Contacts of the strand formed by residues 463 - 470 (chain A) in PDB entry 2HD5
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 GLY 463 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293A GLN* 3.0 16.1 + - - -
456A HIS* 4.0 1.1 - - - -
457A SER 3.0 15.0 - - - -
458A GLY* 4.2 2.5 - - - -
462A GLY* 1.3 74.0 - - - -
464A HIS* 1.3 60.3 + - - +
74B ARG 3.5 3.5 + - - -
75B GLY* 3.8 5.4 - - - -
76B GLY* 3.2 18.0 + - - +
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Residues in contact with HIS 464 (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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223A CYS* 3.3 28.8 - - - +
456A HIS* 3.5 4.1 - - - -
457A SER* 2.9 38.3 + - - +
463A GLY* 1.3 74.6 - - - +
465A TYR* 1.3 87.2 + - - +
466A THR* 3.7 9.6 - - + +
481A ASN* 3.2 35.9 + - - -
482A ASP* 4.3 1.8 - - - -
76B GLY* 4.3 9.0 + - - +
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Residues in contact with TYR 465 (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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223A CYS* 3.6 27.6 - - - +
224A PHE* 3.5 17.9 - - + -
227A SER* 4.0 4.3 - - - -
294A GLN 3.5 19.7 - - - -
295A ASP* 3.6 0.2 - - - -
296A ALA* 3.0 34.9 + - + -
454A SER* 3.6 17.0 - - - -
455A ASN 3.0 20.2 - - - -
456A HIS* 3.6 25.8 - + + -
464A HIS* 1.3 98.4 + - - +
466A THR* 1.3 62.4 + - - +
481A ASN* 5.1 1.2 + - - -
482A ASP 5.4 0.5 + - - -
514A TYR* 3.5 20.2 - + - -
73B LEU* 2.6 25.5 + - - +
75B GLY* 3.6 13.2 - - - -
76B GLY 4.7 0.2 - - - +
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Residues in contact with THR 466 (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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227A SER* 2.9 16.2 + - - +
455A ASN* 2.9 51.6 + - - +
464A HIS* 3.7 9.0 - - + +
465A TYR* 1.3 78.2 - - - +
467A ALA* 1.3 62.8 + - - +
468A TYR* 4.3 4.5 + - - -
479A THR* 4.9 7.4 - - + -
480A PHE 3.5 12.1 - - - -
481A ASN* 3.6 30.7 - - + +
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Residues in contact with ALA 467 (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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227A SER* 3.7 29.3 - - - +
230A GLN* 4.3 6.3 - - + -
231A CYS* 4.0 0.9 - - - -
453A VAL 3.3 11.2 - - - +
455A ASN* 4.3 0.2 - - - +
466A THR* 1.3 75.7 - - - +
468A TYR* 1.3 68.6 + - - +
469A CYS* 3.8 19.1 - - - -
478A HIS 3.9 0.2 - - - +
479A THR* 4.0 0.5 - - - +
480A PHE* 2.7 42.6 + - + +
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Residues in contact with TYR 468 (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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452A ALA* 3.3 2.6 - - - -
453A VAL* 2.8 39.7 + - + +
455A ASN* 3.2 32.1 + - - +
466A THR* 4.3 5.8 + - - -
467A ALA* 1.3 78.8 - - - +
469A CYS* 1.3 63.2 + - - +
477A TRP* 3.6 12.4 - - + -
478A HIS 3.4 3.6 - - - -
479A THR* 3.6 33.7 - - + -
488A MET* 3.6 25.1 - - + -
492A GLN 3.9 10.4 + - - -
493A VAL* 3.6 30.1 - - + -
495A THR* 4.1 16.0 + - + +
512A ASP* 5.8 0.9 + - - +
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Residues in contact with CYS 469 (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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230A GLN 3.8 17.0 - - - -
231A CYS* 3.9 7.9 - - - -
234A ASN* 3.4 34.5 - - + +
451A TYR 3.5 5.6 - - - +
452A ALA* 4.2 2.7 - - + -
467A ALA* 3.8 21.8 - - - -
468A TYR* 1.3 81.1 - - - +
470A ARG* 1.3 61.3 + - - +
471A SER 3.8 1.4 + - - -
476A GLU 3.8 0.2 - - - +
477A TRP* 3.4 7.4 - - - -
478A HIS* 2.9 33.3 + - - +
480A PHE* 3.8 14.7 - - + -
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Residues in contact with ARG 470 (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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234A ASN* 3.7 13.9 - - - +
429A LEU 5.3 0.6 + - - -
430A ARG* 3.4 43.6 - - - +
449A ASN* 5.1 6.5 - - - +
450A LEU 4.1 17.6 + - - -
451A TYR* 2.7 29.9 + - - +
469A CYS* 1.3 73.3 - - - +
471A SER* 1.3 68.4 + - - +
472A PRO* 3.3 8.3 - - - +
475A GLY* 3.1 49.3 + - - +
476A GLU 3.4 3.6 - - - +
477A TRP* 3.5 29.8 - - + +
519A GLU* 5.2 7.5 + - - -
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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