Contacts of the strand formed by residues 376 - 381 (chain A) in PDB entry 3CFV
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 ILE 376 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320A PHE* 5.0 3.1 - - - +
321A GLN* 5.7 0.2 - - - +
335A SER* 3.6 22.9 + - - +
336A GLY* 3.4 18.5 + - - +
339A ARG 3.7 12.3 - - - +
340A ARG 3.5 31.4 - - - +
341A LEU* 3.9 14.4 - - + +
369A HIS* 5.0 0.2 - - + -
372A HIS* 3.7 37.2 - - + -
374A ALA 4.1 0.4 - - - +
375A LYS* 1.3 80.9 - - - +
377A SER* 1.3 64.8 + - - +
378A ASP 3.7 15.5 - - - +
379A PHE* 5.0 1.1 - - + -
391A SER* 4.3 8.5 - - - -
392A VAL 3.6 13.2 - - - +
393A SER* 4.1 0.7 - - - +
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Residues in contact with SER 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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43A SER 4.0 7.1 + - - -
44A LEU* 3.6 42.4 - - - +
128A ARG* 4.8 5.7 + - - -
320A PHE* 5.0 8.4 - - - +
321A GLN* 4.5 11.8 - - - +
375A LYS* 3.5 8.0 + - - +
376A ILE* 1.3 75.0 - - - +
378A ASP* 1.3 63.9 + - - +
392A VAL 3.0 10.4 + - - -
394A GLU* 3.6 27.0 + - - +
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Residues in contact with ASP 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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44A LEU 3.6 14.3 - - - +
45A THR* 3.4 7.2 + - - -
46A VAL* 3.2 21.3 + - + +
128A ARG* 4.4 5.5 + - - +
130A ARG* 2.9 30.1 + - - -
321A GLN* 2.9 27.5 - - - +
323A HIS* 3.8 2.4 + - - -
376A ILE* 3.6 5.3 - - - +
377A SER* 1.3 80.5 - - - +
379A PHE* 1.3 92.2 + - - +
391A SER* 3.6 0.7 - - - -
392A VAL* 3.0 28.3 + - + +
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Residues in contact with PHE 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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46A VAL* 3.7 4.4 - - - +
321A GLN* 3.7 24.2 - - + -
323A HIS* 3.2 47.8 + + + -
333A ALA* 3.4 41.1 - - + -
334A SER* 4.1 7.0 - - - -
335A SER* 3.3 27.1 - - - -
341A LEU* 3.6 25.6 - - + -
376A ILE* 5.0 0.2 - - + -
378A ASP* 1.3 92.9 + - - +
380A SER* 1.3 68.5 + - - +
381A TRP* 3.8 6.1 - + - -
389A ILE* 4.3 9.2 - - + -
390A CYS 3.2 14.4 - - - +
391A SER* 3.8 4.3 - - - -
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Residues in contact with SER 380 (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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46A VAL* 3.7 22.0 - - - -
47A GLN* 3.5 9.6 - - - +
48A TRP* 2.9 50.5 + - - -
65A LEU* 5.6 0.4 - - - -
323A HIS* 5.0 2.9 - - - -
379A PHE* 1.3 80.2 - - - +
381A TRP* 1.3 61.0 + - - +
389A ILE* 3.6 4.6 - - - -
390A CYS* 3.0 23.4 + - - -
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Residues in contact with TRP 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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48A TRP* 3.2 10.3 - - - +
323A HIS* 3.1 36.5 + - + +
324A TRP 3.1 17.6 + - - -
325A SER* 3.9 26.5 - - - -
326A PRO* 3.5 21.1 - - + +
327A HIS* 5.9 0.4 - - - -
331A ILE* 3.8 24.5 - - + -
333A ALA* 3.5 25.8 - - + -
343A VAL* 4.3 9.6 - - + -
379A PHE* 3.8 7.9 - + - -
380A SER* 1.3 74.9 + - - +
382A ASN* 1.3 63.1 + - - +
383A PRO* 3.4 6.1 - - - +
387A TRP* 4.2 33.2 - + - -
388A VAL 3.9 7.4 - - - -
389A ILE* 3.7 30.1 - - + -
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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