Contacts of the strand formed by residues 510 - 514 (chain B) in PDB entry 2P1N
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 SER 510 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ASN* 5.7 0.2 - - - -
77B PRO* 5.7 1.7 - - - +
484B ARG 3.5 1.6 + - - -
485B LYS* 3.8 18.4 - - - +
486B LEU 3.4 20.8 + - - +
508B MET* 3.5 13.8 - - - +
509B ARG* 1.4 85.3 - - - +
511B LEU* 1.4 57.6 + - - +
512B TRP* 4.1 1.5 + - - +
557B PHE* 3.6 33.9 - - - -
558B ILE 3.1 9.2 - - - -
559B TYR* 4.2 3.1 - - - +
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Residues in contact with LEU 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473B MET* 4.9 4.3 - - + -
477B LEU* 5.1 3.1 - - + -
486B LEU* 3.3 42.6 - - + +
488B ILE* 4.4 2.2 - - + -
498B LEU* 3.3 34.8 - - + -
505B LEU* 4.0 22.1 - - + +
508B MET* 4.8 3.1 - - + +
510B SER* 1.4 71.1 - - - +
512B TRP* 1.3 58.4 + - - +
513B MET* 3.8 29.2 - - + -
556B VAL 3.8 2.0 - - - +
557B PHE* 3.6 4.6 - - - -
558B ILE* 2.7 53.2 + - + +
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Residues in contact with TRP 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B PRO* 3.8 28.0 - - + -
79B PHE* 3.5 30.9 - + + -
84B LEU* 3.8 24.9 - - + -
85B VAL* 4.1 15.7 - - + -
89B TRP* 5.7 0.2 - - - -
486B LEU 3.0 9.2 + - - +
487B GLU* 3.4 16.3 - - + +
488B ILE* 2.8 38.5 + - - +
510B SER* 4.1 2.0 + - - +
511B LEU* 1.3 70.8 - - - +
513B MET* 1.3 65.8 + - - +
514B SER* 2.9 28.4 + - - -
538B ILE* 3.8 25.4 - - + -
555B ARG* 3.8 28.9 - - + -
556B VAL 3.8 2.0 - - - -
557B PHE* 3.5 28.1 - + + -
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Residues in contact with MET 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473B MET* 3.7 20.2 - - + +
488B ILE* 3.2 13.7 - - + +
493B PHE* 3.5 48.5 - - + +
498B LEU* 4.3 5.2 - - - -
511B LEU* 3.8 32.7 - - + -
512B TRP* 1.3 80.1 - - - +
514B SER* 1.3 60.3 + - - +
515B SER 4.3 0.3 + - - -
516B CYS* 4.1 13.4 + - + +
518B VAL* 3.8 18.8 - - + -
553B VAL* 5.6 0.3 - - - +
554B GLU 4.7 0.2 - - - -
555B ARG* 3.3 1.3 - - - -
556B VAL* 2.9 50.9 + - + +
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Residues in contact with SER 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LEU* 4.2 12.4 - - - +
488B ILE 3.0 4.8 + - - -
489B ARG* 3.1 21.3 - - - +
490B ASP 2.8 25.5 + - - -
512B TRP* 2.9 25.6 + - - +
513B MET* 1.3 72.4 - - - +
515B SER* 1.3 67.2 + - - +
516B CYS* 3.2 2.4 + - - -
554B GLU 3.4 11.2 - - - -
555B ARG* 3.8 15.7 - - - +
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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