Contacts of the strand formed by residues 561 - 565 (chain H) in PDB entry 6V3O
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 561 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532H TYR* 3.5 7.2 - - + +
534H ILE* 3.4 30.1 - - + -
543H VAL* 3.5 26.8 - - + +
546H VAL* 3.9 15.3 - - + -
547H GLU* 3.5 33.0 - - + +
550H GLN* 3.7 8.3 - - - +
559H LEU 3.7 10.1 - - - +
560H PRO* 1.3 73.9 - - - +
562H VAL* 1.3 64.2 + - - +
563H PRO* 4.1 1.0 - - - +
587H TYR* 4.1 4.2 + - - +
590H ARG* 3.7 5.5 - - - +
595H GLN* 3.1 23.2 + - - -
596H GLN 5.1 0.2 + - - -
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Residues in contact with VAL 562 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531H PRO* 3.3 32.5 - - + -
532H TYR 2.9 10.9 + - - +
533H ILE* 3.3 11.4 - - + +
534H ILE* 2.9 27.9 + - - +
560H PRO* 4.0 4.0 - - + +
561H VAL* 1.3 82.0 - - - +
563H PRO* 1.3 63.4 - - - +
596H GLN* 3.5 45.5 - - + +
598H MET* 3.8 26.5 - - + +
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Residues in contact with PRO 563 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534H ILE* 4.0 4.5 - - + +
537H ALA* 3.8 15.9 - - + -
543H VAL* 4.3 21.5 - - + -
561H VAL 4.1 1.3 - - - +
562H VAL* 1.3 86.6 - - - +
564H LEU* 1.3 59.7 + - - +
565H PHE* 3.7 35.0 - - + -
578H VAL* 5.8 1.3 - - + -
581H LEU* 5.9 2.9 - - + -
595H GLN* 3.9 10.1 - - - +
596H GLN 3.5 15.5 - - - +
597H VAL* 3.8 10.8 - - + +
598H MET* 3.0 27.2 + - - +
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Residues in contact with LEU 564 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456H ARG* 3.5 28.7 - - - +
533H ILE* 4.1 9.2 - - + -
534H ILE 2.9 20.2 + - - +
535H SER* 3.9 6.5 - - - +
536H MET 3.6 3.1 + - - -
537H ALA* 3.2 23.5 + - - +
562H VAL 3.8 0.2 + - - -
563H PRO* 1.3 70.9 - - - +
565H PHE* 1.3 63.1 + - - +
566H GLU* 3.3 34.8 + - + +
598H MET* 3.6 41.7 - - + +
599H VAL 4.1 0.4 - - - -
600H GLY* 4.0 15.5 - - - +
603H ASP* 4.0 8.5 - - - +
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Residues in contact with PHE 565 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537H ALA* 3.4 26.5 - - + -
538H THR 4.5 11.4 - - - -
539H ALA 4.9 1.8 - - - -
543H VAL* 6.2 0.7 - - + -
563H PRO* 3.7 35.4 - - + -
564H LEU* 1.3 70.4 - - - +
566H GLU* 1.3 62.3 + - - +
567H ARG 4.0 0.9 - - - -
570H ASP* 3.8 27.6 - - + +
571H LEU* 4.1 24.4 - - + +
574H ALA* 3.6 30.7 - - + -
577H SER* 4.4 13.5 - - - -
578H VAL* 4.7 6.5 - - + -
581H LEU* 6.6 0.2 - - + -
597H VAL* 3.8 22.4 - - + -
598H MET 3.3 7.9 + - - +
599H VAL* 4.2 2.7 - - + -
600H GLY 3.9 17.0 + - - -
604H SER* 4.3 1.0 + - - -
624H MET* 5.0 0.9 - - - -
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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