Contacts of the strand formed by residues 376 - 381 (chain A) in PDB entry 3PE7
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 ALA 376 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ARG* 4.2 5.4 - - + -
27A THR* 3.3 28.5 - - - +
28A PRO 5.1 0.2 - - - -
29A PRO* 4.6 7.6 - - + -
33A CYS 3.3 7.5 + - - -
368A THR* 3.2 6.9 - - - +
369A SER 2.8 28.7 + - - +
374A LYS 4.1 4.7 - - - +
375A PRO* 1.3 75.1 - - - +
377A LEU* 1.3 61.4 + - - +
378A TYR* 3.4 25.9 - - + +
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Residues in contact with LEU 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ARG* 3.5 6.4 - - - +
26A LEU* 2.8 41.7 + - + -
27A THR* 3.0 21.9 + - + +
33A CYS* 3.6 13.2 - - + -
34A HIS* 3.4 35.4 - - - +
35A ARG* 3.9 20.6 - - + +
50A LEU* 4.0 22.9 - - + -
51A LEU 5.2 0.2 - - - +
52A PHE* 3.7 26.9 - - + -
65A LEU* 6.1 0.4 - - + -
366A LEU* 4.0 10.8 - - + -
367A PHE 3.6 3.4 - - - +
368A THR* 4.9 0.2 - - - +
376A ALA* 1.3 71.4 - - - +
378A TYR* 1.3 62.1 + - - +
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Residues in contact with TYR 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TYR* 3.3 27.6 - - - -
23A VAL* 4.1 7.6 - - + -
24A THR 3.3 6.1 - - - +
25A ARG* 3.5 34.6 - - + -
26A LEU* 5.0 0.7 - - - -
29A PRO* 5.3 0.2 - - - +
365A ILE 3.6 0.7 - - - +
366A LEU* 3.3 8.6 - - - +
367A PHE* 2.9 66.0 + + + -
369A SER* 3.4 23.9 + - - -
371A VAL* 3.4 13.8 - - + +
372A HIS* 2.8 31.2 + + - +
374A LYS 5.3 0.2 + - - -
376A ALA* 3.4 29.5 - - + +
377A LEU* 1.3 74.3 - - - +
379A LEU* 1.3 61.9 + - - +
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Residues in contact with LEU 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLN 3.9 1.0 - - - +
23A VAL* 3.3 4.9 - - - -
24A THR* 2.9 44.5 + - - +
26A LEU* 3.9 32.1 - - + -
43A PHE* 4.3 4.0 - - + -
67A LEU* 4.8 15.5 - - + -
359A THR* 3.7 27.8 - - + -
364A GLN* 3.8 28.8 + - + +
365A ILE 3.2 11.2 - - - +
366A LEU* 3.8 20.4 - - + -
378A TYR* 1.3 73.4 - - - +
380A ALA* 1.3 60.7 + - - +
381A THR* 4.1 0.3 + - - -
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Residues in contact with ALA 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ALA* 5.5 0.7 - - + -
22A GLN 3.5 4.7 - - - +
23A VAL* 4.2 8.3 - - + -
335A VAL* 5.7 1.3 - - + -
336A ALA* 4.0 24.2 - - + -
364A GLN* 3.1 6.4 - - - -
365A ILE* 2.9 53.7 + - + +
367A PHE* 3.9 15.6 - - + -
378A TYR 4.2 0.6 - - - -
379A LEU* 1.3 72.0 - - - +
381A THR* 1.3 63.8 + - - +
382A LEU* 3.6 0.4 + - + -
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Residues in contact with THR 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ALA* 3.6 19.4 - - - +
22A GLN* 2.8 43.9 + - + +
335A VAL* 5.1 1.0 - - - +
363A LYS* 3.7 13.2 - - + +
364A GLN* 3.9 18.9 + - + -
379A LEU 5.1 0.5 + - - -
380A ALA* 1.3 71.2 - - - +
382A LEU* 1.3 75.6 + - - +
383A PRO* 3.4 3.1 - - - +
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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