Contacts of the strand formed by residues 584 - 588 (chain E) in PDB entry 6IWQ
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 GLN 584 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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552E THR* 2.5 34.6 - - - +
553E ASN* 2.5 42.0 + - - +
580E MET* 3.2 6.6 - - - +
581E GLN 2.9 34.4 + - - +
582E TYR* 5.6 4.2 - - + +
583E ASP* 1.3 101.1 + - - +
585E CYS* 1.3 60.6 + - - +
597E ILE* 3.2 18.0 - - + +
598E THR 3.3 20.4 - - - +
599E HIS* 3.4 5.8 - - + -
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Residues in contact with CYS 585 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578E GLN* 3.9 9.0 - - + -
579E LEU 3.2 6.7 - - - +
580E MET* 3.0 20.9 - - - -
584E GLN* 1.3 72.9 - - - +
586E LEU* 1.3 67.5 + - - +
587E THR* 4.1 2.5 + - - +
596E MET 3.8 0.2 - - - +
597E ILE* 3.5 3.4 - - - -
598E THR* 2.7 35.2 + - - +
600E CYS* 2.1 59.9 - - + +
605E PHE* 4.1 17.7 - - + -
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Residues in contact with LEU 586 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537E ILE* 6.2 0.4 - - + -
546E ILE* 5.0 7.6 - - + -
557E VAL* 3.5 31.2 - - + -
571E PHE* 3.7 35.7 - - + -
579E LEU* 2.9 46.2 + - + +
580E MET* 4.5 2.9 - - - -
581E GLN 4.7 0.2 - - - +
585E CYS* 1.3 80.2 - - - +
587E THR* 1.3 57.5 + - - +
595E VAL* 3.6 18.6 - - + -
596E MET 3.0 12.3 - - - +
597E ILE* 4.3 9.0 - - + +
605E PHE* 4.3 4.3 - - - +
608E TRP* 2.6 30.0 + - + -
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Residues in contact with THR 587 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585E CYS 4.6 2.7 - - - +
586E LEU* 1.3 74.4 - - - +
588E LYS* 1.3 74.9 + - - +
595E VAL* 3.9 1.4 - - - -
596E MET* 3.1 52.6 + - + +
598E THR* 4.4 6.1 - - - +
605E PHE* 3.2 43.3 - - + -
607E GLU* 3.2 15.9 + - - -
608E TRP* 4.1 7.6 - - - -
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Residues in contact with LYS 588 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587E THR* 1.3 86.0 + - - +
589E GLY* 1.3 81.5 + - - +
590E ALA* 3.5 6.1 + - + +
592E GLY 3.6 14.9 + - - +
594E LYS 4.0 4.9 - - - +
595E VAL* 5.1 1.8 - - - +
596E MET* 4.1 3.3 - - - +
607E GLU* 3.6 5.8 + - - +
608E TRP* 4.3 4.0 - - - -
619E HIS* 3.3 39.3 + - + +
621E PRO* 5.4 3.4 - - - -
622E SER* 5.1 9.1 - - - +
624E LYS* 5.6 4.4 - - - +
637E ILE* 4.1 16.4 - - + +
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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