Contacts of the strand formed by residues 506 - 514 (chain A) in PDB entry 2W7P
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 506 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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422A PHE* 3.7 9.2 - - + -
424A GLU* 3.4 9.9 - - - -
425A ILE* 3.2 32.7 + - + +
431A GLN* 3.2 13.2 - - + +
460A LEU* 3.4 38.1 - - + -
461A LYS 3.7 7.2 - - - +
462A ASN* 4.8 0.7 - - - +
463A VAL* 3.9 2.0 - - - +
492A LEU* 5.3 0.2 - - + -
504A LEU* 2.9 56.5 + - + +
505A ARG* 1.3 73.5 - - - +
507A ARG* 1.3 61.3 + - - +
508A LEU 3.9 14.1 - - - +
509A MET* 3.6 20.4 - - + -
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Residues in contact with ARG 507 (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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421A THR* 2.8 44.4 - - + +
422A PHE* 3.1 30.4 + - - +
424A GLU* 5.3 1.3 - - - +
461A LYS* 2.8 19.7 + - + +
462A ASN 3.4 17.0 - - - +
463A VAL* 3.9 23.8 - - + +
465A PHE* 2.8 41.6 - - - -
506A LEU* 1.3 73.2 - - - +
508A LEU* 1.3 60.5 + - + +
4T C 3.2 34.6 + - - -
5T 8OG 3.0 24.5 + - - -
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Residues in contact with LEU 508 (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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419A GLU* 3.6 21.8 - - - +
420A ARG 2.9 43.1 - - - +
421A THR* 3.8 13.0 - - + +
422A PHE* 3.7 6.3 - - - -
459A LYS* 3.9 20.6 - - + +
460A LEU* 3.8 2.3 - - - -
461A LYS* 3.0 62.0 + - + +
506A LEU* 3.9 5.9 - - - +
507A ARG* 1.3 83.0 - - - +
509A MET* 1.3 85.6 + - - +
6T G 4.5 2.0 - - - +
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Residues in contact with MET 509 (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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419A GLU* 3.5 1.0 - - - -
420A ARG 3.3 16.0 + - - +
422A PHE* 4.2 11.4 - - + -
431A GLN* 4.0 19.5 - - + +
434A LEU* 4.9 7.2 - - + -
435A CYS* 4.0 29.6 - - - -
438A LEU* 3.8 21.5 - - + +
458A ILE* 5.1 3.6 - - + -
459A LYS 3.0 7.2 - - - -
460A LEU* 3.6 16.8 - - + -
492A LEU* 3.8 20.6 - - + -
506A LEU* 3.6 24.7 - - + -
508A LEU* 1.3 93.6 - - - +
510A GLY* 1.3 65.4 + - - +
511A VAL* 5.4 1.1 - - + -
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Residues in contact with GLY 510 (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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418A VAL 3.7 10.5 - - - -
419A GLU* 3.8 8.5 - - - -
438A LEU* 4.2 3.1 - - - -
457A THR 4.4 0.2 - - - -
458A ILE* 3.1 8.3 - - - +
459A LYS* 2.6 45.6 + - - -
509A MET* 1.3 80.0 - - - +
511A VAL* 1.3 67.3 + - - +
512A ARG 4.3 0.2 - - - -
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Residues in contact with VAL 511 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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417A SER* 4.2 2.0 - - - -
418A VAL 3.3 26.4 + - - +
435A CYS* 4.9 7.6 - - - -
438A LEU* 4.0 27.1 - - + -
439A CYS* 4.2 15.0 - - - +
442A LEU* 3.4 31.9 - - + +
456A VAL* 4.3 18.2 - - + -
457A THR 3.2 7.9 - - - +
458A ILE* 5.0 4.7 - - + -
484A ILE* 4.4 12.1 - - + -
488A ALA* 4.6 6.1 - - + -
509A MET* 5.4 1.6 - - + -
510A GLY* 1.3 80.8 - - - +
512A ARG* 1.3 62.2 + - - +
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Residues in contact with ARG 512 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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415A SER* 3.6 24.2 + - - -
416A MET 3.6 8.5 - - - +
417A SER* 3.1 36.3 + - - +
442A LEU* 4.5 1.3 - - - -
456A VAL* 3.7 1.1 - - - -
457A THR* 2.6 63.7 + - - +
459A LYS* 5.9 7.7 - - - +
469A THR* 5.9 4.9 - - - +
510A GLY 4.3 0.2 - - - -
511A VAL* 1.3 74.7 - - - +
513A ILE* 1.3 60.1 + - - +
514A SER* 4.5 9.6 + - - -
8T A 4.7 4.9 + - - -
9T T 3.4 31.5 + - - +
10T C 5.8 1.8 - - - +
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Residues in contact with ILE 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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416A MET* 2.8 41.7 + - + +
442A LEU* 4.1 15.7 - - + +
446A LEU* 3.3 33.0 - - + -
453A GLY 4.6 17.5 - - - +
455A THR 3.3 17.9 - - - +
456A VAL* 3.2 31.0 - - + -
478A VAL* 5.3 7.9 - - + +
484A ILE* 4.8 9.2 - - + -
512A ARG* 1.3 72.3 - - - +
514A SER* 1.3 68.3 + - - +
516A PHE* 3.3 14.2 - - + -
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Residues in contact with SER 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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414A LYS 4.1 3.4 - - - -
415A SER* 4.1 17.9 - - - -
453A GLY* 3.3 5.4 - - - -
454A ARG 3.2 9.9 + - - -
455A THR* 3.1 24.9 + - - +
457A THR* 4.0 11.6 + - - -
512A ARG* 4.5 5.6 + - - -
513A ILE* 1.3 76.1 - - - +
515A SER* 1.3 79.0 + - - +
516A PHE* 3.2 12.3 - - - -
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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