Contacts of the strand formed by residues 365 - 369 (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 LEU 365 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A SER* 3.4 19.1 - - - +
342A ASN* 4.0 20.6 - - + -
343A VAL 4.1 6.3 - - - +
344A TRP* 3.7 35.7 - - + -
360A ASP 3.8 17.3 - - - +
361A GLY* 4.6 2.5 - - - -
362A PRO* 3.1 15.8 + - + +
363A PRO 4.2 2.9 - - - +
364A GLU* 1.3 76.8 - - - +
366A LEU* 1.3 60.3 + - - +
367A PHE 4.4 4.3 - - - +
368A ILE* 3.8 31.4 - - + -
39F ARG* 3.1 34.6 + - + +
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Residues in contact with LEU 366 (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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331A ILE* 4.4 8.3 - - + -
343A VAL* 2.8 24.6 + - + +
345A ASP* 4.2 17.3 - - + +
348A LYS* 4.6 13.0 - - + +
364A GLU 3.1 6.2 + - - +
365A LEU* 1.3 74.8 - - - +
367A PHE* 1.3 62.7 + - + +
387A TRP* 4.0 32.8 - - + -
403A MSE 4.1 8.7 - - + -
407A ILE* 3.6 33.9 - - + +
408A TYR* 4.1 11.2 - - + -
35F ARG 4.9 0.3 - - - +
38F ALA* 4.2 7.3 - - - +
39F ARG* 3.8 15.0 - - - +
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Residues in contact with PHE 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A LEU* 3.8 27.1 - - + -
31A TYR* 3.5 30.7 - + - -
341A LEU 3.7 0.2 - - - +
342A ASN* 3.4 2.8 - - - +
343A VAL* 2.7 44.2 + - + +
365A LEU* 3.6 3.2 - - - +
366A LEU* 1.3 81.2 - - + +
368A ILE* 1.3 71.8 + - - +
369A HIS* 3.6 24.0 - - + -
401A TRP* 3.7 23.1 - + - -
403A MSE 3.8 36.1 - - + -
407A ILE* 4.4 0.7 - - + -
38F ALA* 3.6 30.1 - - + -
39F ARG* 5.0 0.2 - - - +
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Residues in contact with ILE 368 (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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23A TRP* 5.7 0.2 - - - -
30A LEU* 5.6 1.0 - - - +
31A TYR* 4.7 1.0 + - - -
314A SER* 5.0 5.6 - - - +
340A ARG* 3.7 29.6 - - + -
341A LEU 3.5 2.7 - - - -
342A ASN* 3.4 27.8 - - - +
360A ASP 5.3 0.9 - - - +
365A LEU* 3.8 22.7 - - + -
367A PHE* 1.3 86.0 - - - +
369A HIS* 1.3 62.9 + - - +
370A GLY* 3.5 3.0 + - - -
38F ALA 3.1 11.5 + - - +
39F ARG 3.3 24.9 - - - +
40F ARG 5.0 1.6 - - - -
41F GLY* 3.7 25.0 - - - +
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Residues in contact with HIS 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TRP* 3.9 6.5 - + - -
31A TYR* 2.7 32.2 + + - -
34A VAL* 5.4 0.4 - - + -
339A ARG 4.1 1.7 - - - +
340A ARG* 3.5 7.4 - - - -
341A LEU* 2.6 42.9 + - + +
367A PHE* 3.6 6.7 - - + -
368A ILE* 1.3 71.2 - - - +
370A GLY* 1.3 58.2 + - - +
371A GLY* 3.7 10.9 + - - -
372A HIS* 3.6 19.7 - + - -
391A SER* 4.1 1.6 - - - -
399A GLN* 2.7 33.6 + - - -
401A TRP* 3.4 55.4 + + + -
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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