Contacts of the strand formed by residues 271 - 278 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179I PRO* 4.9 0.4 - - + -
180I VAL 3.3 11.9 - - - +
181I TYR* 3.5 20.2 - - + -
182I LYS 4.3 0.4 - - - +
191I VAL* 4.7 8.5 - - + -
214I LEU* 4.5 6.5 - - + -
256I PHE* 6.0 0.2 - - + -
260I SER* 4.1 5.4 - - - +
266I MET* 3.5 44.2 - - + -
270I PRO* 1.3 79.4 - - - +
272I LEU* 1.3 67.5 + - - +
273I ILE* 3.9 24.9 - - + -
291I GLU* 3.3 9.2 - - - +
292I GLY* 2.9 44.4 + - - +
294I ILE* 4.6 9.2 - - + -
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Residues in contact with LEU 272 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118I ASN* 5.0 17.5 - - + +
179I PRO* 3.4 3.3 - - - +
180I VAL* 2.6 41.6 + - + +
181I TYR 5.7 0.2 - - - -
182I LYS* 3.2 46.2 - - + -
271I ILE* 1.3 77.3 - - - +
273I ILE* 1.3 61.4 + - - +
274I ILE* 4.0 11.3 + - + -
289I SER* 4.4 10.1 - - - +
290I PHE* 3.3 34.1 - - - +
291I GLU* 3.9 6.5 - - + +
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Residues in contact with ILE 273 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151I LEU* 5.5 0.9 - - + -
177I ALA* 5.0 4.7 - - + -
178I MET 3.7 2.7 - - - +
179I PRO* 4.1 6.5 - - + -
214I LEU* 5.3 0.2 - - + -
215I ILE* 4.0 24.2 - - + -
254I TYR* 6.4 2.0 - - + -
256I PHE* 3.8 34.3 - - + -
271I ILE* 3.9 23.3 - - + -
272I LEU* 1.3 73.2 - - - +
274I ILE* 1.3 62.6 + - - +
275I ILE* 3.9 21.8 - - + +
289I SER* 3.4 1.9 - - - -
290I PHE* 2.6 53.5 + - + +
292I GLY* 4.5 15.3 - - - -
294I ILE* 5.9 1.1 - - + -
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Residues in contact with ILE 274 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116I PRO* 5.4 5.6 - - + +
117I SER 3.1 28.7 - - - +
118I ASN* 4.2 11.4 - - + -
176I ARG 3.6 2.1 - - - +
178I MET* 2.7 48.8 + - + +
180I VAL* 4.3 14.8 - - + -
272I LEU* 4.3 13.0 - - + +
273I ILE* 1.3 77.0 - - - +
275I ILE* 1.3 60.9 + - - +
276I THR* 4.1 16.0 + - + +
287I ARG* 3.5 18.8 - - + -
288I ARG 3.7 2.9 - - - -
289I SER* 3.5 17.3 - - - -
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Residues in contact with ILE 275 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127I PHE* 3.6 24.9 - - + -
129I VAL* 4.5 9.2 - - + -
161I ILE* 3.7 19.3 - - + -
163I ILE* 4.6 6.3 - - + -
175I ILE* 3.7 22.2 - - + -
176I ARG 3.2 6.3 - - - +
177I ALA* 4.7 3.8 - - + -
254I TYR* 4.5 9.4 - - + +
273I ILE* 3.9 13.5 - - + +
274I ILE* 1.3 76.6 - - - +
276I THR* 1.3 65.2 + - - +
287I ARG* 3.5 2.3 - - - +
288I ARG 2.8 39.5 + - - +
290I PHE* 3.6 37.9 - - + -
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Residues in contact with THR 276 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127I PHE* 4.4 2.7 - - - -
174I ALA 3.5 0.5 - - - +
175I ILE* 3.1 26.5 - - - +
176I ARG* 2.9 36.9 + - + +
178I MET* 6.3 0.2 - - + -
274I ILE* 4.1 14.1 - - + -
275I ILE* 1.3 81.5 - - - +
277I LEU* 1.3 60.7 + - - +
278I GLU* 3.4 19.4 + - - +
284I VAL* 4.9 11.9 - - + -
286I GLY 3.5 6.7 - - - -
287I ARG* 3.9 21.3 - - + -
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Residues in contact with LEU 277 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125I HIS* 5.1 7.9 - - + +
127I PHE* 3.8 37.6 - - + -
165I VAL* 4.3 9.9 - - + -
169I PRO* 4.0 22.7 - - + -
173I THR* 3.1 31.4 - - + -
174I ALA 3.3 7.2 - - - +
175I ILE* 3.3 21.3 - - + -
240I TYR* 4.1 6.3 - - + -
276I THR* 1.3 72.5 - - - +
278I GLU* 1.3 60.4 + - - +
284I VAL* 4.0 0.2 - - - -
285I LEU* 3.0 32.2 + - + +
286I GLY 2.8 20.4 + - - +
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Residues in contact with GLU 278 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173I THR* 3.3 5.7 - - - +
174I ALA* 2.9 53.2 + - + +
175I ILE 4.3 0.5 + - - -
176I ARG* 2.7 40.7 + - - +
237I VAL* 5.0 0.9 - - - +
276I THR* 3.4 18.2 + - - +
277I LEU* 1.3 76.1 - - - +
279I MET* 1.3 61.9 + - - +
282I GLY* 3.3 28.2 - - - +
283I GLN 2.7 23.6 - - - +
284I VAL* 3.6 9.1 - - + +
285I LEU* 4.1 9.9 - - - +
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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