Contacts of the strand formed by residues 342 - 346 (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 GLU 342 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317E GLN 3.1 8.4 + - - +
318E ARG* 2.9 38.2 + - + +
319E LEU 3.0 24.0 + - - -
320E TRP* 2.7 30.5 + - - -
340E LEU* 3.8 6.8 - - - +
341E ARG* 1.3 82.2 - - + +
343E LEU* 1.3 62.1 + - - +
344E ARG* 2.9 25.8 + - + +
374E LEU* 3.9 2.1 - - - +
376E SER* 3.3 25.6 + - - +
401E ARG* 5.7 2.6 + - - -
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Residues in contact with LEU 343 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319E LEU* 3.6 20.6 - - + +
321E VAL* 4.5 4.3 - - + -
330E LEU* 3.9 25.1 - - + -
333E LEU* 4.3 7.6 - - + -
340E LEU* 4.3 4.7 - - + -
342E GLU* 1.3 73.4 - - - +
344E ARG* 1.3 69.7 + - - +
345E VAL* 4.2 22.7 - - + -
364E LEU* 5.0 6.5 - - + -
367E VAL* 3.8 27.4 - - + -
374E LEU* 3.8 15.2 - - + +
376E SER 2.8 10.1 + - - +
377E VAL* 3.5 6.2 - - + +
378E LEU 2.8 27.2 + - - +
379E TYR* 4.7 12.8 - - + -
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Residues in contact with ARG 344 (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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319E LEU 2.8 11.7 + - - -
320E TRP* 3.2 50.2 - - + +
321E VAL* 2.9 33.4 + - - +
342E GLU* 2.9 26.4 + - + +
343E LEU* 1.3 79.8 - - - +
345E VAL* 1.3 63.3 + - - +
346E PHE* 3.7 21.9 - - + -
376E SER* 4.8 5.1 + - - -
378E LEU* 3.2 30.9 - - + +
403E ARG* 4.1 12.6 - - - +
601E IHP 2.7 51.7 + - - -
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Residues in contact with VAL 345 (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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321E VAL* 3.3 15.0 - - + +
322E LEU 3.9 2.2 - - - +
323E ASP* 3.4 39.3 - - + +
325E ILE* 4.4 10.8 - - + -
330E LEU* 4.5 2.2 - - + -
343E LEU* 4.2 13.5 - - + -
344E ARG* 1.3 76.1 - - - +
346E PHE* 1.3 62.8 + - - +
359E LEU* 4.4 11.4 - - + -
378E LEU* 2.8 10.5 + - - +
379E TYR* 3.8 33.7 - - + -
380E PHE* 3.0 31.6 + - - +
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Residues in contact with PHE 346 (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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297E SER* 3.5 26.7 - - - -
320E TRP* 4.2 22.9 - + + -
321E VAL 3.0 17.4 + - - -
322E LEU* 3.4 15.9 - - + -
323E ASP* 2.6 34.6 + - - +
344E ARG* 3.7 33.9 - - + -
345E VAL* 1.3 74.6 - - - +
347E PRO* 1.3 69.1 - - + +
378E LEU* 3.8 21.1 - - + -
380E PHE* 4.3 14.1 - + - -
8F VAL* 6.3 1.1 - - + -
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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