Contacts of the strand formed by residues 535 - 542 (chain U) in PDB entry 6FF7
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 535 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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521U GLU 3.2 8.5 - - - +
522U VAL* 5.1 4.0 - - + -
532U PRO* 5.4 4.3 - - + -
534U ARG* 1.3 75.2 - - - +
536U ARG* 1.3 58.2 + - - +
628U PHE* 3.3 7.0 - - - +
629U LEU* 2.7 57.9 + - + +
631U PRO* 4.9 5.9 - - + +
634U TYR* 4.6 16.2 - - + -
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Residues in contact with ARG 536 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519U VAL* 3.6 4.5 - - - +
520U VAL* 2.9 23.6 + - + -
521U GLU* 2.9 29.3 + - + +
534U ARG 4.3 0.2 - - - -
535U VAL* 1.3 75.8 - - - +
537U ALA* 1.3 63.5 + - - +
626U ARG* 6.0 3.8 - - + -
627U VAL 3.1 11.9 - - - +
628U PHE* 5.1 0.7 - - - -
629U LEU* 5.4 1.6 - - - -
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Residues in contact with ALA 537 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517U PHE* 6.4 0.7 - - + -
518U THR 3.2 16.6 - - - +
519U VAL* 4.0 7.9 - - + +
520U VAL* 3.9 4.0 - - - +
536U ARG* 1.3 77.1 - - - +
538U ASP* 1.3 62.0 + - - +
539U VAL* 5.7 0.9 - - + -
625U PHE 3.6 0.9 - - - +
626U ARG* 3.3 5.1 - - - +
627U VAL* 2.8 38.5 + - + +
629U LEU* 5.8 6.3 - - + -
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Residues in contact with ASP 538 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516U ALA 3.8 0.7 - - - +
517U PHE* 3.3 4.5 - - - -
518U THR* 2.8 40.8 + - - +
520U VAL* 4.9 7.2 - - + +
537U ALA* 1.3 73.4 - - - +
539U VAL* 1.3 61.4 + - - +
540U THR 4.2 0.2 - - - -
624U THR* 5.4 8.1 - - - -
625U PHE 3.4 7.4 - - - +
626U ARG* 4.5 3.1 - - + +
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Residues in contact with VAL 539 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514U ILE* 6.0 4.3 - - + -
516U ALA 3.4 6.5 - - - +
517U PHE* 4.6 6.1 - - + +
537U ALA* 4.1 1.7 + - + -
538U ASP* 1.3 74.3 - - - +
540U THR* 1.3 61.1 + - - +
541U ILE 4.1 0.3 + - - -
623U ARG 3.7 1.0 - - - +
624U THR* 3.3 3.5 - - - -
625U PHE* 2.8 44.6 + - + +
627U VAL* 6.1 4.3 - - + -
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Residues in contact with THR 540 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514U ILE* 3.8 3.8 - - - +
515U VAL* 2.8 32.6 + - - -
516U ALA* 2.9 29.9 + - - +
538U ASP 4.2 0.2 - - - -
539U VAL* 1.3 74.7 - - - +
541U ILE* 1.3 61.9 + - - +
622U SER* 6.1 2.9 - - - -
623U ARG 3.2 8.7 - - - -
624U THR* 4.1 9.6 - - - +
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Residues in contact with ILE 541 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512U GLN* 4.5 15.9 - - + -
513U PRO 4.2 14.4 - - - +
514U ILE* 5.6 0.4 - - - -
515U VAL* 4.5 4.3 - - - -
539U VAL 4.1 0.6 + - - -
540U THR* 1.3 75.7 - - - +
542U ASN* 1.3 63.1 + - - +
543U LEU* 3.9 1.1 + - + -
621U GLU 3.8 0.3 - - - +
622U SER* 3.4 4.4 - - - -
623U ARG* 2.8 38.1 + - + +
656U ILE* 6.5 1.6 - - + -
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Residues in contact with ASN 542 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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512U GLN* 6.0 0.4 - - - +
513U PRO 4.7 3.8 + - - -
515U VAL* 4.6 11.8 - - + +
541U ILE* 1.3 74.3 - - - +
543U LEU* 1.3 53.2 + - - +
544U ASN* 2.7 25.6 + - + +
621U GLU* 3.5 10.1 - - + +
622U SER* 4.4 3.8 - - - +
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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