Contacts of the strand formed by residues 379 - 382 (chain A) in PDB entry 5E97
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 VAL 379 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340A TRP* 3.4 37.6 - - + +
341A LEU 2.9 25.5 + - - +
377A ILE* 3.3 4.7 - - - +
378A GLU* 1.3 80.2 - - - +
380A VAL* 1.3 67.5 + - - +
381A MET* 3.9 29.4 - - + -
53B SER* 3.6 22.2 - - - +
55B SER 3.9 15.5 - - - +
56B PHE* 3.6 5.8 - - - +
58B SER* 3.9 10.5 - - - +
91B TYR* 4.1 8.7 - - + -
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Residues in contact with VAL 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A LEU* 3.6 11.9 - - + -
344A THR* 3.6 25.1 - - + -
365A TRP* 3.8 22.2 - - + -
368A LYS* 4.8 2.9 - - + -
369A LEU* 4.1 9.0 - - + -
372A SER* 3.6 32.5 - - - +
377A ILE* 4.0 4.7 - - + -
379A VAL* 1.3 79.4 - - - +
381A MET* 1.3 63.2 + - - +
56B PHE* 2.7 27.4 + - + +
57B LEU* 3.9 1.0 - - - -
58B SER 2.8 29.1 + - - +
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Residues in contact with MET 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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185A ILE* 3.5 21.1 - - + -
221A GLU* 4.8 4.5 - - - +
294A THR* 5.1 0.4 - - + -
340A TRP* 3.4 35.7 - - + -
341A LEU 2.8 16.7 + - - +
342A GLY* 3.5 30.5 - - - +
343A GLU* 3.4 2.3 - - - -
344A THR* 3.0 29.1 + - - +
379A VAL* 3.9 9.6 - - + -
380A VAL* 1.3 74.5 - - - +
382A ARG* 1.3 60.9 + - - +
383A GLN 3.4 0.3 + - - -
58B SER* 3.6 18.4 - - - -
59B VAL 4.7 1.1 - - - +
60B THR* 4.0 9.4 - - + +
91B TYR* 4.5 4.9 - - + -
93B ARG* 3.6 24.2 - - + -
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Residues in contact with ARG 382 (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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344A THR 3.6 10.1 - - - -
345A SER* 3.5 9.7 + - - +
346A SER* 5.7 2.3 + - - -
356A SER 4.3 7.5 + - - -
361A ALA* 5.4 0.2 - - - +
365A TRP* 3.2 60.0 - - + +
380A VAL 3.8 1.0 + - - -
381A MET* 1.3 70.7 - - - +
383A GLN* 1.3 81.6 + - - +
384A VAL* 3.5 4.7 - - - +
391A TYR* 2.9 25.1 + - - +
392A HIS 4.4 1.2 + - - -
393A LEU* 3.7 30.8 - - + +
403A ASP* 2.8 32.9 + - - +
58B SER 2.9 20.3 + - - +
59B VAL* 3.5 5.7 - - + -
60B THR* 2.9 27.4 + - - -
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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