Contacts of the strand formed by residues 651 - 660 (chain E) in PDB entry 3HR4
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 651 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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618E LYS 3.9 7.7 + - - -
619E PHE 3.4 7.4 + - - -
620E ARG* 3.1 38.3 + - - +
621E TYR* 3.1 26.8 + - - -
649E GLY 4.3 0.2 + - - -
650E ALA* 1.3 73.0 - - - +
652E GLN* 1.3 60.5 + - - +
653E LEU 3.1 3.6 + - - -
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Residues in contact with GLN 652 (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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620E ARG* 4.7 1.2 + - - -
621E TYR* 3.3 29.3 + - + +
622E ALA* 5.4 0.2 - - - -
642E ASP* 3.6 25.1 - - - +
646E SER* 6.0 0.7 - - - +
650E ALA 3.9 1.0 + - - -
651E SER* 1.3 68.8 - - - +
653E LEU* 1.3 68.8 + - - +
654E THR* 3.0 22.4 - - - +
655E PRO* 3.2 29.2 - - - +
656E MET 4.1 3.3 + - - +
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Residues in contact with LEU 653 (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 LEU* 4.5 12.8 - - + -
587E LEU* 6.1 0.2 - - + -
620E ARG* 3.7 29.4 - - + +
621E TYR 2.6 23.4 + - - +
622E ALA* 4.5 4.3 - - + -
651E SER 3.1 4.2 + - - -
652E GLN* 1.3 73.3 - - - +
654E THR* 1.3 61.0 + - + +
655E PRO* 4.8 0.2 - - - +
676E THR* 3.8 11.7 - - - +
679E ALA* 3.4 39.9 - - + +
680E ALA* 4.6 5.8 - - + -
683E THR* 3.7 32.3 - - + +
684E PHE* 5.0 1.3 - - + -
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Residues in contact with THR 654 (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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621E TYR 4.0 1.0 + - - -
622E ALA* 3.3 21.6 - - + -
623E VAL 4.6 0.3 + - - -
642E ASP* 5.6 0.2 - - - +
652E GLN* 3.0 16.8 - - - +
653E LEU* 1.3 86.5 - - + +
655E PRO* 1.3 86.1 + - - +
656E MET* 4.5 0.5 - - - -
672E TRP* 3.7 10.8 + - - +
675E GLN* 3.7 22.0 + - - +
676E THR* 2.9 39.9 - - - +
679E ALA* 5.1 2.5 - - - -
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Residues in contact with PRO 655 (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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652E GLN* 3.2 19.0 - - - +
653E LEU 4.8 0.4 - - - +
654E THR* 1.3 98.1 + - - +
656E MET* 1.3 66.5 + - - +
657E GLY 3.2 3.8 + - - -
672E TRP* 3.3 16.1 + - - -
675E GLN* 5.0 6.1 - - - +
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Residues in contact with MET 656 (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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623E VAL* 3.4 17.9 - - + +
625E GLY 4.6 0.2 - - - +
635E CYS* 3.8 4.7 - - + +
638E ALA* 3.4 48.9 - - + +
639E HIS* 3.2 49.5 - - + +
642E ASP* 3.4 25.4 - - - +
652E GLN* 4.1 6.1 + - - -
654E THR 3.6 1.5 + - - -
655E PRO* 1.3 74.5 - - - +
657E GLY* 1.3 68.1 + - - +
658E GLU* 3.4 26.1 + - + +
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Residues in contact with GLY 657 (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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623E VAL 3.0 9.1 + - - -
624E PHE* 3.3 13.5 - - - -
625E GLY 3.2 20.4 + - - -
655E PRO 3.2 4.6 + - - -
656E MET* 1.3 73.4 - - - +
658E GLU* 1.3 67.9 + - - +
672E TRP* 3.7 21.7 - - - -
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Residues in contact with GLU 658 (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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624E PHE* 3.8 6.4 - - - -
625E GLY 3.5 4.3 - - - -
634E PHE* 4.3 20.9 - - + +
635E CYS* 4.0 18.1 - - - +
639E HIS* 2.6 38.0 + - - -
656E MET* 3.4 20.4 - - + +
657E GLY* 1.3 81.8 - - - +
659E GLY* 1.3 59.4 + - - +
660E ASP 4.0 1.8 + - - -
668E ALA* 3.7 16.6 - - - +
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Residues in contact with GLY 659 (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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624E PHE* 3.6 15.5 - - - -
625E GLY 2.7 16.1 + - - +
626E LEU* 3.5 0.7 - - - -
627E GLY 3.0 26.7 + - - -
634E PHE* 4.5 3.1 - - - -
635E CYS* 4.3 1.4 - - - -
658E GLU* 1.3 72.5 - - - +
660E ASP* 1.3 59.2 - - - -
665E GLN* 3.3 26.9 + - - -
668E ALA* 4.4 1.1 - - - -
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Residues in contact with ASP 660 (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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627E GLY 3.7 1.8 - - - -
628E SER* 3.6 0.7 - - - -
629E SER* 3.2 37.8 + - - -
634E PHE* 3.7 20.8 - - + -
658E GLU 4.0 2.2 + - - -
659E GLY* 1.3 70.3 - - - -
661E GLU* 1.3 72.7 + - - +
662E LEU* 2.9 17.4 + - - +
663E SER* 2.7 56.4 + - - +
665E GLN* 3.3 8.3 - - - +
668E ALA* 5.3 1.0 - - - +
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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