Contacts of the strand formed by residues 576 - 584 (chain B) in PDB entry 3HIG
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 TYR 576 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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674A LEU* 3.1 31.6 + - + -
675A HIS* 3.5 5.0 - - - -
676A ILE* 2.9 50.0 + - + -
678A HIS* 5.5 1.8 + + - -
531B THR* 3.0 30.1 - - - -
532B LEU* 3.2 28.0 + - + +
574B PRO* 4.2 0.2 - - - +
575B LYS* 1.3 85.1 - - + +
577B LEU* 1.3 62.4 + - - +
578B LEU* 3.9 5.6 - - + -
594B ARG* 3.4 46.4 + - + +
699B PHE* 3.6 34.5 - + - -
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Residues in contact with LEU 577 (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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529B PHE* 4.1 11.4 - - + -
530B GLN 4.1 1.8 - - - -
531B THR* 3.8 21.1 - - + -
567B PHE* 4.7 0.9 - - + -
573B LEU* 4.1 21.5 - - + -
574B PRO* 3.8 30.7 - - + +
575B LYS 4.1 1.7 + - - -
576B TYR* 1.3 71.6 - - - +
578B LEU* 1.3 60.0 + - - +
579B PHE* 4.2 2.5 + - + -
593B TYR 3.8 0.2 - - - +
594B ARG* 3.3 6.3 - - - +
595B LEU* 2.9 58.4 + - + +
596B GLN* 5.5 0.7 - - - -
597B ILE* 4.3 16.8 - - + +
622B LEU* 4.0 27.4 - - + -
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Residues in contact with LEU 578 (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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528B SER 3.8 0.3 - - - +
529B PHE* 3.3 9.7 - - - -
530B GLN* 2.8 63.8 + - + +
532B LEU* 3.6 34.8 - - + -
576B TYR* 4.5 10.5 - - + +
577B LEU* 1.3 73.7 - - - +
579B PHE* 1.3 62.1 + - - +
580B THR* 4.0 6.0 + - + -
592B SER* 4.5 5.4 - - - +
593B TYR 3.5 2.7 - - - +
594B ARG* 3.6 33.7 - - + -
699B PHE* 3.7 35.7 - - + -
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Residues in contact with PHE 579 (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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520B LEU* 3.6 36.3 - - + -
522B VAL* 3.6 17.0 - - + +
527B ASN* 5.1 4.9 - - + +
528B SER 3.5 2.2 - - - +
529B PHE* 3.6 34.1 - + + -
577B LEU* 4.4 4.3 - - + -
578B LEU* 1.3 72.1 - - - +
580B THR* 1.3 59.7 + - - +
592B SER* 3.2 2.4 - - - -
593B TYR 2.8 40.1 + - - +
595B LEU* 4.3 24.7 - - + -
622B LEU* 4.6 3.1 - - + -
624B VAL* 3.9 25.8 - - + -
665B LEU* 4.5 21.1 - - + -
667B ALA* 3.7 24.9 - - + -
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Residues in contact with THR 580 (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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522B VAL* 4.9 0.7 - - - -
527B ASN* 3.2 12.6 - - - +
528B SER* 2.8 48.3 + - - +
530B GLN* 3.1 43.2 + - + +
578B LEU* 4.1 6.3 - - + +
579B PHE* 1.3 76.4 - - - +
581B SER* 1.3 66.4 + - - +
582B PRO* 4.5 0.3 - - - +
590B LYS* 4.5 9.2 - - - +
591B ARG 3.6 4.3 - - - -
592B SER* 3.3 20.0 - - - +
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Residues in contact with SER 581 (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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522B VAL* 3.7 22.5 + - - +
523B ALA* 4.2 9.4 + - - +
526B LYS 4.8 0.5 + - - -
527B ASN* 4.1 3.6 - - - +
580B THR* 1.3 75.1 - - - +
582B PRO* 1.3 77.3 - - - +
583B GLN* 3.1 36.6 + - - +
590B LYS* 3.6 19.2 - - - +
591B ARG* 2.8 17.9 + - - -
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Residues in contact with PRO 582 (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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526B LYS* 3.7 16.8 - - + +
527B ASN* 5.3 0.9 - - - -
580B THR 4.5 0.9 - - - +
581B SER* 1.3 89.3 - - - +
583B GLN* 1.3 63.5 + - + +
584B GLU* 3.5 11.4 + - - +
590B LYS* 4.5 8.7 - - + +
662B ASN* 3.7 20.6 - - - +
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Residues in contact with GLN 583 (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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344B GLU* 4.5 2.3 + - - +
523B ALA* 3.4 27.7 + - - +
581B SER* 3.1 15.9 + - - +
582B PRO* 1.3 81.2 - - + +
584B GLU* 1.3 61.2 + - - +
590B LYS* 3.7 1.6 - - - -
591B ARG* 2.7 64.3 + - - +
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Residues in contact with GLU 584 (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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582B PRO 4.0 9.0 - - - +
583B GLN* 1.3 78.1 - - - +
585B ASN* 1.3 69.2 + - - +
588B GLY* 3.6 28.2 - - - +
589B HIS 3.3 14.1 - - - +
590B LYS* 4.6 9.4 - - + +
591B ARG* 3.8 8.7 - - - -
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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