Contacts of the strand formed by residues 561 - 564 (chain B) in PDB entry 3GJN
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 ILE 561 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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475B PRO* 4.4 0.9 - - - +
476B VAL* 3.4 33.8 + - + +
492B PHE* 3.9 26.0 - - + -
495B PHE* 4.0 21.8 - - + -
499B PHE* 6.1 0.2 - - + -
543B LEU* 4.4 19.7 - - + -
544B HIS 3.3 9.9 - - - +
545B ALA* 4.5 9.4 - - + -
556B TYR* 4.4 10.5 - - + -
557B ASP 3.3 25.8 - - - +
558B MET* 3.4 11.1 + - - +
559B ASP 3.5 0.9 - - - -
560B ASN* 1.3 82.7 - - + +
562B SER* 1.3 74.7 + - - +
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Residues in contact with SER 562 (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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472B LEU* 2.2 36.3 + - - +
473B GLY 4.5 0.2 - - - -
474B SER 3.1 22.0 - - - -
475B PRO* 4.3 2.9 - - - -
476B VAL* 4.6 1.1 - - - +
543B LEU* 3.4 9.9 - - - +
544B HIS* 3.0 41.2 + - - +
560B ASN 4.2 0.6 - - - -
561B ILE* 1.3 79.1 - - - +
563B VAL* 1.3 61.7 + - - +
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Residues in contact with VAL 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B TRP* 3.7 25.4 - - + -
465B LEU* 4.2 8.5 - - + -
468B ALA* 3.8 5.2 - - + +
473B GLY* 3.3 2.4 - - - -
474B SER* 2.7 44.6 + - - +
475B PRO 4.9 1.6 - - - +
476B VAL* 5.5 0.9 - - + +
499B PHE* 4.0 17.7 - - + -
500B TRP* 3.7 23.1 - - + -
541B PHE* 3.9 22.0 - - + -
542B GLU 3.3 8.3 - - - +
543B LEU* 4.1 7.2 - - + -
562B SER* 1.3 73.8 - - - +
564B VAL* 1.3 71.3 + - - +
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Residues in contact with VAL 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B ALA* 3.3 8.1 - - - +
472B LEU 3.7 21.1 - - - +
473B GLY* 4.0 6.7 - - - -
541B PHE* 3.7 6.8 - - - -
542B GLU* 2.7 49.1 + - - +
544B HIS* 3.9 16.8 - - + -
562B SER* 4.6 0.2 - - - +
563B VAL* 1.3 82.2 - - - +
565B THR* 1.3 68.2 + - - +
568B ARG* 4.6 3.4 - - + -
569B HIS* 3.5 38.4 - - + +
572B ILE* 4.1 16.4 - - + -
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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