Contacts of the strand formed by residues 365 - 369 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B SER* 3.6 19.1 - - - +
342B ASN* 4.2 8.3 - - + -
343B VAL 4.2 6.7 - - - +
344B TRP* 3.8 32.8 - - + -
360B ASP 3.8 18.8 - - - +
361B GLY* 4.4 3.1 - - - -
362B PRO* 3.1 17.0 + - + +
363B PRO 4.1 3.6 - - - +
364B GLU* 1.3 77.6 - - - +
366B LEU* 1.3 61.1 + - - +
367B PHE 4.2 6.5 - - - +
368B ILE* 3.9 35.4 - - + -
39E ARG* 2.8 42.8 + - + +
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Residues in contact with LEU 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331B ILE* 4.5 9.2 - - + -
343B VAL* 2.9 24.8 + - + +
345B ASP* 4.1 17.5 - - + +
348B LYS* 4.7 15.0 - - - +
364B GLU 3.2 5.8 + - - +
365B LEU* 1.3 72.1 - - - +
367B PHE* 1.3 62.2 + - + +
387B TRP* 3.8 29.8 - - + -
403B MSE 3.4 28.6 - - + +
407B ILE* 3.8 21.2 - - + +
408B TYR* 4.3 6.5 - - + -
35E ARG* 4.8 1.7 - - + +
38E ALA* 4.0 6.4 - - - +
39E ARG* 3.7 15.3 - - - +
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Residues in contact with PHE 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 3.7 27.4 - - + -
31B TYR* 3.5 29.2 - + - -
341B LEU 3.8 0.7 - - - +
342B ASN* 3.4 2.9 - - - -
343B VAL* 2.8 43.9 + - + +
365B LEU* 3.7 3.0 - - - +
366B LEU* 1.3 80.2 - - - +
368B ILE* 1.3 71.6 + - - +
369B HIS* 3.7 23.1 - - + -
401B TRP* 3.8 24.0 - + - -
403B MSE 3.3 39.3 - - + -
407B ILE* 4.0 2.5 - - + -
38E ALA* 3.6 28.5 - - + -
39E ARG* 5.0 0.2 - - - +
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Residues in contact with ILE 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LEU* 5.5 0.7 - - - +
31B TYR* 4.7 0.7 + - - -
314B SER* 5.2 6.3 - - - +
340B ARG* 3.9 27.6 - - + +
341B LEU 3.7 2.2 - - - -
342B ASN* 3.4 27.1 - - - +
360B ASP 5.3 1.6 - - - +
365B LEU* 3.9 22.2 - - + -
367B PHE* 1.3 83.9 - - - +
369B HIS* 1.3 62.1 + - - +
370B GLY 3.5 1.2 + - - -
38E ALA 2.9 15.9 + - - +
39E ARG 3.4 24.9 - - - +
40E ARG 5.0 1.6 - - - -
41E GLY* 3.5 29.0 - - - +
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Residues in contact with HIS 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B TRP* 4.0 4.9 - + - -
31B TYR* 2.9 31.2 + + - -
34B VAL* 5.3 0.2 - - + -
339B ARG 4.2 1.6 - - - +
340B ARG* 3.6 8.3 - - - -
341B LEU* 2.7 44.5 + - + +
367B PHE* 3.7 8.1 - - + -
368B ILE* 1.3 70.7 - - - +
370B GLY* 1.3 56.9 + - - +
371B GLY* 3.8 10.1 + - - -
372B HIS* 3.7 17.3 - + - -
376B ILE* 5.0 0.2 - - + -
391B SER* 4.2 1.6 - - - -
399B GLN* 2.7 33.5 + - - -
401B TRP* 3.4 56.5 + + + -
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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