Contacts of the strand formed by residues 510 - 514 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52E ASN* 5.7 0.2 - - - -
77E PRO* 5.7 0.7 - - - +
484E ARG 3.4 1.2 + - - -
485E LYS* 3.7 11.8 - - - +
486E LEU 3.3 21.1 + - - -
505E LEU* 5.9 0.7 - - - -
508E MET* 3.5 13.5 - - - +
509E ARG* 1.3 91.5 - - - +
511E LEU* 1.3 60.7 + - - +
512E TRP 4.1 0.7 + - - -
557E PHE* 3.5 28.0 - - - -
558E ILE 3.1 13.7 - - - -
559E TYR* 3.9 6.1 - - - +
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Residues in contact with LEU 511 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473E MET* 4.6 6.3 - - - -
477E LEU* 4.9 4.3 - - + -
486E LEU* 3.3 37.2 - - + +
488E ILE* 4.6 1.8 - - + -
498E LEU* 3.1 35.4 - - + -
505E LEU* 3.8 27.3 - - + +
508E MET* 4.7 2.2 - - + -
510E SER* 1.3 71.7 - - - +
512E TRP* 1.3 61.4 + - - +
513E MET* 3.8 30.1 - - + -
556E VAL 3.9 1.6 - - - +
557E PHE* 3.7 4.5 - - - -
558E ILE* 2.9 41.1 + - + +
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Residues in contact with TRP 512 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E PRO* 3.6 27.8 - - + -
79E PHE* 3.4 32.5 - + + -
84E LEU* 3.7 31.4 - - + -
85E VAL* 3.8 17.3 - - + -
89E TRP* 5.7 0.2 - - - -
486E LEU 2.7 13.8 + - - +
487E GLU* 3.4 11.3 - - + -
488E ILE* 2.9 34.3 + - - +
510E SER* 4.1 1.0 + - - -
511E LEU* 1.3 74.2 - - - +
513E MET* 1.3 67.7 + - - +
514E SER* 3.0 24.8 + - - -
538E ILE* 4.0 22.9 - - + -
555E ARG* 3.9 26.0 - - + -
556E VAL 3.7 3.4 - - - -
557E PHE* 3.6 32.0 - + + -
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Residues in contact with MET 513 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473E MET* 3.5 31.2 - - + +
488E ILE* 3.3 14.6 - - + -
493E PHE* 3.6 26.5 - - + +
494E GLY 4.3 0.4 - - - +
498E LEU* 4.5 5.2 - - - -
511E LEU* 3.8 33.6 - - + -
512E TRP* 1.3 80.3 - - - +
514E SER* 1.3 60.9 + - - +
516E CYS* 4.3 13.0 + - + +
518E VAL* 3.7 26.9 - - + -
555E ARG* 3.3 2.3 - - - -
556E VAL* 2.9 49.7 + - + +
558E ILE* 5.8 0.7 - - - -
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Residues in contact with SER 514 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E LEU* 3.9 12.6 - - - +
488E ILE 2.9 10.5 + - - -
489E ARG* 3.3 17.3 - - - +
490E ASP* 2.8 25.1 + - - -
512E TRP* 3.0 30.7 + - - +
513E MET* 1.3 73.2 - - - +
515E SER* 1.3 65.5 + - - +
516E CYS* 3.3 3.0 + - - -
554E GLU 3.5 9.2 - - - -
555E ARG* 4.0 10.3 - - - -
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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