Contacts of the helix formed by residues 577 - 594 (chain B) in PDB entry 3THW
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 LYS 577 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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523B MET* 4.0 19.5 - - - +
524B GLU* 4.2 26.5 - - + +
575B LEU* 4.3 2.4 - - + +
576B LEU* 1.3 79.4 + - - +
578B LEU* 1.3 68.5 + - - +
579B ARG* 3.3 7.9 + - + +
580B GLU* 3.4 16.2 + - + +
581B ILE* 3.3 21.6 + - - +
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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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576B LEU 3.6 4.4 + - - -
577B LYS* 1.3 71.8 - - - +
579B ARG* 1.3 68.5 + - + +
581B ILE* 3.1 16.4 + - + +
582B ASN* 3.1 39.3 + - - +
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Residues in contact with ARG 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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577B LYS* 3.3 7.8 - - + +
578B LEU* 1.3 80.1 - - + +
580B GLU* 1.3 57.6 + - - +
582B ASN* 3.2 4.5 + - - +
583B ALA* 2.8 30.7 + - - +
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Residues in contact with GLU 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570B TRP* 5.8 0.2 - - - -
575B LEU* 3.4 24.0 - - + +
577B LYS* 3.4 16.5 + - + +
578B LEU 3.3 0.6 - - - -
579B ARG* 1.3 79.6 - - - +
581B ILE* 1.3 62.6 + - - +
583B ALA* 3.6 12.2 + - - +
584B ARG* 3.4 41.5 + - - +
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Residues in contact with ILE 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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575B LEU* 3.4 48.0 - - + +
576B LEU* 4.5 2.5 - - - +
577B LYS 3.3 14.6 + - - +
578B LEU* 3.1 18.0 + - + +
580B GLU* 1.3 78.4 - - - +
582B ASN* 1.3 60.0 - - - +
584B ARG* 3.4 8.3 + - - +
585B LEU* 3.2 39.8 + - + +
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Residues in contact with ASN 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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578B LEU* 3.1 34.1 + - - +
579B ARG* 3.8 7.2 - - - +
581B ILE* 1.3 73.5 - - - +
583B ALA* 1.3 56.4 + - - +
584B ARG 2.9 5.3 + - - -
585B LEU* 3.0 20.7 + - - +
586B ASP* 2.6 48.1 + - - +
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Residues in contact with ALA 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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579B ARG 2.8 21.9 + - - +
580B GLU* 3.7 20.9 - - - +
581B ILE 3.4 0.2 - - - -
582B ASN* 1.3 71.1 - - - +
584B ARG* 1.3 60.3 + - - +
586B ASP* 3.6 12.3 + - - +
587B ALA* 3.6 18.0 + - - +
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Residues in contact with ARG 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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570B TRP* 2.9 81.7 + - + +
574B PRO* 6.0 0.6 - - - +
575B LEU* 3.6 36.5 - - - +
580B GLU* 3.4 30.5 + - - +
581B ILE* 3.4 8.7 + - - +
582B ASN 2.9 0.4 - - - -
583B ALA* 1.3 75.8 - - - +
585B LEU* 1.3 61.0 + - + +
586B ASP 3.0 1.3 - - - -
587B ALA* 2.8 8.8 + - - +
588B VAL* 2.8 38.6 + - + +
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Residues in contact with LEU 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581B ILE* 3.2 25.1 + - + +
582B ASN* 3.0 25.7 + - - +
584B ARG* 1.3 79.3 - - + +
586B ASP* 1.3 61.7 + - - +
588B VAL* 4.0 13.5 - - + +
589B SER* 2.8 29.5 + - - -
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Residues in contact with ASP 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582B ASN* 2.6 39.8 + - - +
583B ALA* 3.6 11.4 + - - +
585B LEU* 1.3 72.1 - - - +
587B ALA* 1.3 64.2 + - - +
589B SER* 2.9 8.5 + - - -
590B GLU* 2.9 24.9 + - - +
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Residues in contact with ALA 587 (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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583B ALA 3.6 10.2 + - - +
584B ARG* 2.8 14.7 + - - +
586B ASP* 1.3 75.5 - - - +
588B VAL* 1.3 63.4 + - + +
590B GLU* 3.0 10.7 + - - +
591B VAL* 3.0 31.3 + - + +
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Residues in contact with VAL 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584B ARG* 2.8 33.8 + - + +
585B LEU* 4.0 14.6 - - + +
587B ALA* 1.3 74.2 - - + +
589B SER* 1.3 61.2 + - - +
591B VAL* 3.5 12.3 + - - +
592B LEU* 3.5 23.8 + - + +
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Residues in contact with SER 589 (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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585B LEU 2.8 17.0 + - - -
586B ASP* 2.9 11.0 + - - -
588B VAL* 1.3 75.0 - - - +
590B GLU* 1.3 59.9 + - - +
591B VAL 3.1 1.3 - - - -
592B LEU* 2.9 29.3 + - - +
593B HIS* 3.2 13.5 + - - +
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Residues in contact with GLU 590 (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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586B ASP* 2.9 13.4 + - - +
587B ALA* 3.0 12.8 + - - +
589B SER* 1.3 76.8 - - - +
591B VAL* 1.3 60.6 + - + +
593B HIS* 4.2 7.4 - - + +
594B SER* 3.4 24.3 + - - -
599B PHE* 3.9 21.2 - - + -
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Residues in contact with VAL 591 (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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587B ALA* 3.0 24.0 + - + +
588B VAL* 3.8 9.2 - - - +
589B SER 3.1 0.2 - - - -
590B GLU* 1.3 78.3 - - + +
592B LEU* 1.3 67.5 + - + +
594B SER* 3.3 10.8 + - - +
599B PHE* 4.0 26.6 - - + +
603B GLU* 5.9 2.9 - - - +
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Residues in contact with LEU 592 (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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588B VAL* 3.5 21.3 - - + +
589B SER* 2.9 13.2 + - - +
591B VAL* 1.3 84.6 - - + +
593B HIS* 1.3 65.7 + - - +
594B SER 3.5 4.7 + - - +
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Residues in contact with HIS 593 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589B SER 3.2 10.3 + - - +
590B GLU* 4.6 6.3 - - + +
592B LEU* 1.3 77.4 - - - +
594B SER* 1.3 75.8 + - - +
595B GLU* 3.4 16.0 + - - +
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Residues in contact with SER 594 (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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590B GLU* 3.4 12.6 + - - -
591B VAL 3.3 15.6 + - - +
592B LEU 3.7 5.2 - - - +
593B HIS* 1.3 90.2 - - - +
595B GLU* 1.3 63.8 + - - +
596B SER* 4.5 2.0 - - - -
599B PHE* 3.3 50.6 - - - +
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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