Contacts of the strand formed by residues 238 - 247 (chain A) in PDB entry 2X6B
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 GLU 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A PRO 4.4 1.7 - - - +
13A ARG* 3.7 17.1 + - - +
14A ILE* 2.7 40.9 + - - +
15A LEU* 3.3 37.9 + - + +
180A LEU* 3.5 3.5 - - - +
181A VAL* 2.7 49.8 + - + +
236A HIS 4.1 8.1 - - - +
237A SER* 1.3 77.2 - - - +
239A PHE* 1.3 67.6 + - - +
259A ALA* 4.9 0.5 - - - +
260A TYR 3.6 13.0 - - - +
261A SER* 4.8 4.7 - - - +
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Residues in contact with PHE 239 (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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15A LEU* 4.7 0.8 - - - +
148A MET* 4.2 26.0 - - + -
150A ILE* 6.4 0.7 - - + -
159A LEU* 3.9 27.4 - - + -
178A LEU* 5.1 5.6 - - + -
179A VAL 3.8 3.8 - - - +
180A LEU* 3.9 38.4 - - + -
198A LEU* 4.1 7.9 - - + -
224A ILE* 4.2 17.7 - - + -
232A LEU* 4.4 13.0 - - + -
237A SER* 4.4 12.1 - - - -
238A GLU* 1.3 81.9 - - - +
240A LEU* 1.3 62.1 + - - +
259A ALA* 3.3 5.9 - - - +
260A TYR* 2.9 35.8 + - + +
261A SER 5.3 0.9 - - - -
262A CYS* 5.6 0.7 - - - -
265A ILE* 3.7 31.4 - - + -
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Residues in contact with LEU 240 (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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15A LEU* 3.9 28.0 - - + -
19A GLY* 3.9 27.6 - - - +
177A HIS 3.2 5.5 - - - +
178A LEU* 3.8 1.5 - - - -
179A VAL* 3.1 38.9 + - + +
181A VAL* 5.3 3.6 - - + -
195A PHE* 5.0 15.0 - - + -
239A PHE* 1.3 77.2 - - - +
241A VAL* 1.3 62.9 + - - +
242A LEU* 3.7 33.7 - - + -
257A ARG* 4.5 3.6 - - + -
258A HIS 3.1 24.5 - - - +
259A ALA* 4.4 0.2 - - + -
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Residues in contact with VAL 241 (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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144A PHE* 3.2 32.3 - - + -
161A MET* 3.5 24.7 - - - -
163A LEU* 4.9 4.7 - - + -
176A VAL* 4.9 6.7 - - + -
177A HIS 3.5 5.4 - - - +
178A LEU* 3.5 24.7 - - + -
240A LEU* 1.3 71.4 - - - +
242A LEU* 1.3 72.4 + - - +
243A PHE* 4.3 3.4 - - + +
256A ALA 3.6 0.5 - - - +
257A ARG* 3.3 26.3 - - - +
258A HIS* 2.9 13.9 + - + +
260A TYR* 3.6 21.3 - - + -
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Residues in contact with LEU 242 (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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175A ASP 3.7 0.3 - - - +
176A VAL* 3.1 5.9 - - - -
177A HIS* 2.9 52.2 + - + +
179A VAL* 3.5 26.7 - - + -
195A PHE* 5.3 7.6 - - + -
240A LEU* 3.7 32.1 - - + +
241A VAL* 1.3 80.6 - - - +
243A PHE* 1.3 59.9 + - - +
244A THR* 4.1 4.8 + - + -
256A ALA 4.0 1.8 - - - -
257A ARG* 3.8 22.9 - - + -
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Residues in contact with PHE 243 (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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140A ALA* 4.3 7.6 - - + -
142A VAL* 3.9 20.0 - - + -
144A PHE* 4.3 14.6 - - + -
163A LEU* 3.8 15.3 - - + -
171A ILE* 3.8 25.6 - - + -
174A ALA* 3.7 32.3 - - + -
175A ASP 3.6 2.5 - - - -
176A VAL* 3.7 24.5 - - + +
208A PHE* 4.1 17.0 - + - -
212A TRP* 4.6 2.2 - + - -
241A VAL* 3.8 1.5 + - + -
242A LEU* 1.3 72.4 - - - +
244A THR* 1.3 83.5 + - - +
245A GLY 4.1 2.5 - - - -
254A VAL* 4.4 1.6 - - + -
255A HIS* 3.2 1.9 - - - +
256A ALA* 3.0 48.0 + - + +
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Residues in contact with THR 244 (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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174A ALA* 3.3 3.3 - - - +
175A ASP* 2.8 51.8 + - - +
177A HIS* 5.3 5.4 + - + -
242A LEU* 5.0 5.2 + - + -
243A PHE* 1.3 92.5 - - - +
245A GLY* 1.3 59.4 + - - +
254A VAL 3.4 7.6 - - - -
255A HIS* 3.5 15.9 - - + -
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Residues in contact with GLY 245 (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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171A ILE* 3.7 9.9 - - - -
172A ILE 4.1 0.4 - - - -
173A GLU 4.6 2.7 - - - -
174A ALA* 3.8 15.9 - - - -
175A ASP* 5.3 0.2 - - - -
243A PHE* 4.1 0.6 - - - -
244A THR* 1.3 77.3 - - - +
246A HIS* 1.3 57.6 + - - -
253A ASN* 3.9 7.0 - - - +
254A VAL* 2.7 40.3 + - - +
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Residues in contact with HIS 246 (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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171A ILE* 3.7 2.6 - - - +
172A ILE* 2.9 60.9 + - + +
173A GLU* 5.9 1.3 - - + -
245A GLY* 1.3 69.6 - - - -
247A HIS* 1.3 66.0 + - - +
248A GLU* 4.9 1.3 - - - -
251A ALA* 3.5 14.8 + - - -
252A GLN* 3.3 35.2 + - - -
253A ASN* 3.3 18.8 + - - +
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Residues in contact with HIS 247 (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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140A ALA 3.5 16.7 + - - -
165A ASN* 4.1 4.2 + - - -
167A ARG* 3.4 35.5 - - - -
169A GLU* 3.7 22.2 - - + -
170A ALA 3.9 5.4 - - - -
171A ILE* 3.5 25.8 - - + +
245A GLY 3.7 3.6 + - - -
246A HIS* 1.3 73.7 + - - +
248A GLU* 1.3 65.8 + - - +
249A ALA* 3.2 37.1 + - + +
250A PHE* 3.7 20.9 - + + -
251A ALA 3.0 18.0 + - - -
252A GLN 2.6 18.9 + - - +
254A VAL* 3.9 13.4 - - + +
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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