Contacts of the strand formed by residues 271 - 279 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179D PRO* 4.1 8.7 - - + -
180D VAL 3.1 12.1 - - - +
181D TYR* 3.4 21.8 - - + -
182D LYS 4.1 1.3 - - - +
191D VAL* 4.3 3.4 - - + -
214D LEU* 4.4 1.1 - - + -
256D PHE* 5.6 0.9 - - + -
260D SER* 4.9 1.8 + - - +
266D MET* 3.4 35.0 - - + -
269D ARG 2.8 25.4 - - - +
270D PRO* 1.3 75.1 - - - +
272D LEU* 1.3 74.4 + - - +
273D ILE* 3.2 35.9 - - + -
291D GLU* 3.6 2.5 - - - +
292D GLY* 2.9 41.3 + - - +
294D ILE* 5.9 1.1 - - + -
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Residues in contact with LEU 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D ASN* 4.0 23.3 - - - +
178D MET 3.6 0.7 - - - +
179D PRO* 3.3 3.1 - - - +
180D VAL* 2.7 49.6 + - + +
182D LYS* 4.3 33.2 - - + -
271D ILE* 1.3 86.5 - - - +
273D ILE* 1.3 66.9 + - - +
274D ILE* 4.6 5.6 - - + -
289D SER* 5.1 4.9 - - - +
290D PHE* 3.5 12.6 - - - +
291D GLU* 3.7 23.3 - - + +
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Residues in contact with ILE 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D LEU* 5.7 0.2 - - + -
177D ALA* 4.4 3.8 - - + -
178D MET 3.4 2.0 - - - -
179D PRO* 4.2 1.8 - - + -
214D LEU* 5.0 0.2 - - + -
215D ILE* 3.7 28.5 - - + -
254D TYR* 6.4 0.7 - - + -
256D PHE* 3.3 36.8 - - + -
271D ILE* 3.2 30.1 - - + -
272D LEU* 1.3 74.5 - - - +
274D ILE* 1.3 61.5 + - - +
275D ILE* 3.5 26.7 + - + -
289D SER* 3.6 2.4 - - - -
290D PHE* 2.9 54.7 + - + +
292D GLY* 4.4 9.9 - - - -
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Residues in contact with ILE 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D SER* 3.9 13.7 - - - +
118D ASN* 3.5 37.9 - - + +
176D ARG 3.4 5.0 - - - +
178D MET* 2.5 53.2 + - + +
180D VAL* 4.4 20.9 - - + -
272D LEU* 4.6 2.9 - - + -
273D ILE* 1.3 73.4 - - - +
275D ILE* 1.3 64.5 + - - +
276D THR* 3.5 24.8 + - + +
287D ARG* 4.2 10.3 - - + -
288D ARG 4.4 0.2 - - - +
289D SER* 3.5 22.2 - - - -
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Residues in contact with ILE 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D PHE* 3.9 14.2 - - + -
129D VAL* 4.4 11.2 - - + -
161D ILE* 4.9 2.7 - - + -
163D ILE* 4.3 12.3 - - + -
175D ILE* 3.9 23.1 - - + -
176D ARG 3.4 2.7 - - - +
177D ALA* 4.2 12.1 - - + -
254D TYR* 4.6 16.2 - - + +
273D ILE* 3.5 29.2 - - + -
274D ILE* 1.3 70.9 - - - +
276D THR* 1.3 68.1 + - - +
288D ARG 2.8 40.9 + - - +
290D PHE* 3.4 28.7 - - + -
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Residues in contact with THR 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D SER* 5.3 0.7 - - - +
127D PHE* 4.3 4.5 - - - -
175D ILE* 3.5 4.6 - - - -
176D ARG* 2.9 43.1 + - + +
178D MET* 6.1 0.9 - - + -
274D ILE* 3.5 25.6 - - + +
275D ILE* 1.3 82.6 - - - +
277D LEU* 1.3 60.0 + - - +
278D GLU* 3.3 21.0 + - - +
284D VAL* 4.1 11.8 - - + +
286D GLY 2.9 17.0 - - - +
287D ARG* 4.0 13.5 - - - -
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Residues in contact with LEU 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D HIS* 4.7 25.8 - - + +
127D PHE* 3.8 29.3 - - + -
165D VAL* 6.0 2.5 - - + -
169D PRO* 4.4 17.7 - - + -
170D PRO* 6.1 0.9 - - + -
173D THR* 3.6 21.1 - - - +
174D ALA 3.5 4.3 - - - -
175D ILE* 3.8 17.7 - - + -
240D TYR* 4.7 9.4 - - + -
276D THR* 1.3 72.9 - - - +
278D GLU* 1.3 62.0 + - - +
284D VAL* 4.1 0.7 - - - +
285D LEU* 3.5 26.6 + - + +
286D GLY* 3.0 37.6 + - - +
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Residues in contact with GLU 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173D THR* 2.7 23.1 + - - -
174D ALA* 2.9 30.8 + - + +
175D ILE 5.6 0.2 - - - -
176D ARG* 3.2 42.5 + - + -
237D VAL* 5.3 0.3 - - - +
276D THR* 3.3 20.3 + - - +
277D LEU* 1.3 79.0 - - - +
279D MET* 1.3 63.2 + - - +
282D GLY* 5.3 4.3 - - - -
283D GLN 3.7 5.8 - - - +
284D VAL* 3.7 32.7 - - + +
285D LEU 4.4 1.3 - - - +
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Residues in contact with MET 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D PRO* 3.4 37.7 - - + -
171D PRO* 5.0 3.6 - - - -
172D GLY 5.2 0.4 - - - -
173D THR* 4.3 8.7 - - - +
278D GLU* 1.3 77.2 - - - +
280D ARG* 1.3 97.9 + - - +
281D ASP* 2.7 32.0 + - - +
282D GLY* 2.7 18.0 + - - -
283D GLN* 2.9 32.4 + - + +
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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