Contacts of the strand formed by residues 691 - 699 (chain B) in PDB entry 3HI7
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 691 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478B LYS* 4.0 16.4 - - - +
479B MET 3.0 14.4 - - - -
480B HIS* 3.7 24.0 - - - -
598B HIS* 5.0 0.7 - - - +
600B MET* 6.0 1.4 - - - +
673B PHE* 5.2 0.4 - - - -
687B THR 4.9 2.5 - - - -
689B GLY* 3.4 6.1 - - - +
690B ASN* 1.3 77.6 - - - +
692B VAL* 1.3 72.2 + - - +
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Residues in contact with VAL 692 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B LYS* 3.4 7.9 - - - +
479B MET* 2.9 53.0 + - + +
514B VAL* 5.1 1.3 - - + -
598B HIS* 3.4 18.8 - - - +
599B SER* 4.0 5.4 - - - -
600B MET* 4.5 4.7 - - + +
671B VAL* 3.7 21.5 - - + +
672B GLY* 3.5 31.9 - - - +
673B PHE* 4.0 15.0 - - + -
691B SER* 1.3 80.2 - - - +
693B GLY* 1.3 60.0 + - - +
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Residues in contact with GLY 693 (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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477B ALA 3.2 12.8 - - - -
516B TYR* 5.0 3.6 - - - -
598B HIS* 2.8 36.9 + - - +
671B VAL* 3.5 18.3 - - - +
692B VAL* 1.3 78.7 - - - +
694B PHE* 1.3 68.4 + - - +
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Residues in contact with PHE 694 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B VAL* 3.8 14.4 - - + -
475B MET* 5.9 1.6 - - + -
476B GLU* 3.3 6.0 - - - +
477B ALA* 2.9 55.4 + - + +
516B TYR* 3.5 35.2 - + + -
518B VAL* 3.5 26.2 - - + -
595B LEU* 3.6 24.7 - - + -
596B GLN 3.2 13.7 - - - +
597B ILE* 4.0 8.5 - - + -
598B HIS* 4.3 5.0 + - - +
669B VAL* 4.0 15.3 - - + -
693B GLY* 1.3 80.1 - - - +
695B LEU* 1.3 67.3 + - - +
696B LEU* 4.0 21.5 - - + -
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Residues in contact with LEU 695 (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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689A GLY* 3.3 35.0 - - - +
470B TYR* 4.5 4.0 - - + +
474B VAL* 3.6 20.2 - - + -
475B MET 3.4 1.8 - - - +
476B GLU* 3.4 36.6 - - + +
594B ARG 4.2 0.2 - - - -
595B LEU* 3.4 7.6 - - - +
596B GLN* 2.8 56.5 + - + +
598B HIS* 3.8 17.9 - - + -
694B PHE* 1.3 73.8 - - - +
696B LEU* 1.3 64.7 + - - +
697B ARG* 4.1 13.0 - - + -
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Residues in contact with LEU 696 (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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346B ILE* 5.5 2.0 - - + -
347B ALA* 5.2 1.3 - - + -
350B VAL* 4.5 6.7 - - + -
474B VAL* 3.3 5.4 - - - +
475B MET* 2.8 65.2 + - + +
518B VAL* 4.1 15.0 - - + -
520B LEU* 3.8 39.5 - - + -
593B TYR* 3.8 18.9 - - + -
594B ARG 3.2 8.1 - - - +
595B LEU* 3.7 22.0 - - + -
694B PHE* 4.0 13.2 - - + -
695B LEU* 1.3 81.2 - - - +
697B ARG* 1.3 60.3 + - - +
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Residues in contact with ARG 697 (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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678A HIS* 4.5 19.8 + - + -
688A PRO 3.9 10.6 + - - -
689A GLY 3.0 20.5 + - - -
690A ASN* 3.1 35.4 + - - +
474B VAL* 4.1 15.0 - - + +
593B TYR* 3.4 4.3 - - - -
594B ARG* 2.7 69.7 + - + +
596B GLN* 2.7 39.5 + - - -
695B LEU* 4.1 20.6 - - + -
696B LEU* 1.3 78.8 - - - +
698B PRO* 1.3 75.2 - - + +
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Residues in contact with PRO 698 (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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678A HIS* 3.5 21.0 + - - -
680A GLU* 3.4 24.8 - - + +
472B ASN 3.7 17.7 - - - +
473B GLY 3.4 20.2 - - - +
474B VAL* 3.9 8.1 - - + -
592B SER 3.8 4.3 - - - +
593B TYR* 3.4 26.2 - - + +
697B ARG* 1.3 88.2 - - + +
699B PHE* 1.3 59.5 + - - +
701B PHE* 4.0 1.1 - - + -
702B PHE* 3.8 17.5 - - + -
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Residues in contact with PHE 699 (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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499A THR* 5.0 0.9 - - - -
676A ILE* 3.6 28.0 - - + -
677A PRO 4.3 0.7 - - - -
678A HIS* 3.5 23.3 - + + -
680A GLU* 3.7 2.2 + - - -
532B LEU* 3.8 21.1 - - + -
576B TYR* 3.5 28.7 - + - -
578B LEU* 3.7 42.2 - - + -
592B SER* 2.9 38.1 + - - +
594B ARG* 4.4 6.3 - - + -
697B ARG 4.3 4.7 - - - +
698B PRO* 1.3 74.5 - - - +
700B ASN* 1.3 85.8 + - - +
701B PHE 3.1 2.2 - - - -
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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