Contacts of the strand formed by residues 238 - 249 (chain A) in PDB entry 2VIG
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 THR 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A TRP* 3.4 39.7 - - + +
186A ILE 3.3 4.0 - - - +
187A THR* 4.4 1.3 + - - +
227A LYS* 3.4 3.5 - - - +
228A GLU* 2.8 44.6 + - + +
230A LYS* 2.8 34.8 + - - +
236A SER* 3.9 2.7 + - - -
237A SER* 1.3 76.1 + - - +
239A ALA* 1.3 63.2 + - - +
501A FAD 3.9 23.4 - - + +
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Residues in contact with ALA 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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185A TRP 3.8 2.6 + - - +
186A ILE* 3.0 36.0 + - - +
189A ALA* 3.9 6.1 - - + +
190A TRP* 3.4 22.0 - - + +
224A LEU* 5.3 0.2 - - + -
225A GLY 3.4 23.3 - - - +
226A LYS 3.4 9.6 - - - +
228A GLU* 4.7 5.6 - - - -
238A THR* 1.3 79.8 - - - +
240A ASN* 1.3 69.9 + - - +
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Residues in contact with ASN 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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157A PRO* 4.6 6.5 - - - +
182A THR* 3.7 20.7 - - + +
183A LYS 3.1 14.8 - - - +
184A ALA* 3.3 23.0 - - - +
185A TRP 3.9 1.4 + - - -
224A LEU* 3.4 8.8 - - - +
225A GLY* 2.7 40.5 + - - +
226A LYS 4.7 1.0 + - - -
228A GLU* 4.3 11.7 + - - +
239A ALA* 1.3 75.7 - - - +
241A LEU* 1.3 57.7 - - - +
242A ILE* 4.0 7.6 - - + +
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Residues in contact with LEU 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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151A CYS* 4.5 2.2 - - - -
153A ALA* 4.1 22.0 - - + -
181A GLY 3.7 2.4 - - - +
182A THR* 3.4 2.3 - - - -
183A LYS* 2.8 41.0 + - + -
186A ILE* 3.9 14.3 - - + +
189A ALA* 3.7 32.1 - - + -
195A ALA* 4.2 21.1 - - + -
217A MET* 4.3 10.5 - - + -
222A LEU* 3.9 17.5 - - + -
223A THR 3.8 4.5 - - - -
224A LEU* 3.8 12.6 - - + -
239A ALA 3.8 0.6 + - - -
240A ASN* 1.3 69.5 - - - +
242A ILE* 1.3 60.5 + - - +
243A PHE* 3.9 21.9 - - + -
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Residues in contact with ILE 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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181A GLY 3.7 2.5 - - - -
182A THR* 4.0 27.8 - - + +
221A GLY 3.4 4.3 - - - +
222A LEU* 3.4 2.3 - - - +
223A THR* 2.8 56.7 + - - +
224A LEU 4.0 2.5 - - - +
225A GLY* 3.8 29.6 - - - +
240A ASN* 4.3 6.1 - - + +
241A LEU* 1.3 73.7 - - - +
243A PHE* 1.3 69.2 + - - +
244A GLU* 4.0 5.6 + - + +
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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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168A THR* 4.8 6.7 - - + -
179A LEU* 3.6 39.3 - - + +
180A ASN* 3.5 2.0 - - - +
181A GLY* 2.8 45.6 + - - +
183A LYS* 4.1 9.6 - - + -
197A VAL* 3.9 37.2 - - + -
215A VAL* 4.1 18.4 - - + -
221A GLY 3.2 4.7 - - - +
222A LEU* 3.9 23.3 - - + -
241A LEU* 3.9 27.8 - - + -
242A ILE* 1.3 74.1 - - - +
244A GLU* 1.3 60.1 + - - +
246A CYS* 3.8 22.0 - - + -
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Residues in contact with GLU 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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180A ASN* 3.5 7.4 - - - +
221A GLY* 2.8 25.0 + - - +
242A ILE* 4.0 6.4 + - + -
243A PHE* 1.3 74.0 - - - +
245A ASP* 1.3 84.3 + - - +
246A CYS 3.2 1.4 + - - -
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Residues in contact with ASP 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 ARG* 6.3 0.4 - - - -
178A VAL* 3.9 19.0 - - + +
179A LEU 3.5 0.4 + - - -
180A ASN* 2.9 23.2 + - - +
220A PRO 4.9 0.9 - - - +
221A GLY* 4.6 2.3 - - - -
244A GLU* 1.3 87.3 - - + +
246A CYS* 1.3 61.4 + - - +
247A ARG* 3.4 5.9 + - - +
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Residues in contact with CYS 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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177A TRP 3.4 4.3 - - - +
178A VAL* 4.2 0.9 - - - -
179A LEU* 2.9 43.2 + - + +
215A VAL* 4.9 0.2 - - - -
219A THR* 3.6 23.6 - - - -
220A PRO 3.5 21.1 - - - -
221A GLY 3.7 19.7 - - - +
243A PHE* 3.8 24.9 - - + -
244A GLU 4.0 0.4 - - - -
245A ASP* 1.3 72.7 - - - +
247A ARG* 1.3 59.6 + - - +
248A ILE* 3.8 13.2 + - - +
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Residues in contact with ARG 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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173A GLU* 4.1 11.1 + - - +
174A GLY* 5.8 0.4 - - - -
175A ASP* 3.2 23.4 + - - -
176A SER* 3.1 35.3 + - - +
177A TRP 3.4 6.3 - - - +
178A VAL* 4.5 12.3 - - + +
219A THR* 4.8 5.5 + - - -
220A PRO* 4.4 5.7 + - - +
245A ASP 3.4 7.0 + - - +
246A CYS* 1.3 74.2 - - - +
248A ILE* 1.3 67.3 + - - +
249A PRO* 4.8 0.5 - - - +
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Residues in contact with ILE 248 (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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176A SER* 3.4 5.7 - - - -
177A TRP* 3.0 45.0 + - + +
179A LEU* 3.9 25.6 - - + -
213A PHE* 3.9 24.0 - - + -
214A LEU 4.4 1.3 - - - +
215A VAL* 4.0 22.4 - - + -
216A PRO* 4.9 7.6 - - + -
219A THR* 5.0 4.0 - - + +
246A CYS* 4.2 20.0 - - - +
247A ARG* 1.3 80.8 - - - +
249A PRO* 1.3 70.9 - - + +
252A SER* 3.7 23.1 - - - +
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Residues in contact with PRO 249 (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 4.5 0.2 - - - +
176A SER* 4.5 7.0 - - - +
177A TRP* 3.8 3.5 - - - -
216A PRO* 6.1 2.9 - - + -
247A ARG 4.8 0.7 - - - +
248A ILE* 1.3 88.3 - - + +
250A LYS* 1.3 65.2 + - - +
251A ASP* 3.3 4.5 - - + +
252A SER* 2.6 38.3 + - - +
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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