Contacts of the strand formed by residues 494 - 498 (chain A) in PDB entry 6F3T
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 494 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486A ALA* 4.8 3.8 - - + -
487A GLY 3.4 12.3 - - - +
488A GLY* 5.1 0.4 - - - +
493A THR* 1.3 77.2 - - - +
495A ARG* 1.3 65.5 + - - +
538A ILE* 3.5 0.9 - - - -
539A LEU* 2.6 59.3 + - + +
542A HIS* 4.3 6.7 - - + -
546A VAL* 3.9 22.0 - - + -
549A ALA* 5.8 3.6 - - + -
558A LEU* 3.8 30.3 - - + -
560A SER* 4.0 24.5 - - - +
570A TRP* 4.4 5.2 - - + +
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Residues in contact with ARG 495 (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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466A PHE* 3.7 3.9 - - - -
467A LEU* 3.5 34.2 - - + +
470A TYR* 3.1 35.0 + - - -
485A ILE 3.6 1.7 - - - +
486A ALA* 3.3 2.6 - - - -
487A GLY 2.9 34.5 + - - -
489A PHE* 3.6 21.0 - - + -
491A ASP* 3.1 24.9 + - - -
493A THR* 3.0 21.8 + - - +
494A VAL* 1.3 79.4 - - - +
496A VAL* 1.3 62.3 + - - +
536A LEU* 4.2 7.2 - - + +
537A LYS 3.3 7.4 - - - +
538A ILE* 3.6 35.9 - - + +
540A TYR* 5.2 2.8 + - - -
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Residues in contact with VAL 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A LEU* 4.3 32.5 - - + -
485A ILE 3.3 7.6 - - - +
486A ALA* 4.4 3.1 - - + -
494A VAL* 4.8 0.7 - - + -
495A ARG* 1.3 75.8 - - - +
497A TRP* 1.3 59.9 + - - +
504A LEU* 3.8 6.3 - - + +
536A LEU* 3.4 5.3 - - - +
537A LYS* 2.9 34.7 + - + +
539A LEU* 4.0 17.5 - - + -
551A PHE* 4.5 5.8 - - + -
558A LEU* 3.8 29.6 - - + -
572A LEU* 4.5 7.0 - - + -
575A PHE* 4.2 21.8 - - + -
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Residues in contact with TRP 497 (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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466A PHE* 3.7 29.2 - + + -
467A LEU* 4.6 7.0 - - + -
484A LEU* 3.3 6.8 - - - +
485A ILE* 2.8 52.0 + - + +
495A ARG 4.0 0.2 + - - -
496A VAL* 1.3 74.5 - - - +
498A SER* 1.3 67.7 + - - +
499A VAL* 3.7 34.2 + - + +
526A ARG* 3.4 23.6 - - + -
527A ILE* 5.8 7.0 - - + -
534A SER* 2.8 38.8 + - - +
535A GLU 3.7 10.8 - - - -
536A LEU* 4.1 15.5 - - + -
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Residues in contact with SER 498 (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 SER 3.6 4.9 - - - -
484A LEU* 3.9 10.5 - - - -
496A VAL 4.3 0.4 + - - -
497A TRP* 1.3 79.8 - - - +
499A VAL* 1.3 60.1 + - - +
501A PRO 3.4 15.5 - - - -
502A LYS 3.5 5.0 - - - -
503A LYS 3.6 17.9 - - - -
504A LEU* 4.1 4.6 - - - +
534A SER* 2.6 31.5 + - - -
535A GLU* 2.9 36.7 + - - +
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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