Contacts of the strand formed by residues 288 - 294 (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 ARG 288 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120D ASP* 3.1 32.8 + - - +
122D PRO* 3.2 32.9 - - - +
127D PHE* 2.7 41.8 + - + +
128D GLU* 3.5 19.6 + - - +
129D VAL* 3.0 39.5 - - + +
274D ILE* 5.0 0.7 - - - -
275D ILE* 2.8 37.0 + - - +
287D ARG* 1.3 76.6 - - - +
289D SER* 1.3 60.0 + - - +
290D PHE* 5.3 0.2 - - - -
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Residues in contact with SER 289 (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* 3.5 24.9 + - - -
120D ASP* 4.1 17.2 + - - +
149D LYS* 6.1 0.2 - - - +
272D LEU* 5.1 7.6 - - - +
273D ILE 3.6 4.9 - - - -
274D ILE* 3.5 33.9 - - - -
287D ARG 4.3 0.4 - - - -
288D ARG* 1.3 75.1 - - - +
290D PHE* 1.3 65.6 - - - +
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Residues in contact with PHE 290 (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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129D VAL* 4.0 17.3 - - + -
131D PHE* 4.0 15.5 - + + -
144D TYR* 4.9 8.7 - - + +
149D LYS* 4.3 10.8 - - + +
151D LEU* 3.5 29.8 - - + -
161D ILE* 3.4 29.6 - - + -
256D PHE* 5.6 0.4 - + - -
272D LEU* 3.5 6.0 - - - -
273D ILE* 2.9 59.6 + - + -
275D ILE* 3.4 26.9 - - + -
288D ARG 5.0 0.2 - - - -
289D SER* 1.3 78.0 - - - +
291D GLU* 1.3 71.6 + - - +
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Residues in contact with GLU 291 (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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148D LEU 4.4 4.3 - - - +
149D LYS* 3.1 21.0 + - + +
150D LYS* 2.8 44.2 + - + +
151D LEU 2.6 31.2 + - - -
182D LYS* 3.4 32.3 + - - -
270D PRO* 4.1 11.3 - - + +
271D ILE 3.6 15.3 - - - +
272D LEU* 3.7 13.4 - - + +
290D PHE* 1.3 78.4 - - - +
292D GLY* 1.3 58.7 + - - +
293D ARG* 6.0 0.2 - - - +
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Residues in contact with GLY 292 (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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150D LYS* 5.0 0.2 - - - -
151D LEU* 3.5 10.5 - - - -
256D PHE* 6.0 0.2 - - - -
260D SER* 4.0 2.9 + - - -
270D PRO* 5.1 1.9 - - - +
271D ILE* 2.9 42.4 + - - +
272D LEU* 4.4 0.4 - - - +
273D ILE* 4.4 16.4 - - - -
290D PHE 3.7 1.4 + - - -
291D GLU* 1.3 79.2 - - - +
293D ARG* 1.3 61.5 + - - +
294D ILE* 4.3 5.8 - - - -
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Residues in contact with ARG 293 (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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150D LYS* 4.3 19.7 - - + +
151D LEU 2.8 14.1 + - - +
152D TYR* 3.5 17.5 - - + -
153D CYS 3.1 24.1 + - - +
260D SER* 3.7 19.1 - - - +
261D SER* 5.7 1.6 - - - +
292D GLY* 1.3 72.9 - - - -
294D ILE* 1.3 66.8 + - - +
295D CYS* 3.3 30.0 + - - +
301D ASP* 2.7 38.4 + - - +
305D ASP* 5.7 3.6 + - - +
517H A 4.2 4.4 + - - +
518H T 2.9 36.5 + - - +
519H G 5.9 0.8 + - - -
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Residues in contact with ILE 294 (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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151D LEU 5.9 0.2 - - - +
153D CYS* 3.1 19.5 - - - +
154D GLN 3.9 1.1 - - - -
155D ILE* 3.5 28.0 - - + +
214D LEU* 5.2 1.1 - - + -
256D PHE* 3.3 43.7 - - + +
258D CYS 3.0 29.8 - - - +
259D ASN* 3.8 5.4 + - - -
260D SER* 3.0 40.0 + - - +
261D SER 4.4 0.2 + - - -
266D MET* 4.7 11.0 - - + -
271D ILE* 5.9 1.1 - - + -
292D GLY* 4.9 3.4 - - - +
293D ARG* 1.3 81.3 + - - +
295D CYS* 1.3 62.8 + - - +
519H G 4.3 2.3 + - - -
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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