Contacts of the strand formed by residues 614 - 618 (chain B) in PDB entry 2NVX
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 614 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604B ARG* 3.6 2.2 - - - +
612B GLU 3.3 2.9 + - - -
613B VAL* 1.3 72.7 - - - +
615B MET* 1.3 60.0 + - - +
616B ILE* 3.5 10.6 - - - +
626B ILE* 3.6 2.8 - - - +
627B PHE* 3.0 33.0 + - - +
632B ARG* 2.7 27.4 + - - +
692B TYR 5.6 0.2 - - - -
694B ASP* 2.9 32.2 + - - -
697B GLU* 3.3 15.3 - - - -
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Residues in contact with MET 615 (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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554B ILE* 5.8 0.7 - - - -
597B MET* 3.3 25.5 - - + +
600B LEU* 3.3 60.3 - - + +
601B ARG* 3.6 22.6 + - + +
604B ARG* 3.8 24.0 - - + +
609B ILE* 5.0 13.0 - - - -
613B VAL* 4.0 9.1 + - + +
614B SER* 1.3 79.0 - - - +
616B ILE* 1.3 59.1 - - - +
617B ARG 3.5 2.0 + - - -
624B LEU* 5.0 0.4 - - - -
625B LYS 3.7 4.9 - - - -
626B ILE* 4.1 23.3 - - + -
697B GLU* 3.4 22.2 + - - +
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Residues in contact with ILE 616 (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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614B SER* 3.5 28.7 - - - +
615B MET* 1.3 67.8 - - - +
617B ARG* 1.3 63.6 + - - +
618B ASP* 3.5 8.3 + - + +
623B GLU 4.3 0.3 - - - +
624B LEU* 3.7 1.9 - - - -
625B LYS* 2.8 52.1 + - + +
627B PHE* 3.9 20.6 - - + -
696B GLU* 3.7 34.1 - - + +
697B GLU* 3.6 30.5 - - + +
699B GLU* 5.7 2.5 - - + -
700B SER* 4.8 8.3 - - - +
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Residues in contact with ARG 617 (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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578B THR* 4.1 7.3 + - - +
593B PRO* 3.5 32.0 + - - +
594B ALA* 4.4 14.1 - - - +
597B MET* 3.8 35.3 - - + +
601B ARG* 5.1 5.1 - - - +
615B MET 3.5 4.6 + - - -
616B ILE* 1.3 71.4 - - - +
618B ASP* 1.3 79.0 + - - +
619B ILE* 3.8 35.2 + - + +
622B LYS* 5.8 1.0 - - - +
623B GLU 4.2 6.7 + - - -
624B LEU* 4.2 17.3 - - + -
700B SER* 3.8 22.8 + - - -
61I ASP* 3.4 31.5 + - - +
64I SER* 4.9 2.8 + - - -
65I ASP* 5.6 0.2 - - - +
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Residues in contact with ASP 618 (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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789A LYS* 5.9 1.0 + - - -
616B ILE* 3.5 10.5 + - + +
617B ARG* 1.3 80.4 + - - +
619B ILE* 1.3 73.8 + - - +
620B ARG* 3.4 17.3 + - - +
621B GLU* 3.5 29.0 + - + +
622B LYS* 3.7 1.7 + - - -
623B GLU* 3.0 40.8 + - + +
700B SER* 5.8 0.9 - - - -
65I ASP* 5.5 0.3 - - - +
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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