Contacts of the strand formed by residues 335 - 342 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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549A VAL* 6.2 2.5 - - - -
552A LYS* 5.0 3.1 - - - -
300B PHE* 3.7 5.2 - - - -
304B SER* 6.4 1.8 - - - -
330B SER* 3.5 2.7 - - - -
331B SER 3.0 32.9 + - - -
332B SER 4.5 1.5 + - - -
333B ALA 3.3 3.6 - - - -
334B LEU* 1.3 80.6 - - - +
336B PHE* 1.3 67.5 + - - -
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Residues in contact with PHE 336 (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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300B PHE* 4.0 0.7 - - - -
301B PRO* 3.2 20.6 - - - +
304B SER* 6.1 4.7 - - - -
307B TYR* 3.4 35.0 - + + -
330B SER* 3.3 28.7 - - - -
335B GLY* 1.3 74.4 - - - -
337B GLY* 1.3 57.1 + - - +
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Residues in contact with GLY 337 (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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299B LEU 3.4 10.8 - - - -
300B PHE* 3.4 8.7 - - - -
301B PRO* 4.2 6.1 - - - -
307B TYR* 3.9 11.8 + - - -
310B PHE* 4.5 0.2 - - - -
328B PRO* 4.0 1.4 - - - +
329B GLU 2.8 28.7 + - - +
336B PHE* 1.3 74.1 - - - +
338B PHE* 1.3 77.4 + - - -
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Residues in contact with PHE 338 (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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298B GLY* 3.7 0.8 - - - -
299B LEU* 2.7 43.4 + - - +
300B PHE* 4.3 1.8 - - - -
307B TYR* 3.5 36.1 - + - -
310B PHE* 3.5 22.7 - + + -
311B ARG* 3.6 45.1 - - + -
314B LEU* 3.6 18.6 - - + -
326B TYR* 4.0 23.1 - + + -
327B GLU 3.5 15.3 - - - +
328B PRO* 3.8 15.9 - - + -
329B GLU* 3.9 4.9 + - - +
337B GLY* 1.3 84.1 - - - -
339B ARG* 1.3 59.1 + - - +
340B CYS* 3.8 8.9 + - - -
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Residues in contact with ARG 339 (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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296B TYR* 3.6 36.1 + - + +
297B ALA 3.7 11.0 - - - +
298B GLY* 4.5 0.7 - - - -
325B PHE* 3.9 13.2 - - - -
326B TYR* 3.3 4.2 - - - -
327B GLU* 2.8 70.8 + - - +
329B GLU* 3.5 37.0 - - + +
338B PHE* 1.3 71.8 - - - +
340B CYS* 1.3 60.7 + - - +
385B ASP* 3.4 34.2 + - - +
386B SER* 3.5 26.2 - - - +
389B LYS* 4.8 8.4 - - - +
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Residues in contact with CYS 340 (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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296B TYR* 3.2 11.8 - - - -
297B ALA 2.8 38.7 + - - +
299B LEU* 3.7 24.7 - - + -
314B LEU* 4.4 11.2 - - - -
324B LEU* 5.0 0.9 - - - -
325B PHE* 3.2 4.5 - - - +
326B TYR* 3.9 19.1 - - - -
338B PHE* 4.0 14.6 - - - -
339B ARG* 1.3 80.1 - - - +
341B GLY* 1.3 59.6 + - - +
342B PHE* 3.5 27.1 - - + -
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Residues in contact with GLY 341 (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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293B PRO* 3.7 18.8 - - - -
295B VAL 3.6 5.4 - - - -
296B TYR* 3.8 11.0 - - - -
323B SER 3.9 3.3 - - - +
324B LEU* 4.0 2.3 - - - +
325B PHE* 2.7 39.6 + - - +
340B CYS* 1.3 71.9 - - - +
342B PHE* 1.3 70.5 + - - -
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Residues in contact with PHE 342 (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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293B PRO* 3.7 5.1 - - - +
294B GLN 2.7 30.6 + - - -
295B VAL 2.8 25.4 + - - +
297B ALA* 4.6 6.5 - - + -
299B LEU* 4.4 9.6 - - + -
323B SER 4.9 1.6 - - - -
324B LEU* 4.3 4.9 - - + -
340B CYS* 3.5 36.3 - - + -
341B GLY* 1.3 80.5 - - - -
343B LEU* 1.3 54.2 + - - +
344B GLY 3.1 19.5 - - - +
347B HIS* 3.5 16.4 - + + -
348B MET* 3.5 48.9 - - + +
351B ILE* 3.6 40.8 - - + -
352B GLN* 5.8 0.7 - - + -
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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