Contacts of the strand formed by residues 514 - 520 (chain A) in PDB entry 1QHP
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 VAL 514 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A TYR 5.1 3.4 + - - +
249A LYS* 6.1 1.3 - - - -
250A ASP* 3.4 45.0 - - + +
506A PRO* 4.0 3.6 - - - +
512A GLY 3.7 1.3 + - - +
513A ASN* 1.3 76.5 - - - +
515A VAL* 1.3 67.8 + - - +
539A LYS* 4.1 26.0 - - + -
547A GLU* 4.3 12.8 - - + +
548A VAL 3.3 9.2 - - - +
549A TYR* 3.8 25.6 - - + -
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Residues in contact with VAL 515 (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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504A VAL* 3.4 32.1 - - + -
505A ALA 3.7 8.1 - - - +
506A PRO* 4.5 4.9 - - + -
513A ASN* 4.7 2.0 - - + -
514A VAL* 1.3 78.4 - - - +
516A THR* 1.3 66.3 + - - +
517A ILE* 5.0 1.8 - - + -
531A PHE* 4.3 11.0 - - + -
546A ILE 3.9 0.2 - - - +
547A GLU* 3.5 3.3 - - - +
548A VAL* 2.9 44.0 + - + +
550A VAL* 3.4 30.1 - - + -
574A TYR* 3.4 24.5 - - + +
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Residues in contact with THR 516 (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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1A SER 2.7 21.9 + - - +
4A ALA* 3.8 15.0 - - + -
250A ASP* 2.6 25.2 + - - -
503A SER* 3.7 1.4 + - - +
504A VAL* 3.4 3.6 - - - -
505A ALA* 2.8 34.0 + - - +
514A VAL* 4.7 0.2 - - - +
515A VAL* 1.3 73.3 + - - +
517A ILE* 1.3 64.7 + - - +
518A ASP* 3.5 22.3 + - - +
545A ARG* 3.5 28.0 - - + -
546A ILE 3.5 3.6 - - - +
547A GLU* 3.9 3.7 - - + +
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Residues in contact with ILE 517 (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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501A ILE* 3.9 30.5 - - + -
503A SER 3.3 9.0 - - - +
504A VAL* 4.0 16.2 - - + -
515A VAL* 5.0 0.9 - - + -
516A THR* 1.3 75.2 - - - +
518A ASP* 1.3 62.6 + - - +
522A PHE* 3.8 15.1 - - + -
529A VAL* 3.6 41.3 - - + -
545A ARG* 3.3 5.5 - - - +
546A ILE* 2.7 43.6 + - + +
548A VAL* 4.4 16.4 - - + -
560A VAL* 3.8 10.5 - - + -
562A VAL* 4.0 7.4 - - + -
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Residues in contact with ASP 518 (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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1A SER 5.1 0.5 - - - +
4A ALA* 5.3 0.2 - - - +
5A SER* 3.6 25.6 + - - +
407A TYR* 3.4 18.4 - - + +
501A ILE* 3.9 2.6 - - - +
502A GLY* 2.8 21.1 + - - -
503A SER* 2.8 25.4 + - - +
516A THR* 3.5 18.9 + - - +
517A ILE* 1.3 74.6 - - - +
519A GLY* 1.3 58.2 + - - +
522A PHE* 4.0 2.7 - - - -
544A ASN 3.5 3.3 - - - +
545A ARG* 2.9 40.0 + - - +
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Residues in contact with GLY 519 (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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407A TYR* 3.8 13.9 + - - -
426A PHE* 5.2 0.7 - - - -
500A GLN 3.3 12.3 - - - -
502A GLY 3.8 4.9 - - - -
518A ASP* 1.3 76.5 - - - +
520A LYS* 1.3 67.8 + - - +
522A PHE* 3.6 6.1 - - - -
544A ASN* 2.9 36.1 + - - +
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Residues in contact with LYS 520 (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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403A ALA* 3.7 21.5 - - + +
407A TYR* 5.4 0.4 - - + -
426A PHE* 4.2 4.9 - - + -
429A ASP* 2.5 35.2 + - - +
493A SER* 5.0 2.4 - - - -
494A THR 2.7 26.9 + - - +
495A SER* 4.6 0.2 - - - +
496A ALA* 3.9 7.6 - - + +
500A GLN* 2.9 51.9 + - + +
519A GLY* 1.3 80.5 - - - +
521A GLY* 1.3 63.2 + - - +
522A PHE* 3.3 7.5 + - - -
543A SER 3.8 1.1 - - - -
544A ASN* 3.6 12.3 - - - +
1295A SO4 3.3 21.5 - - - +
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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