Contacts of the strand formed by residues 511 - 516 (chain A) in PDB entry 3W5D
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 LYS 511 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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479A MET* 4.4 8.5 - - + -
496A VAL 3.7 0.3 - - - +
497A TYR* 3.6 2.8 - - - -
498A CYS* 2.7 44.1 + - - +
509A GLY* 3.7 14.9 + - - +
510A ASN* 1.3 81.2 + - - +
512A MET* 1.3 60.8 - - - +
513A PHE* 3.9 30.7 - - + -
529A ARG* 6.2 0.2 - - - +
566A THR* 4.7 2.9 - - - +
567A ARG 3.7 9.2 - - - +
568A ASP* 2.9 46.6 + - - +
570A PRO* 3.9 3.4 - - - -
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Residues in contact with MET 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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483A PHE* 6.1 0.2 - - + -
485A LEU* 3.8 17.7 - - + -
495A SER* 3.4 28.5 - - - +
496A VAL 3.1 10.1 - - - +
497A TYR* 3.6 22.7 - - + -
511A LYS* 1.3 71.7 - - - +
513A PHE* 1.3 62.0 + - - +
514A VAL* 3.9 6.0 + - + -
566A THR* 3.1 8.3 - - - -
567A ARG* 2.8 46.8 + - + -
570A PRO* 3.9 17.9 - - + +
571A PRO* 4.2 3.8 - - - -
576A MET* 4.1 15.9 - - + -
587A TYR* 3.3 32.3 - - + +
588A GLU* 4.0 4.7 - - + -
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Residues in contact with PHE 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A GLU* 4.8 7.4 - - + -
415A THR* 4.1 16.6 - - + -
416A ILE* 3.9 31.2 - - + -
419A LEU* 3.2 39.5 - - + -
420A CYS* 3.4 10.0 - - + -
479A MET* 4.0 12.1 - - + -
495A SER* 3.2 4.3 - - - -
496A VAL* 3.0 34.2 + - + -
498A CYS* 3.7 26.2 - - + -
511A LYS* 3.9 26.5 - - + -
512A MET* 1.3 75.7 - - - +
514A VAL* 1.3 60.7 + - - +
565A ALA 3.7 1.8 - - - -
566A THR* 3.8 18.6 - - + -
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Residues in contact with VAL 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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416A ILE* 4.0 4.1 - - - +
493A SER* 4.2 13.7 - - - -
494A MET 3.4 11.7 - - - +
495A SER* 3.9 13.5 - - - -
512A MET* 4.3 9.6 - - + +
513A PHE* 1.3 75.6 - - - +
515A LYS* 1.3 64.0 + - - +
521A VAL* 4.4 8.9 - - + +
524A ARG* 5.2 0.7 - - - +
563A ALA 3.8 0.5 - - - +
564A LEU* 3.3 4.7 - - - -
565A ALA* 2.7 46.5 + - + +
588A GLU* 4.1 20.2 - - + +
591A LEU* 3.7 40.6 - - + -
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Residues in contact with LYS 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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416A ILE* 4.5 0.9 - - + +
417A CYS* 6.0 0.4 - - - -
420A CYS* 2.9 34.4 + - + +
421A ASN* 4.3 0.2 - - - +
442A GLU* 2.7 39.0 + - - +
445A LEU* 3.6 26.8 - - + +
487A PHE* 5.5 0.3 - - - -
493A SER* 3.2 4.6 - - - -
494A MET* 2.8 55.6 + - - +
514A VAL* 1.3 74.8 - - - +
516A GLY* 1.3 61.7 + - - +
521A VAL* 4.5 0.4 - - - -
562A LEU* 3.8 17.0 - - + -
563A ALA 3.5 4.0 - - - -
564A LEU* 3.8 18.8 - - + -
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Residues in contact with GLY 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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487A PHE* 5.7 2.7 - - - -
492A LYS 3.5 10.3 - - - -
493A SER* 4.0 0.9 - - - -
515A LYS* 1.3 80.2 - - - +
517A ALA* 1.3 64.5 + - - -
521A VAL* 3.9 7.9 - - - +
562A LEU* 3.5 14.0 - - - +
563A ALA* 2.7 41.0 + - - +
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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