Contacts of the strand formed by residues 400 - 403 (chain I) in PDB entry 2GD4
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 VAL 400 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37H GLU* 4.6 23.1 - - + +
39H GLU* 5.2 1.6 - - - -
260I TYR* 3.4 39.0 - - + +
262I ARG* 5.7 0.4 - - - +
268I GLN* 4.5 0.9 - - - +
314I MET* 3.9 25.4 - - + -
315I MET 3.1 4.6 + - - -
316I LEU* 2.7 37.9 - - + +
317I VAL* 2.7 5.2 + - - +
398I ASN 3.6 10.5 - - - +
399I ARG* 1.3 78.8 - - - +
401I THR* 1.3 74.8 + - - +
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Residues in contact with THR 401 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H GLU* 5.8 0.4 + - - -
39H GLU* 2.9 34.3 + - - +
262I ARG* 5.2 1.9 + - - -
268I GLN* 3.5 22.3 + - - +
316I LEU* 5.1 0.2 - - - -
317I VAL* 3.3 19.9 - - + +
319I HIS* 3.7 26.7 - - + +
400I VAL* 1.3 79.8 - - - +
402I PHE* 1.3 65.0 + - - +
403I LYS* 3.9 9.1 + - + +
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Residues in contact with PHE 402 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260I TYR* 4.8 5.4 - + + -
268I GLN* 3.5 46.9 - - + -
270I LEU* 3.3 47.8 - - + -
283I LEU* 3.6 28.0 - - + -
285I LEU* 3.5 20.6 - - + -
316I LEU* 5.0 9.0 - - + -
317I VAL 2.7 12.0 + - - +
318I VAL* 3.4 5.4 - - + -
319I HIS 2.7 28.4 + - - +
401I THR* 1.3 73.8 - - - +
403I LYS* 1.3 52.3 + - - +
404I ALA* 3.4 29.6 + - + -
408I PHE* 5.7 0.2 - - + -
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Residues in contact with LYS 403 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268I GLN* 5.4 0.6 + - - -
285I LEU* 3.7 8.9 - - - +
319I HIS* 3.4 37.9 - - + +
401I THR* 3.9 6.5 + - + +
402I PHE* 1.3 71.0 - - - +
404I ALA* 1.3 52.0 + - - +
405I ASN* 2.6 35.3 + - + +
406I ARG* 4.4 6.2 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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