Contacts of the strand formed by residues 251 - 258 (chain A) in PDB entry 3CL0
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 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218A TRP* 2.8 34.3 + - - -
219A ARG* 3.9 20.6 + - - +
242A THR* 3.4 4.9 - - - -
243A ASP 2.8 38.9 + - - -
250A ALA* 1.3 73.6 - - - +
252A TYR* 1.3 63.2 + - - +
267A GLU* 2.7 29.9 + - - -
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Residues in contact with TYR 252 (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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240A VAL* 5.0 3.6 - - + -
241A MET 3.5 6.3 - - - +
242A THR* 3.7 4.5 - - + +
249A GLN* 3.3 7.3 + - - -
250A ALA* 3.2 48.1 + - + -
251A SER* 1.3 79.1 + - - +
253A LYS* 1.3 63.0 + - - +
267A GLU* 3.3 8.0 + - - +
268A LEU* 2.9 53.0 + - + -
270A ALA* 4.1 17.9 - - + -
273A TYR 2.5 30.0 + - - -
274A TYR* 3.3 8.7 - + - -
275A TYR* 3.5 57.0 - + + -
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Residues in contact with LYS 253 (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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218A TRP* 3.5 53.9 - - + +
240A VAL* 3.3 6.7 - - - +
241A MET 2.9 33.2 + - - -
252A TYR* 1.3 80.1 - - - +
254A ILE* 1.3 64.7 + - - +
255A PHE* 3.7 32.3 - - + -
265A SER* 4.8 9.7 + - - +
266A VAL 3.3 6.1 - - - +
267A GLU* 3.8 29.6 + - + +
268A LEU* 5.4 0.4 - - - -
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Residues in contact with ILE 254 (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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239A THR 3.4 10.8 - - - +
240A VAL* 4.4 9.6 - - + -
253A LYS* 1.3 76.3 - - - +
255A PHE* 1.3 67.4 + - - +
265A SER* 3.1 7.8 - - - -
266A VAL* 2.9 34.4 + - + +
268A LEU* 3.4 33.4 - - + -
303A VAL* 4.3 7.0 - - + -
305A PHE* 3.7 59.7 - - + -
310A LEU* 4.1 22.9 - - + +
312A TYR* 4.5 6.5 - - + -
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Residues in contact with PHE 255 (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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215A ILE* 4.0 39.5 - - + -
218A TRP* 4.3 5.2 - + - -
237A CYS 3.8 0.7 - - - +
238A PHE* 3.3 8.5 - - - +
239A THR* 2.9 51.5 + - + -
241A MET* 3.7 26.7 - - + -
253A LYS* 3.7 39.0 - - + -
254A ILE* 1.3 78.7 - - - +
256A LYS* 1.3 60.3 + - - +
257A MET* 4.0 10.5 + - - +
262A VAL* 4.1 15.3 - - + -
264A LYS 3.6 1.8 - - - +
265A SER* 3.4 24.7 - - - -
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Residues in contact with LYS 256 (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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236A SER* 3.5 28.5 + - - -
237A CYS 3.7 2.9 - - - -
238A PHE* 3.5 23.1 - - + -
255A PHE* 1.3 73.0 - - - +
257A MET* 1.3 63.0 + - - +
258A GLU* 3.5 12.8 + - - -
262A VAL* 3.5 3.9 - - - -
263A VAL* 2.9 37.2 + - + +
264A LYS* 2.7 30.2 + - + +
308A GLN* 2.8 34.4 + - - +
309A ASN* 5.1 2.4 + - - +
310A LEU* 3.9 12.0 - - + +
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Residues in contact with MET 257 (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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190A LEU* 3.7 32.5 - - + -
192A ILE* 3.7 11.4 - - + -
205A LEU* 3.7 23.6 - - + -
230A CYS* 4.8 2.2 - - + -
236A SER* 3.5 0.7 - - - -
237A CYS* 2.9 50.2 + - + +
238A PHE* 4.1 2.9 - - - +
239A THR* 3.6 38.6 - - + +
255A PHE* 4.4 11.4 - - - +
256A LYS* 1.3 73.4 - - - +
258A GLU* 1.3 65.7 + - - +
259A LYS 4.3 0.2 - - - -
260A GLY* 4.4 2.2 - - - -
261A LYS 3.1 26.9 - - - +
262A VAL* 4.0 3.4 - - - +
263A VAL 4.4 0.4 - - - +
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Residues in contact with GLU 258 (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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235A GLY 4.0 11.4 - - - +
236A SER* 2.8 28.5 + - - +
256A LYS* 3.5 15.6 + - - -
257A MET* 1.3 77.2 - - - +
259A LYS* 1.3 75.0 + - + +
260A GLY 3.1 0.7 - - - -
261A LYS* 2.9 23.1 + - - +
263A VAL* 3.9 28.1 - - + +
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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