Contacts of the helix formed by residues 302 - 313 (chain A) in PDB entry 2G5W
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 GLU 302 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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303A ALA* 1.3 78.6 + - + +
304A LYS* 3.0 24.9 - - + +
305A LEU* 3.1 37.8 + - - +
306A MET* 4.1 3.1 + - - +
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Residues in contact with ALA 303 (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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282A GLN* 5.2 8.5 - - - +
302A GLU* 1.3 87.6 + - + +
304A LYS* 1.3 63.3 + - - +
305A LEU 3.3 0.4 - - - -
306A MET* 3.6 12.4 + - - +
307A LYS* 3.4 37.0 + - - +
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Residues in contact with LYS 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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302A GLU* 4.2 17.5 - - + +
303A ALA* 1.3 76.4 - - - +
305A LEU* 1.3 51.7 + - - +
306A MET 3.3 0.2 + - - -
307A LYS* 3.3 15.3 + - + +
308A SER* 2.7 44.8 + - - +
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Residues in contact with LEU 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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241A PRO* 5.0 5.2 - - + -
242A ALA* 3.8 29.4 - - + +
253A PRO* 4.3 16.8 - - + +
254A LEU* 3.7 44.6 - - + +
302A GLU 3.1 24.6 + - - +
304A LYS* 1.3 78.8 - - - +
306A MET* 1.3 66.2 + - + +
308A SER* 3.4 1.7 + - - -
309A LEU* 3.1 49.3 + - + +
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Residues in contact with MET 306 (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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280A VAL* 3.5 37.5 - - + +
281A THR 4.8 2.0 - - - +
282A GLN* 3.2 48.0 - - + +
302A GLU 5.0 4.9 - - - +
303A ALA* 3.6 9.5 + - - +
304A LYS 3.2 0.6 - - - -
305A LEU* 1.3 79.8 - - + +
307A LYS* 1.3 66.8 + - + +
308A SER 3.1 0.5 + - - -
309A LEU* 3.1 8.9 + - - +
310A ARG* 3.1 21.8 + - - +
317A PHE* 4.1 13.5 - - + -
319A SER* 3.6 31.2 - - - -
320A SER 4.7 0.2 - - - +
323A PHE* 5.6 0.4 - - + -
336A ASP 5.8 0.7 - - - -
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Residues in contact with LYS 307 (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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303A ALA* 3.4 24.6 + - - +
304A LYS* 3.3 18.3 + - + +
306A MET* 1.3 79.2 - - + +
308A SER* 1.3 60.8 + - - +
310A ARG* 3.4 8.2 + - - +
311A MET* 3.2 43.0 + - + +
334A GLN* 4.2 9.5 - - - +
336A ASP* 3.4 43.2 + - + +
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Residues in contact with SER 308 (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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254A LEU* 4.0 21.6 - - - +
258A LEU* 4.2 8.1 - - - +
304A LYS* 2.7 30.4 + - - +
305A LEU 3.5 6.3 - - - -
306A MET 3.1 0.2 - - - -
307A LYS* 1.3 70.9 - - - +
309A LEU* 1.3 66.7 + - - +
311A MET* 3.5 11.1 + - - +
312A ALA* 3.2 23.5 + - - +
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Residues in contact with LEU 309 (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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239A VAL* 5.7 1.1 - - + -
241A PRO* 4.1 20.2 - - + -
254A LEU* 4.4 2.0 - - + +
257A GLY* 3.6 31.4 - - - +
258A LEU* 3.6 17.5 - - + +
261A VAL* 4.0 13.2 - - + +
280A VAL* 4.2 25.4 - - + -
305A LEU* 3.1 35.0 - - + +
306A MET* 3.1 6.6 + - - +
308A SER* 1.3 76.0 - - - +
310A ARG* 1.3 56.2 + - - +
312A ALA* 3.3 6.0 + - - +
313A TYR* 2.9 32.1 + - - +
317A PHE* 4.1 10.0 - - + -
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Residues in contact with ARG 310 (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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306A MET 3.1 11.7 + - - +
307A LYS* 3.5 13.0 - - - +
308A SER 3.2 0.2 - - - -
309A LEU* 1.3 74.0 - - - +
311A MET* 1.3 70.0 + - - +
312A ALA 3.2 0.7 + - - -
313A TYR* 3.3 20.7 + - - +
315A GLY 3.8 10.5 + - - -
317A PHE* 3.6 33.4 - - + +
335A GLY* 2.6 29.7 + - - -
336A ASP* 3.0 22.4 + - - +
337A ALA 3.8 3.0 + - - -
338A ASP* 2.8 51.4 + - - +
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Residues in contact with MET 311 (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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307A LYS* 3.2 32.1 + - + +
308A SER* 3.9 7.6 - - - +
310A ARG* 1.3 84.3 - - - +
312A ALA* 1.3 60.7 + - - +
313A TYR 3.6 3.8 + - - +
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Residues in contact with ALA 312 (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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258A LEU* 3.5 24.9 - - + -
261A VAL* 3.4 10.1 - - + +
265A ASN* 2.7 30.7 + - - -
308A SER 3.2 15.4 + - - +
309A LEU 3.5 4.3 - - - +
310A ARG 3.1 0.8 - - - -
311A MET* 1.3 80.2 - - - +
313A TYR* 1.3 53.0 + - - +
314A ASN* 5.1 0.2 - - - +
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Residues in contact with TYR 313 (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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261A VAL* 3.5 15.3 - - + -
264A LEU* 4.3 15.9 - - + -
265A ASN* 3.5 15.9 - - - -
268A GLN* 3.0 31.9 + - - -
274A LYS* 5.4 0.2 - - - +
275A LEU* 3.7 23.1 + - + +
277A TYR* 4.2 3.8 - - - -
278A LEU* 3.8 35.4 - - + -
309A LEU 2.9 15.9 + - - +
310A ARG* 3.3 13.8 + - - +
311A MET 4.2 3.5 - - - +
312A ALA* 1.3 76.1 - - - +
314A ASN* 1.3 59.8 + - - +
315A GLY* 3.2 36.6 + - - +
316A THR 3.1 26.9 - - - -
317A PHE* 4.8 5.6 - + + -
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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