Contacts of the strand formed by residues 376 - 381 (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 376 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341B ARG 3.0 10.4 + - - +
342B GLU* 3.0 27.1 + - - +
343B LEU 2.8 29.6 + - - -
344B ARG* 5.0 4.5 + - - -
374B LEU* 3.6 1.5 - - - +
375B GLU* 1.3 83.4 - - - +
377B VAL* 1.3 61.7 + - - +
399B MET* 3.9 1.0 - - - -
401B ARG* 3.4 38.0 + - - +
601B IHP 5.3 0.5 + - - -
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Residues in contact with VAL 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B LEU* 3.4 9.6 - - + +
344B ARG* 5.3 0.2 - - - -
364B LEU* 4.0 25.4 - - + -
374B LEU* 3.9 30.1 - - + -
376B SER* 1.3 81.5 + - - +
378B LEU* 1.3 63.9 + - - +
379B TYR* 4.0 20.0 - - + -
399B MET* 4.1 10.1 - - + -
401B ARG* 2.6 14.1 + - - +
402B PHE* 4.0 25.6 - - + -
403B ARG* 2.8 34.0 + - - +
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Residues in contact with LEU 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B LEU 2.9 10.7 + - - +
344B ARG* 3.3 28.9 - - + +
345B VAL 2.8 27.5 + - - +
346B PHE* 3.9 31.6 - - + -
377B VAL* 1.3 73.7 - - - +
379B TYR* 1.3 69.3 + - - +
380B PHE* 3.9 15.9 - - + -
403B ARG* 3.2 48.7 - - + +
602B CFA 3.6 27.4 - - - +
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Residues in contact with TYR 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B LEU* 3.8 18.2 - - + +
343B LEU* 4.7 4.9 - - + -
345B VAL* 3.7 32.5 - - + -
359B LEU* 3.5 17.0 - - + +
360B THR 2.8 25.7 + - - -
363B GLY* 3.9 1.0 - - - -
364B LEU* 3.5 40.5 + - + -
377B VAL* 4.0 10.8 - - + -
378B LEU* 1.3 77.1 - - - +
380B PHE* 1.4 62.8 + - - +
381B CYS* 3.9 33.3 + - + -
384B MET* 4.9 2.5 - - + -
403B ARG 2.8 13.0 + - - +
404B LEU* 3.6 14.9 - - + +
405B CYS* 2.8 33.3 + - - +
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Residues in contact with PHE 380 (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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323B ASP* 4.7 7.6 - - - +
345B VAL* 3.1 28.6 + - - +
346B PHE* 4.1 9.0 - + - -
347B PRO* 3.6 39.5 - - + -
359B LEU* 3.5 16.6 - - - +
378B LEU* 3.9 26.9 - - + -
379B TYR* 1.4 75.4 - - - +
381B CYS* 1.4 60.5 + - - +
405B CYS* 3.5 36.1 - - + -
407B ILE* 4.7 10.3 - - + -
602B CFA 3.8 15.5 - - - -
6C PRO* 5.0 0.9 - - + -
7C PRO* 3.6 22.0 - - + -
8C VAL* 3.7 18.8 - - + -
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Residues in contact with CYS 381 (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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359B LEU* 3.7 24.9 - - + +
360B THR* 4.5 2.9 - - - -
361B GLU 5.2 0.2 - - - -
379B TYR* 3.9 15.7 - - + -
380B PHE* 1.4 72.8 - - - +
382B ARG* 1.3 67.2 + - - +
383B GLN 3.5 25.1 - - - +
384B MET* 3.9 18.2 - - - -
404B LEU* 4.6 3.8 - - - -
405B CYS 3.3 5.4 + - - -
406B ILE* 3.5 16.9 - - - -
407B ILE* 3.3 25.6 + - - +
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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