Contacts of the strand formed by residues 620 - 626 (chain A) in PDB entry 6N8Q
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 ARG 620 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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545A VAL* 5.1 1.6 - - - -
614A PHE* 3.7 5.2 - - - -
615A ASP* 2.9 31.8 + - + +
618A GLN* 3.1 43.6 + - + +
619A ARG* 1.3 81.6 - - - +
621A GLN* 1.3 66.1 + - - +
622A VAL* 4.3 0.2 - - - +
756A MET 4.5 6.5 + - - -
757A ASP 5.3 3.2 + - - -
759A PRO* 5.6 5.5 - - - +
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Residues in contact with GLN 621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545A VAL* 4.3 5.0 - - + +
546A GLU 3.5 13.8 + - - +
547A ALA* 3.3 28.8 - - + +
583A VAL* 3.7 5.9 - - - +
605A PHE* 3.3 20.4 - - - -
613A LEU 3.0 19.6 + - - +
614A PHE* 3.3 23.8 - - - +
620A ARG* 1.3 75.3 - - - +
622A VAL* 1.3 66.4 + - - +
623A PHE 3.8 14.5 - - - +
624A VAL* 3.9 12.8 - - + +
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Residues in contact with VAL 622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602A LEU* 4.5 2.9 - - + -
613A LEU* 3.0 28.5 + - + +
614A PHE 4.3 1.8 - - - -
615A ASP* 3.8 31.6 - - + +
621A GLN* 1.3 75.9 - - - +
623A PHE* 1.3 62.7 + - - +
760A VAL* 3.5 41.7 - - + +
762A ALA* 4.1 26.7 - - + +
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Residues in contact with PHE 623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611A PHE* 3.8 25.8 - + - -
612A GLY* 4.6 1.8 - - - -
613A LEU* 3.0 62.2 + - + +
621A GLN* 3.7 2.5 - - - +
622A VAL* 1.3 81.9 - - + +
624A VAL* 1.3 81.6 + - - +
625A LYS* 4.2 8.3 - - + -
733A LEU* 4.2 6.3 - - + -
745A PHE* 3.6 45.1 - + + -
762A ALA* 3.6 31.6 - - + +
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Residues in contact with VAL 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547A ALA* 4.4 15.0 - - + -
548A ASP 3.3 27.1 - - - +
549A LEU* 3.5 31.0 - - + +
551A GLN* 4.6 19.8 - - + +
552A ASP* 5.8 0.2 - - - +
611A PHE 3.7 4.3 - - - -
612A GLY* 4.5 2.0 - - - -
621A GLN* 3.9 22.9 - - + +
623A PHE* 1.3 86.4 - - - +
625A LYS* 1.3 65.1 + - - +
626A CYS 4.9 0.2 - - - +
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Residues in contact with LYS 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549A LEU* 4.7 0.4 - - - +
610A GLY* 3.2 2.1 - - - -
611A PHE* 2.7 61.0 + - + +
623A PHE* 4.2 7.8 - - + -
624A VAL* 1.3 78.0 - - - +
626A CYS* 1.3 74.3 + - - +
627A THR* 4.3 0.4 - - + -
743A TYR* 3.6 37.7 + - - -
745A PHE* 3.5 24.9 - - + -
764A GLN* 3.3 22.1 + - - +
767A GLU* 5.2 1.2 + - - -
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Residues in contact with CYS 626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549A LEU 3.1 25.6 + - - +
550A LEU* 5.0 6.7 - - - -
552A ASP* 5.9 7.6 - - + +
553A GLN* 5.7 5.8 - - - -
609A HIS* 4.0 2.5 - - - -
610A GLY* 4.1 3.8 - - - -
624A VAL* 4.3 0.6 - - - +
625A LYS* 1.3 86.2 + - - +
627A THR* 1.3 64.4 + - - +
628A LEU* 3.5 36.5 + - - -
629A HIS* 4.5 16.5 + - - +
743A TYR* 5.5 0.2 + - - -
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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
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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