Contacts of the helix formed by residues 297 - 312 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138B LYS* 2.8 42.7 - - + +
139B SER* 3.5 9.4 - - - +
295B CYS* 4.1 4.1 - - - +
296B ALA* 1.3 84.9 - - - +
298B PRO* 1.3 63.8 - - - +
300B ARG* 3.6 31.0 + - - +
301B ASP* 3.4 23.2 + - - +
405E G 4.7 0.2 + - - -
406E C 3.7 21.1 - - - -
407E C 5.7 0.7 - - - -
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Residues in contact with PRO 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LYS 3.6 2.9 - - - +
140B ALA* 2.9 28.9 - - + +
141B THR 4.2 0.9 - - - +
143B THR* 3.5 13.9 - - + +
152B TYR* 3.3 42.5 - - + +
153B CYS 4.1 6.1 - - - +
154B GLN* 3.8 17.7 - - + -
295B CYS* 4.0 10.1 - - - +
296B ALA 3.9 0.2 - - - +
297B CYS* 1.3 84.7 - - - +
299B GLY* 1.3 54.5 + - - +
301B ASP* 3.0 0.9 + - - +
302B ARG* 2.5 39.0 + - - +
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Residues in contact with GLY 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B THR* 5.1 0.9 - - - -
137B ALA 2.8 32.0 + - - -
138B LYS* 2.7 14.3 + - - -
143B THR* 4.5 2.3 - - - +
298B PRO* 1.3 73.5 - - - +
300B ARG* 1.3 56.2 + - - -
302B ARG* 3.2 13.1 - - - +
303B LYS* 3.0 33.6 + - - +
411F G 5.9 0.2 - - - -
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Residues in contact with ARG 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LYS* 3.4 38.5 + - + +
295B CYS* 6.2 0.2 - - - +
297B CYS* 3.6 25.4 + - - +
298B PRO 3.3 0.4 - - - -
299B GLY* 1.3 75.1 - - - +
301B ASP* 1.3 77.4 + - - +
303B LYS* 3.9 6.0 - - - +
304B ALA* 3.4 22.4 + - + +
404E T 3.5 32.1 - - - +
405E G 2.7 49.9 + - - -
413F G 3.2 15.3 + - - -
414F C 4.3 1.6 - - - +
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Residues in contact with ASP 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B TYR* 3.3 23.3 - - + -
293B ARG* 2.4 38.5 + - - +
295B CYS* 3.1 23.1 - - - +
297B CYS 3.4 11.7 + - - +
298B PRO 3.0 3.3 + - - +
300B ARG* 1.3 103.2 + - - +
302B ARG* 1.3 59.4 + - - +
304B ALA* 3.6 4.0 + - - +
305B ASP* 3.0 27.2 + - - +
404E T 4.8 8.3 - - - +
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Residues in contact with ARG 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B SER 4.9 3.8 + - - -
136B THR* 2.9 39.0 - - - +
143B THR* 2.9 27.0 + - + +
144B TYR 2.6 27.6 + - - -
145B SER* 3.2 17.6 - - - +
146B PRO* 3.7 11.5 - - - +
152B TYR* 3.3 28.9 - - + -
298B PRO 2.5 17.7 + - - +
299B GLY* 3.2 14.8 - - - +
301B ASP* 1.3 71.6 - - - +
303B LYS* 1.3 86.6 + - + +
305B ASP* 3.1 1.7 + - - +
306B GLU* 3.0 43.6 + - - +
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Residues in contact with LYS 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B THR* 4.5 21.7 + - - +
299B GLY 3.0 15.4 + - - +
300B ARG* 3.9 7.9 - - - +
302B ARG* 1.3 90.5 - - - +
304B ALA* 1.3 61.4 + - - +
306B GLU* 3.5 7.1 + - - +
307B ASP* 3.2 36.2 + - - +
411F G 6.0 2.2 - - - -
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Residues in contact with ALA 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B ARG* 3.4 15.9 + - + +
301B ASP* 3.9 5.4 - - - +
302B ARG 3.2 0.4 - - - -
303B LYS* 1.3 77.7 - - - +
305B ASP* 1.3 66.3 + - - +
307B ASP* 3.2 15.8 + - - +
308B HIS* 3.2 27.2 + - + -
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Residues in contact with ASP 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B LEU* 4.8 8.4 - - + +
150B LYS* 3.6 21.1 + - + -
152B TYR* 2.4 41.5 + - - +
293B ARG* 4.8 10.9 + - - -
301B ASP 3.0 14.3 + - - +
302B ARG 3.1 0.9 + - - +
304B ALA* 1.3 77.7 - - - +
306B GLU* 1.3 62.3 + - - +
307B ASP 3.3 0.3 + - - -
308B HIS* 3.7 3.5 + - - +
309B TYR* 3.4 22.2 + - - +
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Residues in contact with GLU 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B SER* 2.6 31.7 + - - +
146B PRO* 3.7 13.5 - - - +
147B LEU* 3.9 24.2 - - + +
148B LEU* 3.6 15.7 - - + -
152B TYR* 5.5 0.2 - - - +
302B ARG* 3.0 38.2 + - - +
303B LYS* 4.1 5.9 - - - +
305B ASP* 1.3 76.2 - - + +
307B ASP* 1.3 60.0 + - - +
309B TYR* 4.0 2.0 - - - +
310B ARG* 3.0 34.3 + - - +
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Residues in contact with ASP 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B LYS* 3.2 28.1 + - - +
304B ALA* 3.2 11.7 + - - +
306B GLU* 1.3 76.4 - - - +
308B HIS* 1.3 68.8 + - + +
310B ARG* 3.0 22.1 + - - +
311B GLU* 2.9 24.2 + - - +
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Residues in contact with HIS 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B ALA* 3.2 24.1 + - + +
305B ASP* 4.4 2.9 - - - +
307B ASP* 1.3 80.3 - - + +
309B TYR* 1.3 61.1 + - - +
311B GLU* 3.6 7.6 + - - +
312B GLN 3.3 21.3 + - - -
403E A 5.9 0.8 + - - -
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Residues in contact with TYR 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B LEU* 3.4 43.7 + - + +
148B LEU* 4.7 22.0 - - + -
305B ASP 3.4 16.0 + - - +
306B GLU* 4.1 1.3 - - - +
307B ASP 3.3 0.6 - - - -
308B HIS* 1.3 74.1 - - - +
310B ARG* 1.3 81.3 + - - +
312B GLN* 3.1 20.5 + - - +
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Residues in contact with ARG 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B LEU* 5.0 14.4 - - + +
306B GLU* 3.0 24.7 + - - +
307B ASP* 3.6 20.6 + - - +
309B TYR* 1.3 90.2 - - + +
311B GLU* 1.3 65.3 + - + +
312B GLN* 2.3 18.2 + - - -
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Residues in contact with GLU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B ASP 2.9 10.8 + - - +
308B HIS* 3.9 8.3 - - - +
310B ARG* 1.3 91.2 - - + +
312B GLN* 1.3 74.2 + - + +
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Residues in contact with GLN 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B HIS 3.3 14.6 + - - -
309B TYR* 3.1 16.8 + - - +
310B ARG 2.3 13.4 + - - -
311B GLU* 1.3 85.5 - - + +
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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