Contacts of the helix formed by residues 300 - 313 (chain B) 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 300 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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285B TYR* 4.3 18.6 + - - -
301B GLU* 1.3 60.4 + - - +
302B GLU* 4.3 19.4 - - - +
303B ALA* 3.3 25.2 + - + +
304B LYS* 3.0 51.2 + - - +
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Residues in contact with GLU 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B GLU* 1.3 75.1 - - - +
302B GLU* 1.3 64.2 + - + +
304B LYS* 4.1 5.5 - - - +
305B LEU* 3.5 22.7 + - - +
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Residues in contact with GLU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B GLN* 4.4 14.4 + - - +
283B PRO* 3.4 37.4 - - + +
284B ARG* 4.0 11.6 + - - -
285B TYR* 3.4 47.0 + - + +
300B GLU* 3.3 12.1 - - - +
301B GLU* 1.3 79.0 - - + +
303B ALA* 1.3 62.1 + - - +
304B LYS 3.6 0.2 + - - -
305B LEU* 3.8 6.7 + - - +
306B MET* 3.7 23.9 + - - +
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Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282B GLN* 5.3 3.1 - - - +
300B GLU* 3.3 26.6 + - + +
302B GLU* 1.3 77.1 - - - +
304B LYS* 1.3 62.2 + - + +
306B MET* 3.4 7.1 + - - +
307B LYS* 3.0 28.9 + - - +
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Residues in contact with LYS 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B GLU 3.0 35.4 + - - +
301B GLU* 4.3 5.4 - - - +
302B GLU 3.4 0.2 - - - -
303B ALA* 1.3 75.2 - - + +
305B LEU* 1.3 55.4 + - - +
307B LYS* 3.2 6.4 + - + +
308B SER* 2.8 43.0 + - - +
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Residues in contact with LEU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B PRO* 5.0 6.3 - - + -
242B ALA* 3.8 29.2 - - + -
253B PRO* 4.5 12.3 - - + +
254B LEU* 3.7 42.2 - - + +
283B PRO* 6.1 0.9 - - + -
301B GLU 3.5 15.3 + - - +
302B GLU* 4.1 6.5 - - - +
304B LYS* 1.3 77.6 - - - +
306B MET* 1.3 68.7 + - + +
308B SER* 3.2 6.8 + - - -
309B LEU* 3.0 48.8 + - + +
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Residues in contact with MET 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B VAL* 3.6 45.1 - - + +
282B GLN* 3.8 42.2 - - + +
302B GLU 3.7 13.2 + - - +
303B ALA* 3.4 10.2 + - - +
304B LYS 3.3 0.2 - - - -
305B LEU* 1.3 83.0 - - + +
307B LYS* 1.3 62.4 + - - +
309B LEU* 3.4 5.0 + - - -
310B ARG* 3.1 19.2 + - - +
317B PHE* 3.7 22.0 - - + -
319B SER* 3.7 27.6 - - - +
336B ASP 5.5 1.1 - - - -
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Residues in contact with LYS 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B ALA 3.0 18.4 + - - +
304B LYS* 3.6 7.2 - - + +
306B MET* 1.3 76.5 - - - +
308B SER* 1.3 57.3 + - - +
310B ARG* 3.3 8.6 - - + +
311B MET* 3.0 61.2 + - + +
334B GLN 3.5 16.0 + - - -
335B GLY* 3.6 13.7 + - - -
336B ASP* 3.1 39.7 + - - +
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Residues in contact with SER 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254B LEU* 4.3 17.7 - - - +
258B LEU* 4.4 5.5 - - - +
304B LYS* 2.8 29.7 + - - +
305B LEU* 3.5 7.6 - - - -
307B LYS* 1.3 74.2 - - - +
309B LEU* 1.3 63.0 + - - +
311B MET* 3.4 18.8 + - - +
312B ALA* 3.2 23.6 + - - +
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Residues in contact with LEU 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B VAL* 5.8 1.3 - - + -
241B PRO* 4.2 21.1 - - + -
254B LEU* 4.7 0.9 - - + -
257B GLY* 3.5 35.2 - - - +
258B LEU* 3.6 19.3 - - + +
261B VAL* 3.9 11.6 - - + +
278B LEU* 6.0 0.2 - - + -
280B VAL* 4.3 21.3 - - + -
305B LEU* 3.0 41.5 + - + +
306B MET* 3.8 6.5 - - - +
307B LYS 3.3 0.2 - - - -
308B SER* 1.3 73.2 - - - +
310B ARG* 1.3 61.9 + - - +
312B ALA* 3.4 2.2 + - - -
313B TYR* 3.0 30.3 + - - +
317B PHE* 3.9 10.9 - - + -
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Residues in contact with ARG 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B MET 3.1 10.9 + - - +
307B LYS* 3.3 20.2 - - + +
309B LEU* 1.3 73.4 - - - +
311B MET* 1.3 76.1 + - + +
313B TYR* 3.2 18.6 + - - +
315B GLY 3.8 13.8 + - - +
317B PHE* 3.5 42.7 - - + +
335B GLY* 2.7 43.7 + - - -
336B ASP* 3.2 14.8 - - - +
337B ALA 3.8 5.8 - - - +
338B ASP* 3.0 40.8 + - - -
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Residues in contact with MET 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B LYS* 3.0 45.2 + - + +
308B SER* 3.6 22.0 - - - +
310B ARG* 1.3 90.7 - - + +
312B ALA* 1.3 61.2 + - - +
313B TYR 4.1 3.3 - - - +
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Residues in contact with ALA 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B LEU* 4.0 18.4 - - + -
261B VAL* 3.6 16.6 - - + +
265B ASN* 2.8 19.6 + - - -
308B SER 3.2 13.8 + - - +
309B LEU 4.0 2.2 - - - +
311B MET* 1.3 81.8 - - - +
313B TYR* 1.3 58.5 + - - +
314B ASN* 3.4 1.0 + - - +
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Residues in contact with TYR 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261B VAL* 3.5 14.6 - - + +
264B LEU* 4.7 17.7 - - + -
265B ASN* 3.5 15.7 - - - +
268B GLN* 3.0 32.1 + - - -
275B LEU* 3.8 19.6 + - + +
277B TYR* 3.9 1.1 - - - -
278B LEU* 3.8 41.0 + - + -
309B LEU 3.0 18.5 + - - +
310B ARG* 3.2 13.4 + - - +
311B MET 3.4 3.3 - - - +
312B ALA* 1.3 75.0 - - - +
314B ASN* 1.3 64.8 + - - +
315B GLY* 3.2 30.1 + - - +
316B THR 3.2 25.1 + - - -
317B PHE* 4.6 7.6 - + + -
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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