Contacts of the strand formed by residues 451 - 453 (chain P) in PDB entry 6K71
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 TRP 451 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263J ASN* 5.1 9.4 - - - +
264J PHE 5.1 0.4 - - - -
265J ASP* 3.8 24.3 + - + -
77P ILE* 4.4 28.0 + - + +
140P ILE 5.5 0.5 - - - +
143P ALA* 4.1 11.2 - - + +
144P THR* 5.9 3.6 - - + -
403P VAL* 4.4 6.1 - - + -
404P LEU* 4.0 12.6 - - - -
405P MET* 3.6 46.3 - - + +
444P SER* 3.7 14.4 - - - +
445P ARG* 3.5 27.8 - - - -
446P ARG* 3.5 48.7 - - + +
450P HIS* 1.3 99.1 - - - +
452P ARG* 1.3 67.3 + - - +
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Residues in contact with ARG 452 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139P ASP 4.8 9.3 + - - -
140P ILE* 5.2 0.8 + - - +
142P MET* 3.4 39.9 - - - +
143P ALA* 3.7 7.6 - - - -
172P GLU* 4.7 9.3 + - - +
173P HIS* 6.1 0.4 - - - -
381P LEU* 3.7 39.7 - - + +
382P LEU 5.2 3.6 + - - -
384P VAL* 4.2 16.7 - - - +
444P SER* 2.3 23.5 + - - -
445P ARG 3.1 19.3 + - - +
447P VAL* 3.6 21.3 - - + +
448P GLU* 2.5 33.0 + - - +
450P HIS* 3.9 11.4 + - - -
451P TRP* 1.3 77.4 - - - +
453P LEU* 1.3 59.1 + - - +
454P ILE* 4.1 2.6 - - + +
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Residues in contact with LEU 453 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143P ALA* 3.6 27.7 - - + +
146P LEU* 4.9 10.1 - - + +
147P ASN* 4.6 9.4 - - - +
180P MET* 6.3 1.3 - - + -
378P LEU* 4.4 12.1 - - + +
381P LEU* 5.2 3.8 - - - +
382P LEU* 5.3 5.4 - - - +
407P ASN* 4.8 7.2 - - - +
442P ALA* 3.7 28.9 - - + +
443P LEU 3.4 11.0 - - - +
444P SER* 3.7 8.5 - - - -
452P ARG* 1.3 77.9 - - - +
454P ILE* 1.3 61.4 + - - +
455P GLY 3.3 26.9 - - - +
456P TRP* 4.6 17.9 - - + +
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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
------------------------------------------------------------
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