Contacts of the strand formed by residues 335 - 342 (chain F) in PDB entry 3CB4
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 GLY 335 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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549C VAL* 6.2 2.5 - - - -
552C LYS* 5.2 2.5 - - - -
300F PHE* 3.7 5.5 - - - -
330F SER* 3.3 4.0 - - - -
331F SER 3.0 36.4 + - - -
332F SER 4.5 1.8 + - - -
333F ALA 3.5 1.6 - - - -
334F LEU* 1.3 80.0 - - - +
336F PHE* 1.3 68.7 + - - -
337F GLY 3.6 1.4 + - - -
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Residues in contact with PHE 336 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300F PHE* 4.2 1.1 - - - -
301F PRO* 3.2 20.4 - - - +
304F SER* 6.2 5.0 - - - -
307F TYR* 3.3 37.6 - + + +
329F GLU 3.9 3.6 - - - +
330F SER* 3.7 22.7 - - - -
335F GLY* 1.3 73.7 - - - -
337F GLY* 1.3 59.0 + - - +
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Residues in contact with GLY 337 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299F LEU 3.4 12.3 - - - -
300F PHE* 3.5 11.7 - - - -
301F PRO* 4.1 4.9 - - - -
307F TYR* 4.3 4.2 - - - -
328F PRO* 3.8 1.6 - - - +
329F GLU 2.8 30.3 + - - +
336F PHE* 1.3 75.1 - - - +
338F PHE* 1.3 79.3 + - - -
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Residues in contact with PHE 338 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298F GLY* 3.5 1.5 - - - -
299F LEU 2.9 32.4 + - - +
300F PHE* 4.4 1.4 - - - -
307F TYR* 3.5 36.8 - + - -
310F PHE* 3.6 17.3 - + + -
311F ARG* 3.6 46.2 - - + -
314F LEU* 3.5 23.6 - - + -
326F TYR* 3.9 21.5 - + + -
327F GLU 3.4 9.2 - - - +
328F PRO* 3.7 27.8 - - + -
329F GLU* 4.3 2.7 - - - +
337F GLY* 1.3 73.9 - - - -
339F ARG* 1.3 61.1 + - - +
340F CYS* 3.6 12.9 - - - -
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Residues in contact with ARG 339 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296F TYR* 3.8 19.6 - - + +
297F ALA 3.8 12.6 - - - +
298F GLY* 4.2 3.6 - - - -
325F PHE* 3.8 26.0 - - - -
326F TYR* 3.4 2.3 - - - -
327F GLU* 2.8 65.0 + - - +
329F GLU* 3.9 35.3 - - + +
338F PHE* 1.3 71.2 - - - +
340F CYS* 1.3 61.9 - - - +
341F GLY 4.4 0.2 + - - -
369F THR* 5.7 0.8 - - - +
385F ASP* 3.3 44.6 + - - +
386F SER* 3.8 21.8 - - - +
389F LYS* 5.1 7.5 - - - +
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Residues in contact with CYS 340 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295F VAL 3.8 0.2 - - - +
296F TYR* 3.0 10.3 - - - +
297F ALA 2.7 44.1 + - - +
299F LEU* 3.7 18.4 - - + -
310F PHE* 5.2 0.2 - - - -
314F LEU* 4.5 11.4 - - - -
324F LEU* 5.3 1.3 - - + -
325F PHE* 3.3 5.4 - - - +
326F TYR* 3.8 20.0 - - - -
338F PHE* 3.6 19.3 - - - -
339F ARG* 1.3 78.7 - - - +
341F GLY* 1.3 60.6 + - - +
342F PHE* 3.6 24.5 - - + -
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Residues in contact with GLY 341 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293F PRO* 3.8 20.2 - - - -
295F VAL 3.4 5.8 - - - -
296F TYR* 3.8 9.0 - - - -
323F SER 4.8 0.2 - - - -
324F LEU* 4.0 4.5 - - - +
325F PHE* 2.7 40.7 + - - +
340F CYS* 1.3 70.6 - - - +
342F PHE* 1.3 73.6 + - - -
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Residues in contact with PHE 342 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293F PRO* 3.8 4.8 - - - +
294F GLN 2.9 23.1 + - - -
295F VAL* 2.6 31.4 + - + +
297F ALA* 4.6 8.3 - - + -
299F LEU* 4.2 15.5 - - + -
323F SER 5.1 1.3 - - - -
324F LEU* 4.9 4.7 - - + -
340F CYS* 3.6 35.9 - - + -
341F GLY* 1.3 80.1 - - - -
343F LEU* 1.3 60.8 + - - +
344F GLY 3.3 16.2 - - - +
347F HIS* 3.5 8.5 - + + -
348F MET* 3.6 48.0 - - + +
351F ILE* 3.6 41.5 - - + -
352F GLN* 5.9 0.4 - - + -
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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