Contacts of the strand formed by residues 271 - 278 (chain C) in PDB entry 3VD1
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 ILE 271 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C PRO* 4.7 0.2 - - + -
180C VAL 3.0 15.0 - - - +
181C TYR* 4.1 17.7 - - + -
182C LYS* 4.3 2.1 - - - +
191C VAL* 4.1 12.8 - - + -
214C LEU* 4.1 10.8 - - + -
256C PHE* 5.4 0.7 - - + -
260C SER* 5.3 1.8 + - - +
266C MET* 3.6 38.6 - - + -
269C ARG 3.5 1.4 + - - +
270C PRO* 1.3 77.1 - - - +
272C LEU* 1.3 65.4 + - - +
273C ILE* 3.8 27.6 - - + -
291C GLU* 3.1 26.0 - - - +
292C GLY* 3.3 28.7 + - - +
294C ILE* 5.1 8.1 - - + -
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Residues in contact with LEU 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C ASN* 4.9 15.5 - - + +
178C MET 3.8 0.3 - - - +
180C VAL* 2.8 33.1 + - + +
181C TYR 4.6 2.7 - - - +
182C LYS* 4.1 29.8 - - + +
271C ILE* 1.3 81.4 - - - +
273C ILE* 1.3 65.1 + - - +
274C ILE* 3.6 12.4 + - + +
289C SER* 3.3 37.5 - - - +
290C PHE* 3.2 22.4 - - - +
291C GLU* 4.1 4.5 - - + +
292C GLY 4.3 0.4 - - - +
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Residues in contact with ILE 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151C LEU* 5.8 0.2 - - + -
177C ALA* 4.7 2.7 - - + -
178C MET 3.6 3.1 - - - +
179C PRO* 4.1 6.1 - - + -
214C LEU* 4.8 0.2 - - + -
215C ILE* 3.6 30.1 - - + -
254C TYR* 6.4 1.6 - - + -
256C PHE* 3.5 36.3 - - + -
271C ILE* 3.8 24.0 - - + -
272C LEU* 1.3 71.8 - - - +
274C ILE* 1.3 63.6 + - - +
275C ILE* 4.2 21.1 - - + -
289C SER* 3.5 2.9 - - - -
290C PHE* 2.9 54.1 + - + +
292C GLY* 4.7 7.2 - - - +
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Residues in contact with ILE 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C PRO* 3.9 11.0 - - + +
117C SER 3.4 23.8 - - - +
118C ASN* 4.2 10.8 - - + -
176C ARG* 3.1 7.1 - - - +
177C ALA* 3.5 0.5 - - - -
178C MET* 2.8 42.7 + - + +
180C VAL* 3.8 23.8 - - + -
272C LEU* 3.9 12.8 - - + +
273C ILE* 1.3 78.6 - - - +
275C ILE* 1.3 61.3 + - - +
276C THR* 4.8 3.5 - - - +
287C ARG* 3.7 23.1 - - + -
288C ARG 3.5 15.0 - - - +
289C SER* 4.1 10.5 - - - -
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Residues in contact with ILE 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C PHE* 3.3 26.2 - - + -
129C VAL* 4.6 6.7 - - + -
161C ILE* 3.7 24.9 - - + -
163C ILE* 3.9 10.3 - - + -
175C ILE* 3.8 18.4 - - + -
176C ARG 3.2 1.6 - - - +
177C ALA* 3.8 26.0 - - + -
254C TYR* 3.9 6.1 - - + +
273C ILE* 4.2 9.9 - - + -
274C ILE* 1.3 72.4 - - - +
276C THR* 1.3 63.1 + - - +
287C ARG* 3.3 4.6 - - - -
288C ARG* 3.0 34.2 + - + +
290C PHE* 4.1 22.0 - - + -
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Residues in contact with THR 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C PHE* 4.4 4.3 - - - -
174C ALA 3.2 0.9 - - - +
175C ILE* 3.2 8.7 - - - -
176C ARG* 2.7 46.8 + - - +
274C ILE* 4.0 4.6 + - - +
275C ILE* 1.3 72.6 - - - +
277C LEU* 1.3 69.9 + - - +
278C GLU* 2.9 36.6 - - + +
284C VAL* 4.8 10.3 - - + +
286C GLY 3.6 10.6 + - - +
287C ARG* 3.8 19.4 + - - +
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Residues in contact with LEU 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C PRO 5.2 0.2 - - - +
125C HIS* 4.3 23.8 - - + -
127C PHE* 3.8 32.4 - - + -
163C ILE* 5.8 0.2 - - + -
165C VAL* 5.1 7.2 - - + -
169C PRO* 4.7 11.7 - - + -
173C THR* 3.5 25.8 - - + -
174C ALA 3.3 2.0 - - - -
175C ILE* 3.9 18.8 - - + -
240C TYR* 4.9 4.5 - - + -
276C THR* 1.3 72.0 - - - +
278C GLU* 1.3 57.5 + - - +
284C VAL 3.9 0.5 - - - -
285C LEU* 2.9 51.0 + - + +
286C GLY* 3.0 20.0 + - - +
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Residues in contact with GLU 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C THR* 2.9 14.4 - - - +
174C ALA* 2.8 47.6 + - + +
176C ARG* 2.7 51.9 + - + +
276C THR* 2.9 23.3 + - + +
277C LEU* 1.3 73.8 - - - +
279C MET* 1.3 65.5 + - - +
282C GLY* 3.2 36.8 - - - +
283C GLN 3.6 2.9 - - - +
284C VAL* 4.8 3.5 - - + +
285C LEU* 4.9 1.3 - - - -
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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