Contacts of the strand formed by residues 511 - 517 (chain A) in PDB entry 3QFR
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 LEU 511 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286A LEU* 4.0 47.8 - - + +
287A ALA 3.4 6.1 - - - +
288A ALA* 4.2 12.1 - - + -
500A LYS* 2.7 27.9 + - - +
510A ALA* 1.3 91.2 - - + +
512A VAL* 1.3 62.0 + - - +
513A PRO* 4.0 5.0 - - - +
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Residues in contact with VAL 512 (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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285A PHE 3.1 2.6 - - - +
286A LEU* 4.0 1.8 - - - -
287A ALA 2.7 39.3 + - - +
289A VAL* 3.6 24.9 - - + -
308A LEU* 4.4 14.6 - - + -
325A VAL* 3.8 25.6 - - + -
496A TRP* 3.5 21.8 - - + -
497A LEU* 4.2 11.2 - - + -
500A LYS* 3.9 19.1 - - + -
511A LEU* 1.3 79.8 - - - +
513A PRO* 1.3 65.5 - - - +
514A MET* 3.4 6.6 + - + +
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Residues in contact with PRO 513 (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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272A TYR* 3.6 40.8 - - + +
284A PRO* 4.0 12.1 - - + -
285A PHE 3.4 9.2 - - - +
286A LEU* 4.1 11.7 - - + -
325A VAL* 3.3 4.7 - - - +
326A TYR* 3.0 47.7 + - + +
496A TRP* 3.7 10.5 - - + -
511A LEU 4.0 4.7 - - - +
512A VAL* 1.3 82.6 - - - +
514A MET* 1.3 58.0 + - - +
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Residues in contact with MET 514 (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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284A PRO* 3.5 3.5 - - - +
285A PHE* 2.8 54.1 + - - +
287A ALA* 3.8 18.4 - - + -
308A LEU* 4.1 11.4 - - + -
310A ILE* 3.6 26.9 - - + -
315A ILE* 4.5 5.0 - - + +
323A VAL* 3.7 26.0 - - + -
324A ALA 3.0 17.7 - - - +
325A VAL* 4.2 7.0 - - + -
472A VAL* 4.6 7.6 - - + -
512A VAL* 3.7 10.3 - - + +
513A PRO* 1.3 73.9 - - - +
515A PHE* 1.3 79.7 + - - +
516A VAL* 4.6 11.4 - - + -
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Residues in contact with PHE 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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279A PHE 4.5 3.4 - - - +
280A ASP* 3.8 23.3 - - + +
281A ALA* 3.7 40.4 - - + -
284A PRO* 5.0 0.2 - - + -
315A ILE* 4.7 5.4 - - - -
323A VAL* 3.6 2.0 - - - -
324A ALA* 2.9 56.0 + - + +
326A TYR* 3.9 25.1 - + - -
456A ALA* 4.1 6.3 - - + -
458A TYR* 4.0 20.4 - + - -
514A MET* 1.3 90.0 - - - +
516A VAL* 1.3 74.6 + - - +
517A ARG* 4.8 9.4 - - + -
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Residues in contact with VAL 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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279A PHE 5.6 0.6 + - - -
315A ILE* 3.5 30.5 - - + +
316A ARG 3.8 9.6 - - - +
317A TYR* 3.8 29.8 - - + -
321A ASP* 4.0 15.3 - - + +
322A HIS 3.3 8.7 - - - +
323A VAL* 5.1 0.9 - - + -
461A ILE* 4.3 9.9 - - + -
472A VAL* 4.7 5.8 - - + -
514A MET* 4.6 11.4 - - + -
515A PHE* 1.3 84.7 - - - +
517A ARG* 1.3 65.5 + - - +
518A LYS* 4.1 4.2 + - + +
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Residues in contact with ARG 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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90A GLN* 3.5 32.0 + - - +
143A TYR* 5.5 3.8 - - - +
150A ASP* 3.1 38.8 + - - -
321A ASP* 3.7 1.4 - - - +
322A HIS* 2.8 49.1 + - + +
458A TYR* 3.9 38.6 + - + -
515A PHE* 3.9 10.3 + - + +
516A VAL* 1.3 75.0 - - - +
518A LYS* 1.3 74.9 + - - +
519A SER 3.6 0.3 + - - -
751A FMN 6.2 2.6 - - - +
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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