Contacts of the helix formed by residues 302 - 316 (chain A) in PDB entry 2MWI
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 TRP 302 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A TRP* 4.9 18.8 - + + -
300A PRO* 3.4 27.0 - - + +
301A SER* 1.3 102.1 - - - +
303A MET* 1.3 62.1 + - - +
305A GLU* 2.9 28.5 - - - +
306A LYS* 3.9 7.7 + - - +
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Residues in contact with MET 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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242A TYR* 4.5 4.7 - - - +
248A ASP* 3.1 29.6 - - - +
251A TRP* 4.0 23.7 - - + -
252A LEU* 3.6 21.3 - - + +
268A LEU* 4.0 15.0 - - - -
297A PHE* 4.4 3.1 - - + -
299A LEU* 3.2 43.3 - - + -
300A PRO* 3.5 25.4 + - + +
302A TRP* 1.3 73.7 - - - +
304A VAL* 1.3 66.1 + - - +
305A GLU 3.0 2.0 - - - -
306A LYS* 2.9 27.5 - - - +
307A MET* 3.0 8.9 + - + +
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Residues in contact with VAL 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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213A PHE* 5.5 1.8 - - + -
299A LEU* 3.5 26.7 - - + +
300A PRO 2.9 25.3 + - - +
301A SER* 3.3 23.3 - - - +
303A MET* 1.3 76.9 - - - +
305A GLU* 1.3 60.3 + - + +
307A MET* 3.5 23.2 - - + +
308A ARG* 2.7 38.7 + - + +
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Residues in contact with GLU 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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301A SER 2.9 21.2 - - - +
302A TRP* 2.9 26.0 - - - +
303A MET 2.9 0.2 + - - -
304A VAL* 1.3 81.1 - - - +
306A LYS* 1.3 62.5 + - + +
308A ARG* 3.5 4.1 + - - +
309A LYS* 3.4 24.9 + - + +
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Residues in contact with LYS 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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242A TYR* 3.0 21.5 - - - +
245A ASP* 5.7 2.0 - - + -
247A GLN* 5.7 3.5 - - - +
248A ASP* 2.9 35.4 - - - +
251A TRP* 3.9 16.6 - - - -
302A TRP 3.9 4.9 + - - +
303A MET* 2.9 28.0 - - - +
305A GLU* 1.3 79.5 - - - +
307A MET* 1.3 58.7 + - - +
308A ARG 3.2 0.2 - - - -
309A LYS* 3.3 16.6 - - + +
310A TYR* 2.9 31.7 + - - +
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Residues in contact with MET 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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210A SER* 5.0 5.6 - - - +
213A PHE* 3.4 36.6 - - + -
240A PHE* 4.6 12.1 - - - -
242A TYR* 3.6 34.1 - - + -
299A LEU* 3.8 19.1 - - + -
303A MET 3.0 13.2 + - - +
304A VAL* 3.1 25.5 + - + +
306A LYS* 1.3 79.9 - - - +
308A ARG* 1.3 63.3 + - + +
310A TYR* 3.8 1.9 - - - +
311A MET* 3.1 26.8 + - - +
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Residues in contact with ARG 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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304A VAL* 2.7 21.9 + - + +
305A GLU* 3.8 4.5 - - - +
306A LYS 3.2 0.2 - - - -
307A MET* 1.3 79.3 - - + +
309A LYS* 1.3 66.3 + - - +
310A TYR 3.0 2.0 + - - -
311A MET* 3.2 6.5 + - - +
312A GLU* 3.2 28.4 + - + +
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Residues in contact with LYS 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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305A GLU 3.4 15.1 + - - +
306A LYS* 3.3 22.6 - - + +
308A ARG* 1.3 79.2 - - - +
310A TYR* 1.3 63.7 + - - +
312A GLU* 3.5 20.8 - - - +
313A THR* 3.7 9.2 - - - +
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Residues in contact with TYR 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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240A PHE* 4.4 3.4 - + - -
241A LYS 3.5 22.5 + - - -
242A TYR* 3.5 31.0 - + + -
243A ALA* 4.2 20.1 + - + +
245A ASP* 6.2 0.2 - - - -
267A TYR* 5.1 2.6 + - - -
306A LYS 2.9 21.7 + - - +
307A MET 3.8 3.8 - - - +
309A LYS* 1.3 76.1 - - + +
311A MET* 1.3 67.8 + - + +
312A GLU 3.1 1.8 - - - -
313A THR* 2.5 42.5 + - + +
314A LEU* 3.3 23.0 - - + +
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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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240A PHE* 3.3 35.2 - - + -
307A MET* 3.1 18.9 + - - +
308A ARG* 3.2 5.8 + - - +
310A TYR* 1.3 80.4 - - - +
312A GLU* 1.3 51.1 + - + +
314A LEU* 2.8 35.6 + - + +
315A ARG* 2.7 82.4 + - + +
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Residues in contact with GLU 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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308A ARG* 3.3 18.2 - - + +
309A LYS* 3.5 16.8 - - - +
310A TYR 3.1 0.2 - - - -
311A MET* 1.3 77.5 - - - +
313A THR* 1.3 56.9 + - - +
315A ARG* 3.9 20.2 - - - +
316A THR* 2.9 49.6 + - - +
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Residues in contact with THR 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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309A LYS 3.7 11.9 - - - +
310A TYR* 2.5 32.6 + - + +
312A GLU* 1.3 77.4 - - + +
314A LEU* 1.3 66.0 + - - +
315A ARG 3.3 0.2 - - - -
316A THR 3.5 15.1 - - - +
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Residues in contact with LEU 314 (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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240A PHE* 3.5 35.4 - - + -
241A LYS* 5.0 4.3 - - + +
310A TYR* 3.3 37.9 - - + +
311A MET* 2.8 26.3 + - + +
313A THR* 1.3 92.9 + - - +
315A ARG* 1.3 59.5 + - - +
316A THR 4.9 0.7 - - - -
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Residues in contact with ARG 315 (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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209A GLU* 4.9 10.1 + - - -
311A MET* 2.7 46.2 + - + +
312A GLU* 3.9 22.9 - - - +
314A LEU* 1.3 81.0 - - - +
316A THR* 1.3 75.8 + - + +
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Residues in contact with THR 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A GLU* 2.9 38.0 + - - +
313A THR* 3.5 14.5 - - - +
314A LEU 4.9 0.5 - - - -
315A ARG* 1.3 92.4 + - + +
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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