Contacts of the helix formed by residues 291 - 298 (chain C) in PDB entry 2GD4
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 SER 291 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289C GLU 3.9 1.7 + - - -
290C LYS* 1.3 76.7 - - - +
292C LEU* 1.3 54.6 + - - +
293C ALA* 2.5 25.1 + - - +
294C LYS* 2.6 32.4 + - - +
295C VAL 3.4 5.5 + - - -
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Residues in contact with LEU 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242C ALA* 6.2 2.0 - - + -
286C PRO* 4.1 21.4 - - + +
290C LYS 3.9 2.8 + - - -
291C SER* 1.3 69.2 - - - +
293C ALA* 1.3 59.3 + - - +
295C VAL* 3.5 12.1 - - + +
296C GLU* 3.0 26.6 + - - +
407C PRO* 3.6 52.4 - - + +
408C PHE* 3.7 4.3 - - - +
409C LEU* 3.7 28.9 - - + +
425C ARG* 3.8 31.0 - - + +
426C VAL 4.9 0.2 - - - +
427C ALA* 5.9 0.9 - - + -
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Residues in contact with ALA 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C ASP* 4.6 19.1 - - + +
291C SER* 2.5 14.0 + - - +
292C LEU* 1.3 71.4 - - - +
294C LYS* 1.3 53.9 + - - +
295C VAL 3.0 1.3 - - - -
296C GLU* 2.5 35.7 + - - +
297C LYS* 2.6 19.2 + - - -
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Residues in contact with LYS 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290C LYS* 3.6 23.1 - - + +
291C SER* 2.6 27.9 + - - +
293C ALA* 1.3 73.7 - - - +
295C VAL* 1.3 51.6 + - - +
297C LYS* 3.6 15.1 - - + +
298C GLU* 2.7 61.1 + - - +
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Residues in contact with VAL 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265C GLU* 4.0 2.7 - - - +
267C THR* 4.0 31.2 - - + +
284C ILE* 5.0 1.8 - - + -
286C PRO* 4.2 11.2 - - + -
290C LYS* 4.5 4.4 - - + +
291C SER 3.4 2.4 + - - -
292C LEU* 3.5 21.3 - - + +
293C ALA 3.0 0.2 - - - -
294C LYS* 1.3 78.4 - - - +
296C GLU* 1.3 59.0 + - - +
298C GLU* 3.2 22.0 - - - +
299C LEU* 2.9 29.0 + - + +
307C TRP* 4.2 17.0 - - + -
409C LEU* 3.7 29.2 - - + -
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Residues in contact with GLU 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C TYR* 2.4 49.8 + - + +
64C GLN* 3.3 22.3 + - - +
67C ALA* 3.9 10.1 - - + +
72C ASP* 5.7 0.2 - - - +
292C LEU* 3.0 30.5 + - - +
293C ALA* 2.5 20.9 + - - +
295C VAL* 1.3 76.3 - - + +
297C LYS* 1.3 63.1 + - - +
299C LEU* 3.4 13.2 + - + +
409C LEU* 4.1 12.3 - - + -
425C ARG* 3.2 27.6 + - - -
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Residues in contact with LYS 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C GLN* 3.1 19.4 + - - +
293C ALA* 2.6 16.4 + - + +
294C LYS* 3.6 24.5 - - + +
296C GLU* 1.3 72.5 - - - +
298C GLU* 1.3 58.0 + - - +
299C LEU 3.3 0.2 - - - -
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Residues in contact with GLU 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265C GLU* 3.1 31.4 - - - +
290C LYS* 3.4 14.5 + - - -
294C LYS* 2.7 47.4 + - - +
295C VAL* 3.2 18.7 - - + +
297C LYS* 1.3 76.7 - - - +
299C LEU* 1.3 61.0 + - - +
300C THR* 3.3 15.2 - - - +
303C VAL* 4.2 6.8 - - + +
307C TRP* 5.7 3.2 - - + -
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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