Contacts of the strand formed by residues 295 - 299 (chain B) in PDB entry 4CCN
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 SER 295 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B ASP 3.4 0.3 - - - +
264B ALA* 3.1 7.3 - - - +
265B ALA* 2.7 36.9 + - - -
293B GLY 4.0 0.6 + - - -
294B CYS* 1.3 74.5 - - - +
296B LEU* 1.3 63.3 + - - +
329B LEU 3.3 10.1 - - - -
330B THR* 3.2 28.6 + - - +
331B PRO* 4.0 1.1 - - - +
334B SER* 5.0 0.2 + - - -
336B GLY* 3.2 23.2 - - - -
337B PHE* 3.8 19.9 - - - -
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Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B LEU* 4.8 9.6 - - + -
251B LEU* 5.4 1.3 - - + -
258B PHE* 5.1 0.4 - - + -
262B LEU* 4.0 32.8 - - + -
263B ASP 3.4 0.7 - - - -
264B ALA* 4.2 17.5 - - + -
286B ALA* 4.2 34.1 - - + +
287B TRP* 4.3 12.8 - - + -
289B LEU* 4.9 3.1 - - + -
290B TYR* 4.5 6.5 - - + -
294B CYS 5.0 3.8 - - - +
295B SER* 1.3 82.2 - - - +
297B ARG* 1.3 60.0 + - - +
298B LEU 4.1 0.7 - - - -
327B VAL 3.6 0.7 - - - +
328B TYR* 3.4 4.3 - - - -
329B LEU* 2.9 61.7 + - + +
337B PHE* 5.2 0.7 - - - -
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Residues in contact with ARG 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B HIS 3.4 1.4 - - - +
262B LEU* 3.2 6.6 - - - +
263B ASP* 2.8 74.7 + - + +
272B ARG* 3.9 2.4 - - - +
296B LEU* 1.3 74.5 - - - +
298B LEU* 1.3 64.9 + - - +
299B CYS* 3.8 5.0 + - - +
326B ASN* 3.5 21.5 - - - +
327B VAL 3.3 6.5 - - - +
328B TYR* 3.3 27.3 - - + -
337B PHE* 3.7 23.0 - - + -
214D GLY* 2.9 34.1 + - - +
215D ASN 3.6 11.8 + - - -
217D GLN* 3.6 23.2 + - - +
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Residues in contact with LEU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B PHE* 4.4 11.7 - - + -
247B LEU* 3.4 24.9 - - + -
250B MET* 3.3 41.7 - - + -
256B VAL* 4.2 7.4 - - + -
261B HIS* 3.1 28.7 - - + +
262B LEU* 4.3 10.1 - - + +
296B LEU 4.1 1.0 - - - -
297B ARG* 1.3 73.2 - - - +
299B CYS* 1.3 71.1 - - - +
300B SER 3.6 0.3 + - - -
301B PRO* 3.8 12.8 - - + +
304B PHE* 4.9 2.7 - - + -
326B ASN* 3.5 2.4 - - - -
327B VAL* 2.9 39.0 + - + +
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Residues in contact with CYS 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B GLN 4.1 7.2 - - - +
261B HIS* 2.7 23.7 + - - +
297B ARG* 3.8 7.1 + - - +
298B LEU* 1.3 79.7 - - - +
300B SER* 1.3 77.8 + - - +
301B PRO 3.6 0.2 - - - -
304B PHE* 5.3 1.4 - - - -
326B ASN* 3.6 9.4 - - - +
217D GLN* 3.6 26.2 - - + -
220D CYS* 1.9 62.1 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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