Contacts of the strand formed by residues 680 - 685 (chain B) in PDB entry 6M17
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 680 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349A ASP* 2.9 27.0 + - - -
619B LYS* 4.3 15.0 - - - -
620B VAL 3.2 13.9 - - - -
621B ARG* 4.7 8.1 - - - -
674B ASN 2.9 15.4 - - - +
675B LEU* 3.4 1.5 - - - +
676B LYS* 2.9 30.5 + - - +
678B ARG* 4.2 2.4 - - - +
679B ILE* 1.3 79.1 + - - +
681B PHE* 1.3 67.8 + - - +
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Residues in contact with PHE 681 (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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618B ILE 3.8 0.2 - - - +
619B LYS* 3.5 5.6 - - - +
620B VAL* 3.0 47.7 + - + +
622B ILE* 4.2 20.2 - - + -
635B TRP* 4.6 0.9 - + - -
640B MET* 3.8 24.9 - - + -
643B PHE* 3.7 39.5 - + - -
672B VAL* 3.8 25.4 - - + -
673B ALA 3.4 10.1 - - - +
674B ASN 3.4 10.1 - - - +
675B LEU* 3.7 20.9 - - + -
679B ILE* 4.8 4.5 - - + -
680B SER* 1.3 82.6 - - - +
682B ASN* 1.3 70.9 + - - +
683B PHE* 4.8 3.6 - + + -
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Residues in contact with ASN 682 (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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613B TYR* 6.4 1.3 - - + -
614B ALA* 6.2 1.4 - - - +
617B SER* 4.0 26.6 + - - +
618B ILE 3.4 3.6 - - - -
619B LYS* 4.1 26.9 - - - +
672B VAL* 3.3 6.9 - - - +
673B ALA* 2.9 40.1 + - + +
674B ASN* 4.0 19.0 - - - +
681B PHE* 1.3 81.7 - - - +
683B PHE* 1.3 62.0 + - - +
684B PHE* 6.0 0.2 - - - -
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Residues in contact with PHE 683 (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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616B GLN 4.2 0.5 - - - +
617B SER* 3.3 4.1 - - - -
618B ILE* 3.0 61.1 + - + +
620B VAL* 3.6 28.0 - - + -
643B PHE* 4.8 7.4 - + + -
647B VAL* 3.7 25.6 - - + -
670B VAL* 3.7 26.5 - - + -
671B ARG 3.3 10.8 - - - +
672B VAL* 4.4 8.5 - - + -
681B PHE* 4.8 4.0 - + + -
682B ASN* 1.3 77.1 - - - +
684B PHE* 1.3 66.5 + - - +
685B VAL* 4.1 11.2 - - + -
700B VAL* 4.2 6.1 - - + -
704B ILE* 3.6 25.8 - - + -
724B PHE* 4.2 6.7 - + - -
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Residues in contact with PHE 684 (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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490B PRO 5.1 0.4 - - - -
491B VAL* 5.0 9.9 - - + -
492B PRO* 3.8 20.2 - - + -
613B TYR* 3.7 32.3 - + + -
616B GLN* 3.6 21.3 - - + +
617B SER* 3.8 17.0 - - - +
669B ASP 3.8 0.7 - - - +
670B VAL* 3.7 2.6 - - - -
671B ARG* 3.1 56.0 + - + +
673B ALA* 6.1 0.7 - - + -
682B ASN 6.0 0.2 - - - -
683B PHE* 1.3 77.6 - - - +
685B VAL* 1.3 63.1 + - - +
686B THR* 3.6 21.8 - - - -
694B ILE* 4.0 33.7 - - + -
700B VAL* 6.3 0.4 - - - -
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Residues in contact with VAL 685 (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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647B VAL* 4.5 6.7 - - + -
648B ALA* 6.3 0.2 - - - -
651B MET* 4.1 18.6 - - + -
665B PHE* 4.1 26.9 - - + -
669B ASP* 3.5 10.1 - - + +
670B VAL* 4.8 7.6 - - + -
683B PHE* 4.1 14.1 - - + -
684B PHE* 1.3 79.0 - - - +
686B THR* 1.3 65.4 + - - +
694B ILE* 3.7 7.3 - - - +
695B ILE* 3.0 36.2 + - + +
700B VAL* 4.0 35.1 - - + +
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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