Contacts of the helix formed by residues 259 - 267 (chain A) in PDB entry 3CWL
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 LYS 259 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A SER* 3.6 42.0 + - - +
255A PRO* 3.7 4.2 - - - +
256A ASP* 3.1 17.0 + - + +
257A GLU 4.0 9.2 - - - +
258A GLY* 1.3 88.0 - - - +
260A LEU* 1.3 59.8 + - - +
261A GLN 3.4 2.2 - - - -
262A HIS* 3.4 28.5 + - + +
263A LEU* 2.9 30.8 + - - +
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Residues in contact with LEU 260 (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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46A ASN* 5.9 2.5 - - + +
255A PRO* 3.6 28.7 - - + +
256A ASP 4.2 0.2 + - - -
258A GLY 3.7 1.8 - - - +
259A LYS* 1.3 76.0 - - - +
261A GLN* 1.3 58.2 + - - +
263A LEU* 3.2 5.4 + - + +
264A GLU* 2.9 43.4 + - - +
369A PRO* 4.4 19.5 - - + +
371A VAL* 3.9 26.9 - - + -
387A LYS* 4.2 25.4 - - + +
389A VAL* 5.7 1.6 - - + -
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Residues in contact with GLN 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ALA* 6.0 0.9 - - - +
46A ASN* 4.9 15.2 + - - +
258A GLY 5.2 1.5 + - - +
259A LYS* 3.4 0.6 - - - +
260A LEU* 1.3 74.8 - - - +
262A HIS* 1.3 61.3 + - - +
264A GLU* 3.2 23.0 + - - +
265A ASN* 2.8 59.0 + - - +
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Residues in contact with HIS 262 (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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234A LYS 2.8 26.2 + - - -
235A LEU* 3.5 24.0 - - - -
236A SER* 4.1 14.2 + - - -
258A GLY 5.3 0.8 + - - +
259A LYS* 3.4 35.5 + - + +
261A GLN* 1.3 77.1 - - - +
263A LEU* 1.3 56.7 - - - +
265A ASN* 3.1 10.9 + - - +
266A GLU* 2.9 61.5 + - + +
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Residues in contact with LEU 263 (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 LEU* 3.8 28.7 - - + +
237A SER* 3.2 26.7 - - - +
253A PHE* 3.8 37.5 - - + +
255A PRO* 4.3 9.6 - - + -
259A LYS 2.9 20.7 + - - +
260A LEU* 3.3 6.5 - - + +
262A HIS* 1.3 75.4 - - - +
264A GLU* 1.3 62.5 + - - +
266A GLU 3.3 0.7 + - - +
267A LEU* 3.2 28.8 + - + +
371A VAL* 3.6 33.2 - - + -
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Residues in contact with GLU 264 (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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38A TYR* 2.4 46.2 + - + +
39A ARG* 2.7 40.6 + - + +
42A ALA* 4.2 9.6 - - + +
46A ASN* 5.4 1.7 - - - +
260A LEU* 2.9 31.3 + - + +
261A GLN* 3.2 31.0 + - - +
263A LEU* 1.3 73.4 - - - +
265A ASN* 1.3 52.6 + - - +
267A LEU* 3.9 9.4 + - - +
371A VAL* 4.3 6.3 - - + -
387A LYS* 2.8 27.9 + - - +
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Residues in contact with ASN 265 (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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39A ARG* 3.3 20.3 + - - +
261A GLN* 2.8 47.6 + - - +
262A HIS* 3.4 11.4 - - - +
264A GLU* 1.3 75.4 - - - +
266A GLU* 1.3 71.0 + - - +
267A LEU 3.5 0.6 - - - +
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Residues in contact with GLU 266 (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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234A LYS* 5.0 7.5 - - + +
235A LEU* 3.8 18.7 - - + +
262A HIS* 2.9 49.8 + - + +
263A LEU 3.3 0.4 + - - -
265A ASN* 1.3 87.1 + - - +
267A LEU* 1.3 66.5 + - - +
268A THR* 3.4 7.7 + - - +
271A ILE* 3.6 18.2 - - + +
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Residues in contact with LEU 267 (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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35A PHE* 4.1 19.2 - - + -
39A ARG* 3.1 20.1 + - - +
235A LEU* 4.2 7.4 - - + +
253A PHE* 3.5 46.2 - - + -
263A LEU* 3.2 28.1 + - + +
264A GLU* 4.2 10.1 - - - +
265A ASN 3.5 1.5 - - - +
266A GLU* 1.3 77.9 - - - +
268A THR* 1.3 65.3 + - - +
271A ILE* 4.9 3.6 - - + -
272A ILE* 4.8 9.0 - - + -
371A VAL* 4.3 15.7 - - + -
373A LEU* 4.4 5.2 - - + -
385A MET* 4.0 26.5 - - + -
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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