Contacts of the strand formed by residues 691 - 699 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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478A LYS* 4.0 16.4 - - - +
479A MET 3.0 14.6 - - - -
480A HIS* 3.7 23.7 + - - -
598A HIS* 5.8 0.7 - - - +
673A PHE* 5.4 0.4 - - - -
687A THR 5.0 2.7 + - - -
689A GLY* 3.5 6.8 + - - +
690A ASN* 1.3 80.1 + - - +
692A VAL* 1.3 73.0 + - - +
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Residues in contact with VAL 692 (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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478A LYS* 3.4 6.8 - - - +
479A MET* 2.8 51.8 + - + +
514A VAL* 5.3 0.9 - - + -
516A TYR* 5.1 0.2 + - - -
598A HIS* 3.5 17.5 - - - +
599A SER* 4.1 5.6 - - - -
600A MET* 4.5 2.5 - - + +
671A VAL* 3.6 23.1 - - + +
672A GLY* 3.5 32.1 - - - +
673A PHE* 3.9 15.5 - - + -
691A SER* 1.3 82.3 - - - +
693A GLY* 1.3 59.1 + - - +
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Residues in contact with GLY 693 (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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477A ALA 3.2 13.5 - - - -
516A TYR* 5.0 2.9 - - - -
598A HIS* 2.8 40.8 + - - +
671A VAL* 3.5 19.2 - - - +
692A VAL* 1.3 78.0 - - - +
694A PHE* 1.3 63.1 + - - +
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Residues in contact with PHE 694 (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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350A VAL* 3.8 14.1 - - + -
475A MET* 5.6 1.3 - - + -
476A GLU* 3.3 4.4 + - - +
477A ALA* 2.9 56.3 + - + +
516A TYR* 3.5 34.5 - + + -
518A VAL* 3.6 27.8 - - + -
595A LEU* 3.5 26.0 - - + -
596A GLN 3.1 13.7 - - - +
597A ILE* 4.0 8.3 - - + -
598A HIS 4.3 1.1 - - - +
669A VAL* 4.1 14.8 - - + -
671A VAL* 4.8 0.2 - - + -
693A GLY* 1.3 77.3 - - - +
695A LEU* 1.3 67.3 + - - +
696A LEU* 4.1 25.8 - - + -
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Residues in contact with LEU 695 (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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470A TYR* 5.1 2.2 - - + +
474A VAL* 3.9 20.0 - - + -
475A MET 3.3 5.2 - - - +
476A GLU* 3.9 28.7 - - + +
594A ARG 3.5 0.7 - - - +
595A LEU* 3.4 6.2 - - - +
596A GLN* 2.7 41.8 + - + +
598A HIS* 3.1 42.0 - - + +
694A PHE* 1.3 78.6 - - - +
696A LEU* 1.3 65.3 + - - +
697A ARG* 4.1 14.4 - - + -
689B GLY* 3.6 32.1 - - - +
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Residues in contact with LEU 696 (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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346A ILE* 5.4 2.2 - - + -
347A ALA* 5.2 0.7 - - + -
350A VAL* 4.6 7.0 - - + -
474A VAL* 3.3 5.5 - - - +
475A MET* 2.7 62.4 + - + +
518A VAL* 4.1 15.5 - - + -
520A LEU* 3.8 34.5 - - + -
593A TYR* 3.8 17.3 - - + -
594A ARG 3.3 8.1 - - - +
595A LEU* 3.8 24.0 - - + -
694A PHE* 4.1 14.8 - - + -
695A LEU* 1.3 79.6 - - - +
697A ARG* 1.3 60.7 + - - +
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Residues in contact with ARG 697 (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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474A VAL* 4.1 20.3 - - + +
593A TYR* 3.4 5.6 - - - -
594A ARG* 2.7 70.3 + - + +
596A GLN* 2.7 41.8 + - - -
695A LEU* 4.2 14.6 - - + -
696A LEU* 1.3 76.6 - - - +
698A PRO* 1.3 74.2 - - + +
699A PHE 3.5 0.2 + - - -
600B MET* 5.1 2.2 - - - +
678B HIS* 4.6 19.2 + - + -
688B PRO 3.8 13.6 + - - -
689B GLY 3.3 15.9 + - - -
690B ASN* 3.0 36.1 + - - +
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Residues in contact with PRO 698 (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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472A ASN 3.7 17.9 - - - +
473A GLY 3.4 22.0 - - - +
474A VAL* 4.0 8.5 - - + -
592A SER 3.8 0.4 - - - +
593A TYR* 3.5 30.7 - - + +
697A ARG* 1.3 89.1 - - + +
699A PHE* 1.3 60.8 + - - +
701A PHE* 3.9 1.8 - - + -
702A PHE* 3.7 16.8 - - + -
678B HIS* 3.5 15.1 + - - -
680B GLU* 3.4 30.0 - - + +
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Residues in contact with PHE 699 (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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530A GLN* 5.8 0.2 - - - -
532A LEU* 3.8 21.5 - - + -
576A TYR* 3.5 21.3 - + - -
578A LEU* 3.8 41.7 - - + -
590A LYS 5.5 0.2 - - - -
592A SER* 2.8 41.1 + - - +
594A ARG* 4.3 12.1 - - + -
697A ARG 3.5 0.2 + - - -
698A PRO* 1.3 75.0 - - - +
700A ASN* 1.3 86.1 + - - +
701A PHE 3.1 1.8 - - - -
499B THR* 5.0 0.7 - - - -
676B ILE* 3.5 34.3 - - + -
677B PRO 4.2 1.6 - - - -
678B HIS* 3.5 22.9 - + + -
680B GLU* 3.6 1.7 + - - -
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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