Contacts of the strand formed by residues 537 - 542 (chain A) in PDB entry 3F8I
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 537 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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462A ALA* 3.8 5.2 - - + +
463A TYR 3.8 2.5 - - - -
464A SER* 3.7 16.2 - - - +
465A LEU* 4.0 23.6 - - + -
513A LEU* 4.4 11.4 - - + -
516A ASN* 2.9 37.9 - - + +
535A LYS 3.9 3.4 - - - +
536A PRO* 1.3 73.3 - - - +
538A ARG* 1.3 75.6 + - - +
539A VAL* 3.4 6.3 + - + +
562A ILE* 3.6 5.5 - - - +
563A TYR 3.1 36.2 + - - +
564A LYS* 5.4 0.2 - - - -
565A VAL* 4.8 5.8 - - + -
584A LEU* 4.8 4.5 - - + -
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Residues in contact with ARG 538 (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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420A ALA 5.5 2.0 + - - -
422A HIS* 3.3 22.0 + - - +
424A GLY* 2.6 43.2 + - - +
425A PRO* 4.4 3.1 - - - -
426A ILE* 3.7 30.9 - - - +
445A GLY 3.6 10.1 + - - -
446A VAL* 2.8 38.7 + - + +
447A HIS* 5.3 0.2 - - - +
448A ARG* 5.5 3.0 - - - +
455A HIS* 4.9 4.8 + - - -
463A TYR* 3.0 37.0 + - - +
464A SER* 2.9 13.1 + - - -
465A LEU 2.9 26.5 + - - +
536A PRO 4.3 0.2 - - - -
537A VAL* 1.3 72.4 - - - +
539A VAL* 1.3 60.1 + - - +
540A VAL* 5.4 0.8 - - - +
559A TYR* 4.0 14.8 - - + +
561A GLY 3.9 4.9 - - - -
562A ILE* 4.0 13.2 - - + +
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Residues in contact with VAL 539 (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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465A LEU* 3.5 30.1 - - + -
467A LEU* 4.4 8.3 - - + -
481A PHE* 4.1 15.7 - - + -
537A VAL* 3.7 8.5 - - + +
538A ARG* 1.3 79.2 - - - +
540A VAL* 1.3 70.4 + - - +
541A ARG* 4.5 7.6 - - + +
559A TYR* 3.4 7.9 - - - -
560A ASP* 3.0 25.9 + - + -
561A GLY 3.1 7.8 + - - +
563A TYR* 3.3 46.4 - - + -
584A LEU* 5.0 0.2 - - + -
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Residues in contact with VAL 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A TRP* 4.7 2.5 - - + -
438A ARG* 5.8 0.9 - - - -
441A VAL* 4.1 18.2 - - + -
446A VAL* 3.9 26.5 - - + -
447A HIS* 4.6 6.7 - - + -
464A SER* 6.1 0.7 - - - -
465A LEU 2.9 13.2 + - - +
466A VAL* 3.1 14.2 - - + +
467A LEU* 2.8 26.9 + - - +
538A ARG 5.4 1.3 - - - +
539A VAL* 1.3 80.2 - - - +
541A ARG* 1.3 66.8 - - - +
557A ASN* 3.8 32.1 - - + +
558A ARG 3.4 11.9 - - - +
559A TYR* 4.5 5.6 - - - -
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Residues in contact with ARG 541 (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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467A LEU* 3.7 29.9 - - + +
476A ASP* 2.6 42.6 + - - -
478A GLY* 3.1 22.3 + - - -
481A PHE* 3.8 6.7 - - - -
539A VAL* 4.3 3.9 + - + +
540A VAL* 1.3 73.6 - - - +
542A ASN* 1.3 60.7 + - - +
551A TYR* 3.9 23.6 - - - +
552A ALA* 4.4 2.9 - - + +
553A PRO* 3.4 18.9 - - + +
557A ASN* 3.4 1.6 - - - -
558A ARG* 2.8 36.4 + - - +
560A ASP* 2.9 35.8 + - - +
563A TYR* 3.1 23.0 + - - -
594A TRP* 3.6 9.3 - - - -
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Residues in contact with ASN 542 (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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438A ARG* 5.1 1.6 - - - +
466A VAL* 4.1 6.7 - - + -
467A LEU 2.8 17.7 + - - +
468A ALA* 3.7 14.4 - - + +
540A VAL 4.0 0.8 + - - -
541A ARG* 1.3 74.2 - - - +
543A MET* 1.3 63.0 + - - +
544A LYS* 2.7 59.5 + - - +
545A GLY* 3.0 19.9 + - - -
552A ALA* 3.8 7.1 - - - +
553A PRO* 4.0 2.2 - - - -
556A GLY 3.5 7.2 + - - -
557A ASN* 2.9 31.4 + - - +
408D G 4.8 3.0 + - - -
409D C 4.6 5.1 + - - -
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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