Contacts of the helix formed by residues 297 - 310 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A LYS* 3.3 21.8 - - - +
139A SER* 4.6 2.7 - - - +
295A CYS* 3.6 2.8 - - - +
296A ALA* 1.3 89.0 - - - +
298A PRO* 1.3 65.5 - - - +
299A GLY 2.8 4.9 + - - -
300A ARG* 2.8 52.6 + - + +
301A ASP* 2.9 14.1 + - - +
418F C 3.3 31.6 - - - -
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Residues in contact with PRO 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LYS 4.3 1.3 - - - +
139A SER 4.5 0.4 - - - -
140A ALA* 3.2 28.0 - - + +
141A THR 4.5 0.4 - - - +
143A THR* 3.5 11.8 - - + +
152A TYR* 3.4 40.1 - - + +
153A CYS* 4.3 0.9 - - - -
154A GLN* 3.4 20.0 - - + +
295A CYS* 3.7 13.6 - - - +
296A ALA 3.2 10.8 - - - +
297A CYS* 1.3 88.3 - - - +
299A GLY* 1.3 57.0 + - - +
302A ARG* 3.0 29.5 + - - +
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Residues in contact with GLY 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A THR 4.4 7.6 - - - -
137A ALA 3.7 15.3 + - - -
138A LYS* 2.8 19.0 + - - -
140A ALA* 4.6 0.6 - - - +
143A THR* 4.5 4.7 - - - +
297A CYS 2.8 4.2 + - - -
298A PRO* 1.3 70.9 - - - +
300A ARG* 1.3 63.2 + - - -
301A ASP 3.0 2.0 - - - -
302A ARG* 3.8 7.8 + - - -
303A LYS* 2.9 31.9 + - - +
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Residues in contact with ARG 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LYS* 3.3 31.8 + - + +
297A CYS* 2.8 41.1 + - + +
299A GLY* 1.3 71.5 - - - +
301A ASP* 1.3 68.7 + - - +
303A LYS* 3.7 14.1 - - - +
304A ALA* 3.2 26.0 + - + +
401E G 4.1 4.2 + - - -
402E C 4.6 1.2 - - - +
416F T 3.4 41.0 - - - +
417F G 2.9 53.1 + - - -
418F C 3.9 5.3 - - - +
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Residues in contact with ASP 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A TYR* 3.8 20.2 - - + -
293A ARG* 3.0 25.5 + - - +
295A CYS* 2.9 28.6 - - - +
297A CYS 2.9 15.4 + - - +
298A PRO 3.8 0.7 - - - +
300A ARG* 1.3 101.8 + - - +
302A ARG* 1.3 60.9 + - - +
304A ALA* 3.0 6.3 + - - +
305A ASP* 2.8 32.3 + - - +
416F T 4.3 4.8 + - - +
417F G 5.0 0.3 + - - -
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Residues in contact with ARG 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A THR* 5.0 24.0 + - - +
143A THR* 3.5 25.8 - - + -
144A TYR 3.9 12.9 + - - -
145A SER* 4.6 1.1 - - - -
152A TYR* 3.4 30.2 - - + -
298A PRO 3.0 20.5 + - - +
299A GLY* 3.8 8.1 + - - +
301A ASP* 1.3 74.2 - - - +
303A LYS* 1.3 95.4 - - - +
305A ASP* 3.2 1.7 + - - +
306A GLU* 3.0 58.8 + - - +
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Residues in contact with LYS 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A THR 5.3 5.1 + - - -
138A LYS* 5.1 9.5 - - - +
299A GLY 2.9 15.1 + - - +
300A ARG* 3.7 18.7 - - - +
302A ARG* 1.3 103.0 - - - +
304A ALA* 1.3 64.5 + - + +
306A GLU* 4.4 2.7 - - - +
307A ASP* 3.3 32.4 + - - +
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Residues in contact with ALA 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A ARG* 3.2 18.6 + - + +
301A ASP* 3.0 6.2 + - - +
303A LYS* 1.3 81.2 - - + +
305A ASP* 1.3 66.4 + - - +
307A ASP* 4.0 4.4 - - - +
308A HIS* 3.3 24.3 + - - +
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Residues in contact with ASP 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A LEU* 3.7 13.3 - - + +
150A LYS* 2.8 22.0 + - - -
152A TYR* 2.6 35.6 + - - +
293A ARG* 3.9 8.3 + - - -
301A ASP 2.8 15.5 + - - +
302A ARG 3.5 2.0 - - - +
304A ALA* 1.3 78.5 - - - +
306A GLU* 1.3 60.5 + - - +
308A HIS* 3.2 9.2 + - - +
309A TYR* 3.0 24.4 + - - +
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Residues in contact with GLU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A SER* 2.3 41.6 + - - -
146A PRO* 5.2 0.7 - - - +
147A LEU* 3.6 30.2 - - + +
148A LEU* 3.7 13.9 - - + -
152A TYR* 5.8 0.4 - - - -
302A ARG* 3.0 51.5 + - - +
303A LYS* 4.4 2.9 - - - +
305A ASP* 1.3 73.6 - - - +
307A ASP* 1.3 60.8 + - - +
309A TYR* 3.2 3.7 + - - +
310A ARG* 2.8 45.6 + - - +
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Residues in contact with ASP 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A LYS* 3.3 23.5 + - - +
304A ALA* 4.0 6.5 - - - +
306A GLU* 1.3 73.3 - - - +
308A HIS* 1.3 57.9 + - - +
309A TYR 2.9 4.0 - - - -
310A ARG* 2.6 41.1 + - - +
311A GLU* 3.3 11.7 + - - +
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Residues in contact with HIS 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A ALA 3.3 13.7 + - - +
305A ASP* 3.2 14.6 - - - +
307A ASP* 1.3 79.2 - - - +
309A TYR* 1.3 57.2 + - - +
311A GLU* 2.9 29.8 + - - +
312A GLN* 2.8 31.8 + - - +
415F A 5.0 13.1 + - - -
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Residues in contact with TYR 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A LEU* 3.8 37.5 - - + -
148A LEU* 3.7 31.0 - - + -
305A ASP 3.0 12.0 + - - +
306A GLU 3.4 7.2 - - - +
307A ASP 2.9 1.0 - - - -
308A HIS* 1.3 74.3 - - - +
310A ARG* 1.3 58.0 + - + +
311A GLU 2.8 11.9 + - - -
312A GLN* 3.0 39.2 + - + +
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Residues in contact with ARG 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A LEU* 3.4 36.2 - - + +
306A GLU* 2.8 30.5 + - - +
307A ASP* 2.6 21.7 + - - +
309A TYR* 1.3 70.5 - - + +
311A GLU* 1.3 58.3 + - - +
312A GLN 3.6 0.9 - - - -
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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