Contacts of the helix formed by residues 297 - 312 (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 CYS 297 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138D LYS* 3.1 26.6 - - + +
139D SER* 3.3 21.8 - - - +
295D CYS* 4.1 2.6 - - - +
296D ALA* 1.3 77.0 - - - +
298D PRO* 1.3 66.8 - - - +
300D ARG* 3.2 44.2 + - - +
301D ASP* 3.8 15.8 + - - +
519H G 4.9 0.2 + - - -
520H C 3.4 20.4 - - - -
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Residues in contact with PRO 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D SER 3.8 0.7 - - - -
140D ALA 2.6 38.6 - - - +
141D THR 3.9 12.8 - - - +
142D TRP* 4.1 2.2 - - - -
143D THR* 4.2 6.1 - - - +
152D TYR* 3.5 35.4 - - + +
153D CYS 4.2 0.9 - - - +
154D GLN* 3.9 15.0 - - + +
295D CYS* 3.7 14.0 - - - +
297D CYS* 1.3 81.3 - - - +
299D GLY* 1.3 68.9 + - - +
300D ARG 3.2 2.3 + - - -
301D ASP 3.3 1.7 + - - -
302D ARG* 3.0 23.9 + - - +
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Residues in contact with GLY 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136D THR 4.7 3.1 - - - -
137D ALA 3.5 10.4 + - - -
138D LYS* 2.8 28.3 + - - -
143D THR* 4.2 13.1 + - - +
298D PRO* 1.3 74.9 - - - +
300D ARG* 1.3 61.6 + - - -
302D ARG* 3.6 4.8 - - - +
303D LYS* 3.0 28.1 + - - +
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Residues in contact with ARG 300 (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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138D LYS* 3.0 39.4 + - + +
297D CYS* 3.2 31.6 + - - +
298D PRO 3.2 0.4 + - - -
299D GLY* 1.3 75.1 - - - +
301D ASP* 1.3 77.5 + - - +
303D LYS* 3.0 15.5 - - + +
304D ALA* 2.9 26.8 + - + +
503G G 3.3 17.6 + - - -
504G C 4.8 2.4 - - - +
518H T 4.3 26.9 - - - +
519H G 2.9 50.7 + - - -
520H C 3.7 0.8 - - - +
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Residues in contact with ASP 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D TYR* 3.6 9.0 - - + -
293D ARG* 2.7 43.5 + - - +
295D CYS* 3.0 22.6 - - - +
297D CYS 3.8 7.0 + - - +
298D PRO 3.3 4.5 + - - +
300D ARG* 1.3 92.9 + - - +
302D ARG* 1.3 53.1 + - - +
304D ALA* 3.1 7.8 + - - +
305D ASP* 2.7 43.9 + - - +
517H A 6.0 1.0 - - - +
518H T 5.0 7.8 - - - +
519H G 4.7 2.4 + - - -
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Residues in contact with ARG 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D SER* 4.9 2.8 + - - -
143D THR* 3.7 21.0 - - - +
144D TYR 2.3 37.7 + - - +
145D SER* 3.7 22.4 - - - -
146D PRO* 4.1 13.1 - - - +
152D TYR* 3.1 25.3 - - + -
298D PRO 3.0 17.2 + - - +
299D GLY* 3.6 5.4 - - - +
301D ASP* 1.3 75.0 - - - +
303D LYS* 1.3 65.3 + - - +
305D ASP* 2.9 13.7 + - - +
306D GLU* 2.9 40.0 + - - +
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Residues in contact with LYS 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D LYS* 5.1 7.9 - - + -
299D GLY 3.0 14.8 + - - +
300D ARG* 3.0 30.3 - - + +
302D ARG* 1.3 81.8 - - - +
304D ALA* 1.3 57.0 + - + +
306D GLU* 4.6 7.4 - - - +
307D ASP* 2.5 56.6 + - - +
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Residues in contact with ALA 304 (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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300D ARG* 2.9 22.0 + - + +
301D ASP* 3.4 9.2 - - - +
303D LYS* 1.3 79.5 - - + +
305D ASP* 1.3 65.3 + - - +
307D ASP* 3.9 6.0 - - - +
308D HIS* 3.5 29.0 + - + +
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Residues in contact with ASP 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D LEU* 3.8 10.3 - - + -
150D LYS* 3.4 21.6 + - - +
152D TYR* 2.8 32.4 + - - +
293D ARG* 5.7 4.0 + - - -
301D ASP* 2.7 24.9 + - - +
302D ARG 2.9 4.5 + - - +
304D ALA* 1.3 76.8 - - - +
306D GLU* 1.3 60.9 + - - +
308D HIS* 4.4 1.4 - - - +
309D TYR* 3.3 31.6 + - + +
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Residues in contact with GLU 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D SER* 2.4 27.4 + - - +
146D PRO* 5.1 0.7 - - - +
147D LEU* 3.8 29.9 + - + +
148D LEU* 3.2 22.4 - - + -
302D ARG* 2.9 47.1 + - - +
303D LYS* 4.1 5.6 - - - +
305D ASP* 1.3 75.1 - - - +
307D ASP* 1.3 69.6 + - - +
309D TYR* 3.2 2.6 + - - +
310D ARG* 3.0 23.6 + - - +
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Residues in contact with ASP 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303D LYS* 2.5 56.5 + - - +
304D ALA* 3.9 8.2 - - - +
306D GLU* 1.3 77.1 - - - +
308D HIS* 1.3 64.3 + - + +
310D ARG* 3.2 16.5 - - - +
311D GLU* 3.3 8.2 + - - +
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Residues in contact with HIS 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304D ALA* 3.5 16.4 + - + +
305D ASP* 4.6 1.6 - - - +
306D GLU 3.3 0.2 - - - -
307D ASP* 1.3 79.2 - - + +
309D TYR* 1.3 56.5 + - + +
310D ARG 3.1 1.8 - - - -
311D GLU* 3.2 26.8 + - - +
312D GLN* 2.7 44.4 + - + +
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Residues in contact with TYR 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D LEU* 6.0 4.5 - - + -
148D LEU* 4.0 27.1 - - + -
150D LYS* 6.0 1.3 - - - -
305D ASP* 3.3 22.9 + - + +
306D GLU* 3.2 7.5 + - - +
308D HIS* 1.3 74.9 - - + +
310D ARG* 1.3 72.4 + - - +
312D GLN* 3.8 24.6 + - + +
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Residues in contact with ARG 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D LEU* 5.3 22.5 - - + +
306D GLU 3.0 11.8 + - - +
307D ASP* 3.2 13.5 - - - +
309D TYR* 1.3 85.3 + - - +
311D GLU* 1.3 60.1 + - - +
312D GLN 4.7 1.2 - - - -
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Residues in contact with GLU 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307D ASP 3.3 8.0 + - - +
308D HIS* 3.2 32.4 + - - +
310D ARG* 1.3 82.5 - - - +
312D GLN* 1.3 61.4 + - - +
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Residues in contact with GLN 312 (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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308D HIS* 2.7 29.9 + - + +
309D TYR* 4.1 24.0 - - + -
310D ARG 3.5 1.5 - - - -
311D GLU* 1.3 78.6 + - - +
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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