Contacts of the strand formed by residues 376 - 381 (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 ILE 376 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B PHE* 5.1 3.6 - - - +
321B GLN* 5.8 0.3 - - - +
335B SER* 3.7 26.4 + - - +
336B GLY* 3.3 13.7 + - - +
339B ARG* 3.9 9.6 - - - +
340B ARG 3.8 30.3 - - - +
341B LEU* 3.9 14.6 - - + +
369B HIS* 5.0 1.1 - - + -
372B HIS* 3.7 39.5 - - + +
374B ALA 4.2 1.3 - - - +
375B LYS* 1.3 86.2 - - - +
377B SER* 1.3 62.6 + - - +
378B ASP 3.4 21.8 - - - +
379B PHE* 4.8 0.9 - - + -
391B SER* 4.3 8.5 - - - -
392B VAL 3.5 7.0 - - - +
393B SER* 4.1 0.2 - - - +
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Residues in contact with SER 377 (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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43B SER 3.9 7.7 + - - -
44B LEU* 3.6 42.0 - - - +
128B ARG* 4.9 7.1 + - - -
320B PHE* 5.4 5.7 - - - +
321B GLN* 4.8 7.2 - - - +
375B LYS* 3.6 7.1 + - - +
376B ILE* 1.3 73.0 - - - +
378B ASP* 1.3 64.6 + - - +
392B VAL 2.8 8.2 + - - -
394B GLU* 3.4 32.1 + - - +
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Residues in contact with ASP 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU 3.5 12.9 - - - +
45B THR* 3.6 5.0 + - - -
46B VAL* 3.3 21.5 + - + +
128B ARG* 4.5 5.3 + - - -
130B ARG* 3.1 28.6 + - - -
321B GLN* 2.8 33.5 - - - +
323B HIS* 4.0 1.9 + - - -
376B ILE* 3.4 10.1 - - - +
377B SER* 1.3 81.4 - - - +
379B PHE* 1.3 82.8 + - - +
392B VAL* 3.0 27.1 + - + +
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Residues in contact with PHE 379 (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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46B VAL* 3.5 6.7 - - - +
321B GLN* 3.7 25.6 - - + -
323B HIS* 3.6 41.8 + - + -
333B ALA* 3.4 41.7 - - + -
334B SER* 4.2 0.7 - - - -
335B SER* 3.3 32.5 - - - -
341B LEU* 3.5 16.6 - - + -
376B ILE* 4.8 0.2 - - + -
378B ASP* 1.3 90.2 + - - +
380B SER* 1.3 70.2 + - - +
381B TRP* 3.8 6.7 - + - -
389B ILE* 4.1 10.8 - - + -
390B CYS 3.0 13.9 - - - +
391B SER* 3.7 14.1 - - - -
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Residues in contact with SER 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B VAL* 3.8 19.1 - - - -
47B GLN* 3.5 9.7 - - - +
48B TRP* 2.9 48.9 + - - -
65B LEU* 5.7 0.2 - - - -
323B HIS* 5.3 2.2 - - - -
379B PHE* 1.3 80.7 - - - +
381B TRP* 1.3 63.0 + - - +
389B ILE* 3.5 5.4 - - - -
390B CYS* 2.7 27.4 + - - -
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Residues in contact with TRP 381 (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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48B TRP* 3.2 10.0 - - - +
323B HIS* 3.0 35.4 + - + +
324B TRP 3.2 16.7 + - - +
325B SER* 3.9 15.7 - - - -
326B PRO* 3.5 28.4 - - + +
327B HIS* 5.9 0.7 - - - -
331B ILE* 3.8 29.8 - - + -
333B ALA* 3.6 27.7 - - + +
343B VAL* 4.4 9.9 - - + -
379B PHE* 3.8 4.6 - + - -
380B SER* 1.3 74.2 + - - +
382B ASN* 1.3 64.9 + - - +
383B PRO* 3.4 6.1 - - - +
387B TRP* 4.1 33.0 - + - -
388B VAL 3.9 6.3 - - - -
389B ILE* 3.6 32.1 - - + -
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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