Contacts of the helix formed by residues 256 - 262 (chain A) in PDB entry 1E0C
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 256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A ALA* 4.2 10.4 - - - +
60A PRO* 5.8 0.7 - - - +
61A GLY 5.2 1.6 + - - -
62A LEU* 3.7 17.2 - - - +
149A ALA 5.1 0.6 + - - -
231A GLN 3.7 4.9 - - - +
232A THR* 4.8 0.9 - - - -
254A TYR* 3.2 5.6 - - - -
255A ALA* 1.3 78.5 - - - +
257A SER* 1.3 73.2 + - - +
259A GLY* 3.8 0.7 + - - -
260A GLU* 3.3 38.0 + - - +
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Residues in contact with SER 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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229A HIS* 3.4 3.0 - - - +
230A CSS 3.1 26.6 + - - -
231A GLN 3.2 17.5 - - - -
232A THR 3.7 1.6 - - - -
233A HIS* 3.2 10.7 + - - -
254A TYR* 2.8 47.6 + - - -
255A ALA 3.7 3.1 - - - -
256A GLY* 1.3 83.0 - - - +
258A TRP* 1.3 60.9 + - - +
261A TRP 2.8 22.7 + - - -
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Residues in contact with TRP 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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169A ARG* 3.4 31.5 - - - +
180A LEU* 5.0 3.9 - - + +
181A ALA* 3.9 14.3 - - + +
183A LYS 3.0 28.5 + - - -
184A GLY* 4.5 2.4 - - - -
185A GLY 3.3 29.8 + - - -
186A HIS* 3.6 9.9 - - - -
187A ILE* 3.7 19.1 - - + -
229A HIS* 4.2 10.4 + + - -
230A CSS 2.8 20.8 + - - +
231A GLN* 3.4 22.4 + - - +
257A SER* 1.3 67.6 - - - +
259A GLY* 1.3 62.1 + - - +
260A GLU 3.0 1.8 - - - -
261A TRP* 3.4 35.4 - + + +
262A GLY* 2.7 39.2 + - - -
263A ASN 4.1 0.2 + - - -
269A VAL* 3.8 14.8 - - + -
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Residues in contact with GLY 259 (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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58A PRO 3.9 12.9 - - - +
59A ALA* 5.5 1.1 - - - -
60A PRO* 5.6 8.1 - - - -
231A GLN* 2.8 32.6 + - - -
232A THR* 5.6 1.3 - - - -
256A GLY 4.1 1.8 - - - -
258A TRP* 1.3 77.2 - - - +
260A GLU* 1.3 56.9 + - - +
263A ASN* 2.9 29.0 + - - +
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Residues in contact with GLU 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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58A PRO* 4.3 9.1 + - + +
59A ALA* 4.2 16.1 - - + +
62A LEU* 5.7 0.8 - - - +
151A ARG* 2.8 48.0 + - - +
254A TYR* 2.6 33.2 + - - +
256A GLY* 3.3 21.1 + - - +
257A SER 3.1 6.5 + - - +
258A TRP 3.0 0.2 - - - -
259A GLY* 1.3 77.5 - - - +
261A TRP* 1.3 60.5 + - - +
263A ASN* 3.0 4.8 + - - +
264A HIS* 2.9 32.9 + - + +
373A SO4 4.5 1.7 + - - -
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Residues in contact with TRP 261 (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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151A ARG* 3.9 18.6 - - + -
154A LEU* 3.9 17.5 - - + -
155A LEU* 3.4 24.9 - - + -
158A LEU* 3.9 11.4 - - + -
183A LYS* 3.7 3.8 - - - -
187A ILE* 3.6 33.2 - - + +
254A TYR* 3.4 28.5 - + + +
257A SER 2.8 19.4 + - - +
258A TRP* 3.4 35.2 - + + -
260A GLU* 1.3 73.6 - - - +
262A GLY* 1.3 60.8 + - - +
263A ASN 3.2 1.0 + - - -
264A HIS 3.6 0.3 + - - -
267A THR* 2.6 49.8 + - + -
268A PRO* 2.7 40.0 + - + -
269A VAL* 4.3 2.0 - - + -
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Residues in contact with GLY 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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181A ALA* 3.7 2.7 - - - -
182A ALA* 3.4 3.6 + - - +
183A LYS* 2.9 40.8 + - - +
258A TRP* 2.7 49.2 + - - -
261A TRP* 1.3 73.3 - - - +
263A ASN* 1.3 61.7 + - - +
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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