Contacts of the strand formed by residues 397 - 403 (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 397 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A THR* 5.1 6.5 - - - -
37A HIS 4.1 11.7 - - - +
38A ALA* 4.2 17.7 - - + -
39A LEU* 5.2 1.0 - - - +
371A GLY 5.4 1.8 - - - +
372A HIS* 3.7 12.8 - - + +
373A THR* 5.1 3.8 - - - +
391A SER 3.9 0.2 - - - +
392A VAL* 3.2 5.0 - - - +
393A SER* 2.9 40.1 + - - +
395A ASP* 3.2 24.2 + - - +
396A ASN* 1.3 78.3 - - - +
398A MSE 1.3 63.9 + - - +
399A GLN* 3.6 30.5 - - + +
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Residues in contact with MSE 398 (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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35A MSE 3.8 0.3 - - - +
36A THR* 3.4 2.6 - - - -
37A HIS* 2.9 77.1 + - + +
39A LEU* 3.5 22.9 - - + -
65A LEU* 5.3 4.7 - - - -
67A LEU* 4.3 17.0 - - - -
114A ILE* 3.5 21.5 - - + -
390A CYS* 3.8 25.1 - - - -
391A SER 3.4 4.9 - - - -
392A VAL* 3.9 12.1 - - + -
397A ILE* 1.3 75.0 - - - +
399A GLN* 1.3 65.1 + - - +
400A ILE* 4.4 11.8 + - + -
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Residues in contact with GLN 399 (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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20A TYR* 4.8 2.4 + - - -
23A TRP* 3.9 9.8 - - - -
34A VAL* 6.3 1.1 - - - -
35A MSE 3.1 6.3 - - - +
36A THR* 3.1 31.8 - - + +
369A HIS* 2.7 39.5 + - + -
371A GLY* 3.2 22.4 - - - +
372A HIS* 3.3 19.0 + - + -
389A ILE 3.5 1.2 - - - +
390A CYS* 3.1 5.6 - - - -
391A SER 2.9 32.5 + - - -
397A ILE* 3.6 14.5 - - + +
398A MSE 1.3 76.9 - - - +
400A ILE* 1.3 63.0 + - - +
401A TRP* 3.6 11.9 - - + -
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Residues in contact with ILE 400 (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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33A LEU* 4.1 1.8 - - + +
34A VAL* 3.7 1.0 - - - -
35A MSE 2.8 74.0 + - + +
48A TRP* 3.9 20.6 - - + -
65A LEU* 4.3 4.9 - - + -
83A VAL* 4.3 27.4 - - + -
85A ILE* 4.3 1.1 - - + -
388A VAL* 3.9 24.0 - - + -
389A ILE 3.2 3.6 - - - +
390A CYS* 4.0 18.4 - - + -
398A MSE 4.3 10.5 - - + -
399A GLN* 1.3 75.0 - - - +
401A TRP* 1.3 61.0 + - - +
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Residues in contact with TRP 401 (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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31A TYR* 3.6 16.2 - + + -
33A LEU* 3.1 13.5 - - - +
34A VAL* 3.9 16.6 - - + -
35A MSE 5.0 0.2 - - - +
341A LEU* 3.9 17.9 - - + -
343A VAL* 4.6 4.7 - - + -
367A PHE* 3.7 24.2 - + - -
369A HIS* 3.4 45.9 + + + -
387A TRP 3.6 2.7 - - - +
388A VAL* 3.4 4.7 - - - -
389A ILE* 2.7 81.0 + - + +
391A SER* 3.2 18.4 + - - -
399A GLN* 3.6 22.4 - - + -
400A ILE* 1.3 75.1 - - - +
402A GLN* 1.3 64.2 + - - +
403A MSE 4.1 11.4 - - + -
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Residues in contact with GLN 402 (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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31A TYR* 3.3 8.7 - - - +
32A ASP* 2.8 44.4 + - + +
33A LEU* 2.8 25.2 + - + +
385A GLU* 4.5 7.9 + - - -
386A PRO 2.8 24.9 + - - -
387A TRP* 3.5 23.8 - - + +
388A VAL* 3.5 19.5 - - + +
401A TRP* 1.3 77.0 - - - +
403A MSE 1.3 68.5 + - - +
408A TYR* 4.7 7.0 + - - +
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Residues in contact with MSE 403 (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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30A LEU 3.3 12.1 - - - +
31A TYR* 4.1 3.4 - - - +
32A ASP* 3.8 5.2 - - - +
343A VAL* 5.3 4.3 - - - -
366A LEU* 4.1 8.5 - - + -
367A PHE* 3.8 41.1 - - + -
387A TRP* 4.0 26.9 + - + +
401A TRP* 4.1 9.7 - - + -
402A GLN* 1.3 84.3 - - - +
404A ALA* 1.3 64.9 + - - +
405A GLU 3.5 1.2 + - - -
407A ILE* 2.9 57.0 - - + -
408A TYR* 3.7 26.6 - - + +
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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