Contacts of the helix formed by residues 335 - 341 (chain D) in PDB entry 1C2O
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 335 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333D ASP 3.2 1.0 + - - -
334D GLU* 1.3 78.3 - - - +
336D SER* 1.3 64.3 + - - +
337D TYR 3.5 0.2 - - - -
338D PHE* 3.4 15.6 + - - +
339D LEU* 3.5 14.6 + - - +
399D SER* 3.4 22.9 + - - -
402D VAL* 3.9 9.8 - - - +
403D GLY* 3.3 17.9 - - - -
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Residues in contact with SER 336 (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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333D ASP* 2.5 27.1 + - - -
335D GLY* 1.3 71.9 - - - +
337D TYR* 1.3 68.0 + - - +
339D LEU* 2.8 21.8 + - - +
399D SER* 3.3 20.3 + - - -
442D TRP* 4.1 8.8 - - - -
443D MET* 3.2 50.7 + - - +
446D PRO* 3.6 7.4 - - - +
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Residues in contact with TYR 337 (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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83D THR* 4.9 1.6 - - - +
86D TRP* 3.7 32.0 - + - +
124D TYR* 5.8 0.3 + - - -
334D GLU 4.0 2.9 + - - +
335D GLY 3.5 0.8 - - - -
336D SER* 1.3 77.5 + - - +
338D PHE* 1.3 90.7 + + + +
339D LEU 2.9 7.3 + - - -
340D VAL* 3.0 25.3 - - - +
341D TYR* 3.8 26.2 + + - -
439D TRP* 3.2 43.1 - + - -
443D MET* 3.6 10.9 - - - +
446D PRO* 4.4 13.8 - - + +
447D HIS* 4.5 11.9 - + + +
449D TYR* 4.5 8.7 - + - -
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Residues in contact with PHE 338 (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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203D SER* 5.4 0.9 - - - -
294D ILE* 3.5 27.5 - - + +
295D PHE* 3.1 64.4 - + + -
297D PHE* 4.5 11.9 - + - -
334D GLU 3.7 23.1 - - - -
335D GLY* 3.8 9.6 - - - +
336D SER 3.3 0.4 - - - -
337D TYR* 1.3 87.3 - + - +
339D LEU* 1.3 62.3 + - - +
341D TYR* 3.5 16.3 + + + +
402D VAL* 4.3 11.0 - - + -
447D HIS* 3.6 33.0 - + + -
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Residues in contact with LEU 339 (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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294D ILE* 3.9 10.1 - - + -
335D GLY 3.5 10.1 - - - +
336D SER* 2.8 13.4 + - - +
338D PHE* 1.3 77.8 - - - +
340D VAL* 1.3 62.6 + - - +
341D TYR 3.2 0.3 + - - -
343D VAL* 3.0 37.1 + - + +
346D PHE* 3.6 43.2 - - + +
395D ARG 4.6 0.2 - - - +
398D MET* 4.0 12.1 - - + +
399D SER* 3.5 36.6 - - - +
402D VAL* 3.6 30.5 - - + -
442D TRP* 4.5 4.9 - - + -
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Residues in contact with VAL 340 (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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76D LEU* 4.0 16.4 - - + +
77D TYR* 4.4 12.8 + - + +
337D TYR 3.0 20.0 - - - +
339D LEU* 1.3 76.8 - - - +
341D TYR* 1.3 81.8 + - + +
342D GLY 3.1 6.2 + - - -
346D PHE* 4.3 15.5 - - - +
347D SER 4.1 5.6 - - - -
348D LYS* 4.0 22.0 - - + +
439D TRP* 4.4 14.1 - - + -
442D TRP* 4.4 4.9 - - + -
443D MET* 3.4 27.1 - - + -
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Residues in contact with TYR 341 (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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74D ASP* 3.0 39.0 + - - -
76D LEU* 3.3 22.9 - - + -
83D THR* 3.2 16.6 - - - +
124D TYR* 5.8 3.4 - - - -
293D SER 4.9 1.4 - - - +
294D ILE* 3.5 13.9 - - + +
337D TYR* 3.8 40.3 + + - -
338D PHE* 3.5 17.9 + + + +
339D LEU 3.1 2.1 - - - -
340D VAL* 1.3 108.3 - - + +
342D GLY* 1.3 54.8 + - - -
439D TRP* 4.6 2.5 - + - -
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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