Contacts of the strand formed by residues 374 - 379 (chain A) in PDB entry 3I7P
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 GLN 374 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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364A VAL* 3.2 6.9 - - - +
365A VAL 2.8 30.7 + - - +
366A ASP* 4.8 0.9 - - - -
367A LEU* 2.7 45.6 - - + +
368A GLU* 3.8 14.2 + - - +
370A GLN* 5.0 0.3 + - - -
372A GLN* 3.5 12.1 - - - +
373A GLY* 1.3 74.6 - - - -
375A LEU* 1.3 62.3 + - - +
376A VAL* 5.1 1.3 - - + -
389A ILE* 3.5 17.9 - - + +
390A ILE 3.3 8.7 - - - +
391A ARG* 2.8 52.2 + - - +
713A ARG* 6.2 0.2 - - - +
1012A LEU* 4.6 0.7 - - - -
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Residues in contact with LEU 375 (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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362A MET* 4.0 29.6 - - + -
363A CYS 3.5 9.6 - - - +
364A VAL* 3.1 36.3 - - + -
374A GLN* 1.3 75.9 - - - +
376A VAL* 1.3 64.0 + - - +
377A THR* 4.2 9.0 - - + -
389A ILE* 3.3 3.3 - - - -
390A ILE* 2.7 51.0 + - + +
1008A CYS* 5.1 0.2 - - - -
1012A LEU* 4.0 14.6 - - + -
1029A LEU* 4.0 13.9 - - + -
1037A ILE* 3.8 33.4 - - + -
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Residues in contact with VAL 376 (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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362A MET* 3.3 2.0 - - - -
363A CYS* 2.9 40.1 + - - +
365A VAL* 5.1 3.1 - - + -
367A LEU* 4.8 8.1 - - + -
374A GLN 5.1 1.1 - - - -
375A LEU* 1.3 82.4 - - - +
377A THR* 1.3 60.7 + - - +
387A LEU* 4.3 15.5 - - + -
388A ARG 3.3 5.8 - - - +
389A ILE* 3.9 25.8 - - + -
724A ILE* 3.7 28.8 - - + +
733A PHE* 4.0 30.5 - - + -
799A PHE* 4.8 0.2 - - + -
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Residues in contact with THR 377 (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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356A LEU* 5.2 1.1 - - + +
359A ILE* 4.0 30.0 - - + +
361A ASP 3.5 4.0 - - - -
362A MET* 3.8 13.7 - - + -
375A LEU* 4.2 18.2 - - + -
376A VAL* 1.3 78.3 - - - +
378A CYS* 1.3 61.7 + - - +
379A SER* 2.9 19.3 + - - -
387A LEU* 3.3 8.5 - - - -
388A ARG* 2.9 40.8 + - - +
390A ILE* 4.4 11.2 - - + +
1037A ILE* 4.8 0.2 - - + -
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Residues in contact with CYS 378 (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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358A PRO 3.4 0.9 - - - +
359A ILE* 3.6 1.9 - - - -
360A VAL* 3.1 28.0 + - + +
361A ASP* 2.9 21.5 + - - +
377A THR* 1.3 72.0 - - - +
379A SER* 1.3 58.4 + - - +
386A SER 3.7 5.4 - - - -
387A LEU* 4.2 3.6 - - - -
721A PRO* 3.2 31.6 - - + +
722A ARG 4.3 0.2 - - - +
723A LYS* 3.4 19.7 - - - -
724A ILE* 3.4 41.5 - - - -
735A VAL* 4.8 0.2 - - - -
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Residues in contact with SER 379 (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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355A ASN 5.1 1.6 - - - -
356A LEU* 3.2 23.8 + - - -
358A PRO 3.2 6.0 + - - -
359A ILE* 4.5 0.7 - - - +
377A THR* 2.9 24.1 + - - -
378A CYS* 1.3 71.2 + - - +
380A GLY* 1.3 69.4 + - - +
384A GLU 4.7 0.2 - - - -
385A GLY* 3.1 1.4 - - - -
386A SER* 2.8 50.6 + - - +
388A ARG* 3.7 13.6 - - - +
721A PRO* 3.4 4.6 - - - +
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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