Contacts of the strand formed by residues 288 - 295 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120K ASP* 3.2 38.6 + - + +
122K PRO* 4.2 17.9 - - - +
127K PHE* 2.6 34.1 + - + +
128K GLU* 3.4 23.0 + - - +
129K VAL* 3.0 39.9 - - + +
274K ILE* 4.8 0.2 - - - -
275K ILE* 2.8 38.7 + - + +
287K ARG* 1.3 89.2 - - - +
289K SER* 1.3 61.3 + - - +
290K PHE* 4.7 0.3 - - - -
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Residues in contact with SER 289 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118K ASN* 2.9 28.6 + - - +
120K ASP* 3.3 13.7 + - - +
129K VAL* 5.7 1.2 - - - +
149K LYS* 6.0 0.5 - - - +
272K LEU* 4.1 8.9 - - - +
273K ILE 3.1 4.9 - - - -
274K ILE* 3.3 32.8 - - - -
287K ARG* 5.8 0.2 - - - -
288K ARG* 1.3 75.5 - - - +
290K PHE* 1.3 68.2 + - - +
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Residues in contact with PHE 290 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129K VAL* 4.6 8.1 - - + -
131K PHE* 3.5 20.6 - + + -
144K TYR* 4.4 12.8 - + + +
149K LYS* 4.0 13.0 - - + +
151K LEU* 3.3 40.8 - - + -
161K ILE* 3.5 23.3 - - + -
256K PHE* 5.4 1.3 - + - -
272K LEU* 4.0 4.5 - - - -
273K ILE* 2.5 72.0 + - + -
275K ILE* 3.7 28.7 - - + -
288K ARG 4.7 0.7 - - - -
289K SER* 1.3 83.2 + - - +
291K GLU* 1.3 59.9 + - - +
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Residues in contact with GLU 291 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148K LEU* 5.1 3.5 - - - +
149K LYS* 3.1 17.6 + - + +
150K LYS* 2.6 46.3 + - + +
151K LEU* 2.8 30.0 + - - +
182K LYS* 3.1 35.2 + - + +
270K PRO* 4.0 10.6 - - + +
271K ILE 3.6 13.2 - - - +
272K LEU* 3.9 9.6 - - + +
290K PHE* 1.3 74.9 - - - +
292K GLY* 1.3 67.6 + - - +
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Residues in contact with GLY 292 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150K LYS* 5.4 0.2 + - - -
151K LEU* 3.8 8.5 - - - -
153K CYS* 5.8 1.3 - - - -
260K SER* 5.7 1.0 - - - -
270K PRO* 5.1 3.3 - - - +
271K ILE* 2.9 40.4 + - - +
272K LEU* 3.9 1.0 - - - +
273K ILE* 4.2 12.3 - - - -
290K PHE* 3.5 3.8 + - - -
291K GLU* 1.3 80.8 - - - +
293K ARG* 1.3 66.2 + - - +
294K ILE* 5.4 2.7 - - - -
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Residues in contact with ARG 293 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150K LYS* 4.2 26.2 - - + +
151K LEU 3.3 11.4 + - - +
152K TYR* 3.7 12.6 - - + -
153K CYS* 3.3 18.6 + - - +
260K SER* 3.9 17.1 + - - +
270K PRO* 6.5 1.3 - - + -
271K ILE* 5.6 0.2 - - - -
292K GLY* 1.3 76.8 - - - +
294K ILE* 1.3 67.7 + - - +
295K CYS* 3.3 35.5 + - - +
301K ASP* 3.0 42.2 + - - +
305K ASP* 4.7 6.2 + - - -
705O A 5.7 0.4 - - - +
706O T 2.7 42.9 + - - +
707O G 5.2 1.2 + - - -
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Residues in contact with ILE 294 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153K CYS* 3.4 19.7 - - - +
154K GLN 3.6 24.7 - - - +
155K ILE* 3.7 11.2 - - - -
214K LEU* 4.9 4.3 - - + -
256K PHE* 3.3 38.1 - - + +
258K CYS 3.0 29.2 - - - +
259K ASN* 3.0 11.3 - - - +
260K SER* 2.8 33.3 + - - +
261K SER 4.4 0.9 + - - -
266K MET* 4.2 9.9 - - + -
271K ILE* 5.4 4.9 - - + -
273K ILE* 6.0 0.9 - - + -
292K GLY* 5.1 3.4 - - - -
293K ARG* 1.3 74.3 + - - +
295K CYS* 1.3 57.9 + - - +
707O G 4.5 0.9 + - - -
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Residues in contact with CYS 295 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152K TYR* 4.4 4.3 - - - -
153K CYS 3.1 15.0 + - - +
154K GLN* 3.7 13.7 - - - +
155K ILE 4.0 0.5 + - - -
259K ASN* 3.7 12.1 + - - +
293K ARG* 3.4 49.4 - - - +
294K ILE* 1.3 74.1 - - - +
296K ALA* 1.3 62.1 + - - +
298K PRO* 3.9 30.0 - - - +
301K ASP* 3.9 8.1 - - - +
707O G 3.9 14.8 - - - +
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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