ASN* 1.3 62.5 + - - +
557B ILE* 5.3 3.8 - - + -
1237B THR 3.0 6.3 + - - -
1238B GLU* 3.1 26.2 - - + +
1239B PHE 2.8 26.2 + - - -
1240B ARG* 5.3 6.3 - - - +
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Residues in contact with ASN 556 (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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154B ARG* 3.7 21.7 + - + +
157B LEU* 5.7 0.2 - - - +
158B GLN* 3.7 26.1 + - - +
161B ARG* 3.3 36.4 - - - +
554B PRO* 4.9 1.7 - - - +
555B ALA* 1.3 84.1 - - - +
557B ILE* 1.3 77.3 + - - +
558B GLN* 3.6 16.6 - - - +
1235B ILE* 5.6 2.8 - - - +
1236B PRO 4.8 0.5 - - - +
1237B THR 4.1 5.2 - - - +
1239B PHE* 3.3 24.6 + - - +
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Residues in contact with ILE 557 (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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555B ALA* 5.3 2.9 - - + -
556B ASN* 1.3 91.9 - - - +
558B GLN* 1.3 68.9 + - - +
559B LEU* 4.1 29.2 - - + -
1239B PHE 3.2 7.4 + - - +
1240B ARG* 3.2 38.4 - - + +
1241B VAL 2.9 25.5 + - - +
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Residues in contact with GLN 558 (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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154B ARG* 3.4 28.9 + - - +
158B GLN* 3.0 30.3 + - - +
192B SER* 5.0 1.2 + - - -
193B PRO 4.5 6.8 - - - +
195B LEU* 3.8 29.3 + - + +
196B PHE* 5.7 1.0 - - - -
556B ASN* 3.6 3.6 - - - +
557B ILE* 1.3 91.9 + - - +
559B LEU* 1.3 69.4 + - - +
560B PHE* 4.3 7.1 + - + -
1192B ILE* 3.7 26.5 - - + -
1196B GLU* 4.7 3.6 - - - +
1239B PHE 4.8 0.6 + - - -
1241B VAL* 3.2 7.0 - - + +
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Residues in contact with LEU 559 (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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192B SER* 3.9 26.2 - - - +
193B PRO 5.7 0.2 - - - -
557B ILE* 4.1 20.2 - - + -
558B GLN* 1.3 82.0 - - - +
560B PHE* 1.3 62.8 + - - +
970B GLU* 5.6 3.1 - - - +
974B SER* 6.2 3.6 - - - -
1192B ILE* 4.6 1.5 - - - +
1241B VAL 2.9 10.1 + - - +
1242B SER* 3.3 24.6 - - - +
1243B LEU* 2.8 30.1 + - - +
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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