Contacts of the helix formed by residues 297 - 311 (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 CYS 297 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138K LYS* 5.0 7.9 - - + -
139K SER* 4.4 19.3 - - - +
295K CYS* 3.6 0.6 - - - -
296K ALA* 1.3 86.4 - - - +
298K PRO* 1.3 66.4 - - - +
299K GLY 3.2 3.7 + - - -
300K ARG* 3.6 30.9 - - + +
301K ASP* 3.0 27.4 + - - +
707O G 4.4 0.8 + - - -
708O C 3.6 36.1 - - - -
709O C 6.0 0.7 - - - -
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Residues in contact with PRO 298 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139K SER* 4.2 2.9 - - - -
140K ALA 3.4 21.1 - - - +
142K TRP* 4.5 0.7 - - - -
143K THR* 3.6 9.7 - - + +
152K TYR* 3.5 32.5 - - + +
153K CYS 3.9 19.3 - - - +
154K GLN* 3.3 22.0 - - - +
295K CYS* 3.9 15.0 - - - +
296K ALA 3.7 1.3 - - - -
297K CYS* 1.3 87.4 - - - +
299K GLY* 1.3 56.9 + - - +
301K ASP* 3.6 0.9 - - + -
302K ARG* 2.8 33.1 + - - +
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Residues in contact with GLY 299 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137K ALA 3.1 27.8 - - - -
138K LYS* 3.7 8.7 - - - -
139K SER 3.7 7.0 - - - +
140K ALA* 4.5 0.8 - - - +
143K THR* 4.4 2.8 - - - +
297K CYS 3.2 2.6 + - - -
298K PRO* 1.3 73.7 - - - +
300K ARG* 1.3 53.0 + - - -
302K ARG* 2.6 29.0 + - - +
303K LYS* 2.7 20.5 + - - +
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Residues in contact with ARG 300 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138K LYS* 3.6 27.8 - - - +
297K CYS* 3.6 26.6 - - + +
299K GLY* 1.3 70.7 - - - +
301K ASP* 1.3 79.0 + - - +
303K LYS* 3.3 17.7 - - + +
304K ALA* 2.5 39.6 + - - +
706O T 3.5 33.6 + - - +
707O G 2.8 42.4 + - - -
708O C 3.6 5.5 - - - +
715P G 3.4 22.4 + - - -
716P C 4.9 0.6 - - - +
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Residues in contact with ASP 301 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152K TYR* 3.1 10.6 - - + -
293K ARG* 3.0 38.3 + - - +
295K CYS* 3.9 8.0 - - - +
297K CYS 3.0 24.5 + - - +
298K PRO* 3.6 3.8 - - + +
299K GLY 3.0 1.2 - - - -
300K ARG* 1.3 102.6 + - - +
302K ARG* 1.3 62.0 + - - +
304K ALA* 3.9 8.7 - - - +
305K ASP* 2.8 26.7 + - - +
705O A 5.8 1.6 - - - +
706O T 4.7 9.6 - - - +
707O G 4.6 4.2 + - - -
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Residues in contact with ARG 302 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134K SER* 6.0 3.4 - - - -
137K ALA* 5.7 4.6 + - - +
143K THR* 2.9 30.1 + - + -
144K TYR 2.7 30.3 + - - +
145K SER* 3.6 24.2 - - - -
152K TYR* 3.3 32.0 + - + -
298K PRO 2.8 16.5 + - - +
299K GLY* 2.6 8.2 + - - +
301K ASP* 1.3 74.0 - - - +
303K LYS* 1.3 65.5 + - - +
304K ALA 3.3 0.2 - - - -
305K ASP* 3.5 2.8 + - - +
306K GLU* 3.0 36.4 + - - +
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Residues in contact with LYS 303 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137K ALA* 4.9 13.1 - - - +
138K LYS* 3.9 21.2 - - - +
299K GLY 2.7 8.8 + - - +
300K ARG* 3.3 32.3 - - + +
302K ARG* 1.3 85.4 - - - +
304K ALA* 1.3 57.2 + - - +
306K GLU* 2.8 42.2 - - - +
307K ASP* 3.3 11.1 - - - +
713P G 5.1 2.4 + - - -
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Residues in contact with ALA 304 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300K ARG* 2.5 24.0 + - - +
301K ASP* 4.1 10.5 - - - +
303K LYS* 1.3 70.3 - - - +
305K ASP* 1.3 63.2 + - - +
306K GLU 3.0 1.1 - - - -
307K ASP* 2.8 24.7 + - - +
308K HIS* 3.2 19.2 + - + +
705O A 5.3 9.4 - - - +
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Residues in contact with ASP 305 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148K LEU* 3.8 19.3 - - + +
150K LYS* 3.6 21.6 + - - -
152K TYR* 3.4 23.1 - - - +
293K ARG* 4.7 6.8 + - - -
301K ASP* 2.8 21.3 + - - +
302K ARG 3.5 2.1 + - - +
304K ALA* 1.3 78.3 - - - +
306K GLU* 1.3 61.6 + - - +
308K HIS* 3.4 10.2 + - - +
309K TYR* 3.2 22.9 + - - +
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Residues in contact with GLU 306 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147K LEU* 4.9 16.4 - - + +
148K LEU* 5.6 0.9 - - - -
302K ARG* 3.0 25.8 + - - +
303K LYS* 2.8 35.2 - - - +
304K ALA 3.0 0.2 - - - -
305K ASP* 1.3 79.7 - - - +
307K ASP* 1.3 68.0 + - - +
309K TYR* 3.4 5.5 + - - +
310K ARG* 2.9 33.6 + - - +
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Residues in contact with ASP 307 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303K LYS* 3.3 7.7 - - - +
304K ALA* 2.8 12.9 + - - +
306K GLU* 1.3 96.5 - - - +
308K HIS* 1.3 65.5 + - + +
309K TYR 3.1 2.0 - - - -
310K ARG* 3.1 40.3 + - - +
311K GLU* 3.1 8.3 + - - +
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Residues in contact with HIS 308 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304K ALA* 3.2 19.6 + - + +
305K ASP* 3.4 10.3 + - - +
307K ASP* 1.3 79.0 - - + +
309K TYR* 1.3 58.2 + - - +
311K GLU* 3.1 42.4 - - - +
704O C 4.5 14.6 + - - -
705O A 3.1 30.8 + - - -
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Residues in contact with TYR 309 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147K LEU* 3.8 44.5 + - + -
148K LEU* 4.2 31.4 - - + -
305K ASP 3.2 16.1 + - - +
306K GLU 3.8 4.0 - - - +
307K ASP 3.1 0.4 - - - -
308K HIS* 1.3 74.2 - - - +
310K ARG* 1.3 66.9 + - - +
311K GLU 2.8 12.8 - - - +
312K GLN* 4.1 26.2 + - - +
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Residues in contact with ARG 310 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147K LEU* 6.3 0.4 - - - -
306K GLU* 2.9 22.2 + - - +
307K ASP* 3.1 37.2 + - - +
309K TYR* 1.3 77.8 - - - +
311K GLU* 1.3 61.0 + - - +
312K GLN* 3.7 4.3 + - - +
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Residues in contact with GLU 311 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307K ASP 3.1 8.1 + - - +
308K HIS* 3.1 40.4 - - - +
309K TYR* 2.9 13.5 - - - +
310K ARG* 1.3 78.8 - - - +
312K GLN* 1.3 68.7 + - - +
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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