Contacts of the strand formed by residues 632 - 637 (chain D) in PDB entry 5UHG
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 632 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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591D GLU* 3.2 38.7 + - + +
592D VAL 4.3 6.1 + - - +
598D GLU* 3.5 15.9 - - + +
599D TYR* 3.0 26.4 + - + +
630D ARG 4.1 0.6 + - - -
631D ALA* 1.3 71.5 - - - +
633D ILE* 1.3 65.4 + - - +
665D GLU* 3.8 39.2 + - - +
666D THR 3.4 9.9 - - - +
667D THR* 4.0 4.5 - - - +
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Residues in contact with ILE 633 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597D GLY 3.4 25.1 - - - +
598D GLU* 4.4 0.2 - - - -
599D TYR* 4.0 10.3 - - - +
610D GLY 3.7 8.7 - - - +
612D TYR* 4.0 8.1 - - + -
618D ALA* 4.5 1.6 - - + -
627D LEU* 3.7 35.0 - - + -
631D ALA 3.8 7.0 - - - +
632D LYS* 1.3 80.5 - - - +
634D LYS* 1.3 64.6 + - - +
635D VAL* 3.7 25.7 + - + +
665D GLU* 3.4 6.1 - - - +
666D THR* 2.7 41.5 + - - +
667D THR 4.7 0.2 - - - -
668D LEU* 4.1 21.3 - - + +
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Residues in contact with LYS 634 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599D TYR* 4.3 40.1 + - + +
608D GLU* 5.3 2.1 + - - +
610D GLY 3.3 10.6 + - - +
611D VAL* 3.4 20.0 - - + +
612D TYR 3.1 23.9 + - - -
633D ILE* 1.3 77.8 - - - +
635D VAL* 1.3 64.9 + - - +
663D MET* 4.5 13.0 - - + -
664D ALA 3.2 14.1 - - - +
665D GLU* 3.3 37.2 + - + -
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Residues in contact with VAL 635 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612D TYR* 3.6 17.5 - - + +
614D SER 3.9 22.2 - - - +
615D PRO* 4.0 3.4 - - + -
618D ALA* 4.9 4.5 - - + -
633D ILE* 3.7 29.4 + - + -
634D LYS* 1.3 80.5 - - - +
636D ARG* 1.3 75.2 + - - +
637D LEU* 3.7 25.2 + - + +
662D TRP 3.6 1.9 - - - +
663D MET* 3.7 6.4 - - - +
664D ALA* 3.2 29.6 + - + +
666D THR* 6.1 0.9 - - - +
668D LEU* 6.1 1.8 - - + -
671D VAL* 5.6 8.1 - - + -
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Residues in contact with ARG 636 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B GLU* 3.6 26.5 + - - +
78B LEU* 4.4 13.5 - - + +
79B ASN* 3.1 48.1 + - - +
612D TYR 3.4 7.7 + - - +
613D SER* 3.1 30.9 - - - +
614D SER* 3.5 12.8 - - - -
615D PRO* 3.8 0.7 - - - +
635D VAL* 1.3 75.9 - - - +
637D LEU* 1.3 62.5 + - - +
638D THR* 5.8 0.6 - - - +
661D ALA* 3.9 28.4 - - + +
662D TRP 3.3 8.9 - - - +
663D MET* 3.7 19.7 - - - +
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Residues in contact with LEU 637 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615D PRO* 4.0 15.7 - - + -
635D VAL* 3.7 31.9 - - + +
636D ARG* 1.3 75.5 - - - +
638D THR* 1.3 61.6 + - - +
639D GLN 4.8 2.5 - - - +
640D LEU* 4.5 13.5 - - + -
661D ALA* 3.2 24.8 - - - +
662D TRP* 3.0 51.5 + - + +
664D ALA* 4.5 9.4 - - + -
671D VAL* 4.1 25.1 - - + -
683D PHE* 4.3 20.0 - - + -
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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