Contacts of the strand formed by residues 401 - 406 (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 ARG 401 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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342E GLU* 5.7 2.8 + - - -
375E GLU* 3.2 40.3 + - - +
376E SER* 3.5 27.2 + - - +
377E VAL 2.8 28.6 + - - +
399E MET* 4.0 2.0 - - - +
400E THR* 1.3 98.4 - - + +
402E PHE* 1.3 60.6 + - - +
403E ARG* 4.1 6.1 - - - -
434E LEU* 4.0 0.4 - - - -
435E ARG* 3.6 14.6 - - + +
436E ARG* 3.5 25.1 - - + -
601E IHP 3.0 47.7 + - - +
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Residues in contact with PHE 402 (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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364E LEU* 4.1 18.4 - - + -
377E VAL* 3.8 29.2 - - + -
389E LEU* 4.0 13.5 - - + -
392E ILE* 4.0 22.7 - - + -
399E MET* 4.1 18.6 - - + -
401E ARG* 1.3 74.7 - - - +
403E ARG* 1.3 61.3 + - - +
404E LEU* 4.0 21.5 - - + -
424E PHE* 4.1 5.4 - + - -
427E ILE* 3.5 45.1 - - + -
434E LEU* 3.5 17.2 - - + +
436E ARG 2.8 10.1 + - - -
437E LEU* 3.4 14.3 - - + +
438E SER 3.2 22.5 + - - +
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Residues in contact with ARG 403 (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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78E HIS* 5.0 3.0 + - - -
344E ARG* 4.1 13.3 - - - +
377E VAL* 2.7 20.8 + - - +
378E LEU* 3.4 32.4 - - + +
379E TYR 2.9 27.0 + - - -
401E ARG* 5.3 5.4 - - - -
402E PHE* 1.3 81.5 - - - +
404E LEU* 1.3 61.5 + - - +
405E CYS 4.2 0.7 - - - -
436E ARG* 3.1 55.9 - - + +
438E SER* 3.0 24.9 - - - +
601E IHP 3.2 27.5 + - - -
602E CFA 2.8 30.0 + - - +
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Residues in contact with LEU 404 (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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364E LEU* 3.6 31.0 - - + -
377E VAL* 5.5 0.2 - - + -
379E TYR* 3.6 15.0 - - + +
381E CYS* 4.8 2.0 - - - -
384E MET* 3.9 35.7 - - + -
389E LEU* 4.5 3.4 - - + -
402E PHE* 4.0 19.5 + - + -
403E ARG* 1.3 75.2 - - - +
405E CYS* 1.3 64.1 + - - +
406E ILE* 4.5 10.5 - - + -
424E PHE* 3.5 27.1 - - + -
438E SER* 3.0 17.7 + - - +
439E LEU* 4.0 0.3 - - - -
440E SER* 2.9 22.2 - - - -
602E CFA 3.2 6.0 - - - +
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Residues in contact with CYS 405 (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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378E LEU* 5.5 0.9 - - + -
379E TYR 2.8 11.7 + - - +
380E PHE* 3.4 29.7 - - + +
381E CYS 3.3 21.8 + - - +
404E LEU* 1.3 74.8 - - - +
406E ILE* 1.3 63.0 + - - +
407E ILE* 3.7 2.2 + - - -
440E SER* 3.5 3.4 - - - -
602E CFA 3.5 21.1 - - + +
5F TRP* 4.0 16.6 - - - -
6F PRO* 4.7 3.6 - - - -
7F PRO* 3.3 33.4 - - - -
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Residues in contact with ILE 406 (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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381E CYS* 3.2 16.6 - - - +
382E ARG 4.0 13.9 - - - +
383E GLN* 4.8 2.2 - - - -
384E MET* 4.0 22.9 - - + +
404E LEU* 4.5 9.0 - - + -
405E CYS* 1.3 72.2 - - - +
407E ILE* 1.3 66.8 + - - +
408E GLU 3.4 23.2 + - - +
409E PRO* 5.1 0.3 - - - +
411E ALA* 3.8 17.0 - - + +
412E PRO 5.8 0.9 - - - +
420E LEU* 3.3 34.1 - - + -
440E SER* 2.9 21.5 + - - +
441E GLY* 3.6 21.1 + - - +
5F TRP* 3.8 11.8 - - - -
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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