Contacts of the strand formed by residues 590 - 594 (chain A) in PDB entry 3I7H
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 590 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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540A CYS* 3.8 7.2 - - - -
589A ARG* 1.3 81.0 - - - +
591A ILE* 1.3 69.8 + - - +
604A CYS* 3.5 6.6 - - - -
605A ALA 3.0 27.0 + - - +
636A THR 3.8 10.3 - - - -
637A VAL* 4.1 11.3 - - - +
638A LEU* 3.6 38.4 + - - +
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Residues in contact with ILE 591 (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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540A CYS* 3.9 9.1 - - - +
541A LEU* 3.8 35.1 + - - +
542A ASP* 3.4 11.8 - - - +
557A ALA* 3.8 23.1 - - + +
558A ILE 4.2 9.6 - - - +
559A GLY 4.7 0.4 - - - +
566A ALA* 3.6 31.2 - - + -
567A ARG 5.2 0.2 - - - +
590A SER* 1.3 79.6 + - - +
592A LEU* 1.3 66.2 + - - +
602A LEU* 3.8 21.1 - - + -
603A LEU 3.1 17.9 - - - +
604A CYS* 3.7 17.7 - - + -
638A LEU* 5.1 0.7 - - - -
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Residues in contact with LEU 592 (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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542A ASP* 3.3 26.0 - - - +
544A THR* 5.6 3.4 - - + +
591A ILE* 1.3 78.4 - - - +
593A MET* 1.3 70.0 + - - +
594A THR* 4.1 10.6 + - + -
601A TYR 3.9 0.3 - - - +
602A LEU* 3.1 8.7 - - - -
603A LEU* 3.0 35.5 + - - +
638A LEU* 3.7 21.7 - - + +
639A ARG* 3.5 43.5 - - - +
640A THR* 4.4 4.3 - - - +
649A VAL* 4.0 16.2 - - + -
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Residues in contact with MET 593 (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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542A ASP* 2.7 43.8 + - - +
543A ILE* 4.3 0.9 - - - -
544A THR* 3.4 37.7 + - - +
546A LEU* 3.5 34.7 - - + +
553A SER* 5.0 0.2 - - - -
555A LEU* 4.4 9.0 - - + +
556A CYS* 3.6 10.5 - - - +
557A ALA* 3.3 28.5 - - + +
592A LEU* 1.3 78.4 - - - +
594A THR* 1.3 67.7 + - - +
601A TYR 3.3 9.0 - - - +
602A LEU* 3.5 9.4 - - + +
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Residues in contact with THR 594 (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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546A LEU* 4.3 6.2 - - - +
592A LEU* 4.1 11.6 + - + +
593A MET* 1.3 79.5 - - - +
595A THR* 1.3 62.1 + - - +
596A PHE* 3.6 28.0 + - + -
599A SER 4.8 0.2 - - - +
600A HIS* 4.2 3.1 + - - +
601A TYR* 3.0 35.8 + - - +
603A LEU* 5.5 1.9 - - - +
640A THR* 3.1 27.6 - - - +
648A ASN 5.5 0.2 - - - +
649A VAL* 4.0 26.1 - - + +
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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