Contacts of the helix formed by residues 294 - 305 (chain A) in PDB entry 3DVA
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 ASP 294 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A ARG* 2.8 45.2 + - - -
268A TYR* 3.1 24.7 + - + +
290A TRP 3.6 0.2 + - - -
291A ALA* 3.7 15.0 - - - +
292A LYS 3.1 1.7 - - - +
293A LYS* 1.3 75.3 - - - +
295A PRO* 1.3 67.7 - - - +
296A LEU* 3.0 13.4 + - - +
297A VAL* 2.9 39.9 + - + +
298A ARG* 3.5 6.4 + - - -
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Residues in contact with PRO 295 (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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53A MET* 4.8 4.7 - - - -
57A ARG* 4.1 1.8 - - - +
80A GLY 3.5 15.7 - - - +
82A GLU* 3.8 14.8 - - + +
83A ALA* 3.7 28.0 - - + +
236A MET* 3.4 45.8 - - + +
238A PRO* 4.1 6.0 - - + +
268A TYR* 4.4 0.7 - - - +
293A LYS 3.1 0.6 - - - +
294A ASP* 1.3 93.3 - - - +
296A LEU* 1.3 60.4 + - + +
298A ARG* 3.7 4.2 - - + +
299A PHE* 3.2 28.1 + - - +
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Residues in contact with LEU 296 (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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50A MET* 3.8 9.9 - - + +
53A MET* 3.5 41.3 - - + +
54A VAL* 3.8 18.8 - - + +
57A ARG* 3.6 49.4 - - + +
82A GLU* 5.1 2.0 - - + +
294A ASP* 3.0 13.1 + - - +
295A PRO* 1.3 79.3 - - + +
297A VAL* 1.3 58.4 + - + +
299A PHE* 4.8 1.1 - - - -
300A ARG* 2.9 54.6 + - - +
314A GLU* 5.5 0.2 - - - +
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Residues in contact with VAL 297 (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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28A GLU 4.4 4.7 - - - +
291A ALA 4.2 9.4 - - - +
292A LYS* 4.1 15.9 - - - +
294A ASP* 2.9 32.5 + - + +
296A LEU* 1.3 77.2 - - + +
298A ARG* 1.3 60.7 + - - +
300A ARG* 3.4 18.9 + - - +
301A LYS* 3.1 52.0 + - - +
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Residues in contact with ARG 298 (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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24A GLN* 4.3 2.4 - - - +
26A LEU* 3.2 29.0 + - + -
27A ASN 3.3 23.6 + - - +
28A GLU* 3.5 31.2 - - - +
30A GLY* 3.2 17.4 - - - +
234A ASP* 2.9 29.3 + - - -
236A MET* 3.2 29.2 + - - +
237A ASP* 3.7 7.5 - - - +
238A PRO* 4.5 4.3 - - + -
292A LYS 5.5 0.4 - - - +
293A LYS* 2.9 45.3 + - - +
294A ASP 3.5 2.8 + - - +
295A PRO 3.7 9.9 - - - +
297A VAL* 1.3 79.3 - - - +
299A PHE* 1.3 62.6 + - - +
301A LYS* 3.5 1.5 + - - -
302A PHE* 3.0 23.7 + - - +
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Residues in contact with PHE 299 (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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26A LEU* 4.0 14.4 - - + -
46A LEU* 3.5 38.6 - - + -
49A LEU* 4.0 14.4 - - + -
50A MET* 3.6 23.3 - - + -
53A MET* 3.3 24.0 - - + -
238A PRO* 3.9 22.0 - - + -
239A LEU* 3.9 25.6 - - + -
295A PRO 3.2 18.0 + - - +
296A LEU 4.4 0.9 - - - +
298A ARG* 1.3 79.4 - - - +
300A ARG* 1.3 64.3 + - - +
302A PHE* 3.8 12.7 - + - +
303A LEU* 3.2 32.8 + - + +
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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
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50A MET* 3.7 12.1 - - + +
296A LEU* 2.9 56.9 + - - +
297A VAL* 3.6 24.7 + - - +
299A PHE* 1.3 77.5 - - - +
301A LYS* 1.3 59.7 + - + +
303A LEU* 3.3 4.7 + - - +
304A GLU* 2.9 58.5 + - - +
309A TRP* 4.1 11.8 - - + +
314A GLU* 2.7 39.9 + - - -
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Residues in contact with LYS 301 (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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28A GLU 4.5 0.8 + - - -
29A GLU* 2.8 59.8 + - - +
30A GLY* 4.9 0.9 - - - -
297A VAL* 3.1 35.0 + - + +
298A ARG 3.8 2.2 - - - +
300A ARG* 1.3 75.8 - - + +
302A PHE* 1.3 65.1 + - - +
304A GLU* 3.9 11.5 - - - +
305A ALA* 3.0 27.2 + - - +
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Residues in contact with PHE 302 (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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26A LEU* 3.6 18.8 - - + -
30A GLY* 3.5 22.6 - - - +
32A VAL* 3.7 24.7 - - + -
38A MET* 4.6 9.0 - - + -
46A LEU* 4.5 13.5 - - + -
239A LEU* 3.9 20.0 - - + -
298A ARG 3.0 18.6 + - - +
299A PHE* 3.8 16.4 - + - +
300A ARG 3.2 0.2 - - - -
301A LYS* 1.3 78.5 - - - +
303A LEU* 1.3 76.6 + - + +
305A ALA* 3.9 4.4 + - - +
306A LYS* 3.3 51.4 + - + +
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Residues in contact with LEU 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 3.7 33.9 - - + +
47A LYS* 4.6 1.3 - - - +
50A MET* 3.6 34.3 - - + -
299A PHE* 3.2 29.3 + - + +
300A ARG 3.9 0.9 - - - +
302A PHE* 1.3 92.2 - - + +
304A GLU* 1.3 60.0 + - - +
305A ALA 3.2 0.4 - - - -
306A LYS* 3.0 14.8 + - + +
308A LEU* 2.9 45.3 + - + +
309A TRP* 3.7 25.6 - - + -
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Residues in contact with GLU 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* 2.9 43.2 + - - +
301A LYS* 4.0 11.5 - - - +
303A LEU* 1.3 76.0 - - - +
305A ALA* 1.3 60.7 + - - +
307A GLY* 3.2 11.7 + - - +
309A TRP* 3.7 33.7 - - + +
310A SER* 4.6 2.8 - - - -
311A GLU* 4.5 14.7 + - - +
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Residues in contact with ALA 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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301A LYS 3.0 17.7 + - - +
302A PHE* 4.2 6.1 - - - +
303A LEU 3.2 0.2 - - - -
304A GLU* 1.3 76.1 - - - +
306A LYS* 1.3 60.2 + - + +
307A GLY 3.3 1.5 + - - -
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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