Contacts of the helix formed by residues 302 - 310 (chain D) in PDB entry 1D2V
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 GLY 302 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298D PRO 2.9 19.1 + - - -
300D VAL 3.5 1.4 - - - -
301D LEU* 1.3 79.8 - - - +
303D PRO* 1.4 77.2 - - - +
304D THR 3.5 2.2 + - - -
305D ALA 3.6 0.2 + - - -
306D MET* 3.0 24.8 + - - +
486D LYS* 5.5 0.2 - - - -
487D ARG 3.7 6.5 - - - -
488D LYS 3.4 12.1 - - - -
489D GLY* 3.7 1.0 - - - -
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Residues in contact with PRO 303 (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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298D PRO 5.0 0.4 - - - +
302D GLY* 1.4 83.9 - - - +
304D THR* 1.3 64.8 + - - +
306D MET* 3.7 4.9 - - + +
307D ARG* 3.1 40.4 + - - +
487D ARG* 3.1 25.6 - - + +
488D LYS* 3.5 31.0 - - + +
2607D ACT 3.5 38.4 - - + +
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Residues in contact with THR 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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302D GLY 3.5 0.8 - - - -
303D PRO* 1.3 79.1 - - - +
305D ALA* 1.3 59.4 + - - +
307D ARG* 2.8 28.2 + - - +
308D LYS* 3.0 32.3 + - + +
486D LYS* 3.9 18.2 - - - +
487D ARG* 6.1 1.0 - - - -
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Residues in contact with ALA 305 (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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301D LEU* 3.4 33.5 - - + +
302D GLY 3.6 1.2 + - - -
303D PRO 3.5 0.4 - - - -
304D THR* 1.3 76.6 - - - +
306D MET* 1.4 60.2 + - - +
308D LYS* 4.2 3.8 - - - -
309D TYR* 2.9 48.0 + - + +
486D LYS* 3.9 13.8 - - - +
496D ALA* 3.9 22.0 - - + -
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Residues in contact with MET 306 (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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293D TYR* 4.1 19.7 - - + +
297D LEU 4.3 0.9 - - - -
298D PRO* 3.9 37.7 - - + -
301D LEU* 4.0 12.4 - - + +
302D GLY 3.0 20.7 + - - +
303D PRO* 3.7 6.3 - - + +
305D ALA* 1.4 73.9 - - - +
307D ARG* 1.3 66.5 + - + +
310D LEU* 3.0 78.5 + - + +
507D ARG* 5.7 1.3 - - - +
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Residues in contact with ARG 307 (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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303D PRO* 3.1 26.7 + - - +
304D THR* 2.8 43.8 + - - +
306D MET* 1.3 78.5 - - - +
308D LYS* 1.3 63.7 + - - +
310D LEU 4.9 1.6 - - - -
311D PRO* 3.8 19.9 - - - +
2607D ACT 2.8 28.1 + - - +
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Residues in contact with LYS 308 (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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304D THR* 3.0 19.5 + - + +
305D ALA* 3.7 6.1 - - - +
307D ARG* 1.3 84.0 - - - +
309D TYR* 1.3 95.4 + - + +
311D PRO* 3.9 6.8 - - - +
440D CYS 5.9 1.6 - - - -
504D ARG* 5.0 2.8 + - - -
4E MAN 2.8 64.7 + - - +
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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
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301D LEU* 5.2 1.3 - - + -
305D ALA* 2.9 40.5 + - + +
308D LYS* 1.3 109.6 - - + +
310D LEU* 1.3 60.7 + - + +
311D PRO* 3.5 4.5 - - - -
440D CYS 4.7 4.3 + - - -
442D LEU* 5.6 3.8 - - - +
486D LYS* 5.9 1.3 - - - -
493D PRO 4.7 2.2 + - - -
496D ALA* 3.7 13.7 - - + -
497D CYS* 3.2 37.8 - - + +
500D GLY* 3.7 22.9 - - - -
501D THR* 3.8 16.3 - - - -
504D ARG* 3.3 33.6 - - - +
3E BMA 3.8 21.2 + - - -
4E MAN 4.9 3.4 - - - -
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Residues in contact with LEU 310 (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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293D TYR* 3.9 13.9 - - + -
297D LEU* 3.7 28.5 - - + -
301D LEU* 4.4 10.3 - - + -
306D MET* 3.0 56.9 + - + +
307D ARG* 4.9 0.7 - - - -
309D TYR* 1.3 82.1 - - + +
311D PRO* 1.3 69.2 - - - +
500D GLY 4.3 4.5 - - - +
503D PHE* 4.4 4.3 - - + -
504D ARG* 3.4 36.6 - - + +
507D ARG* 3.8 20.3 + - - +
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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