Contacts of the helix formed by residues 314 - 327 (chain A) in PDB entry 2BEW
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 HIS 314 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A ASN* 5.0 4.4 + - - -
90A TYR* 5.2 2.4 - - - +
91A GLY 4.0 10.9 + - - -
93A GLU* 3.5 24.8 + - - -
256A ASN* 4.7 0.2 - - - -
288A ILE* 3.5 25.2 - - + +
309A TRP 3.7 5.6 - - - +
310A ASP* 3.6 25.4 + - - +
311A LYS 5.5 0.8 - - - -
312A GLN 4.0 0.6 - - - +
313A ASP* 1.3 76.0 + - - +
315A PRO* 1.3 73.9 - - + +
316A ILE* 3.0 45.3 + - + +
317A SER* 3.6 20.5 - - - +
318A ARG* 3.1 27.4 + - - +
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Residues in contact with PRO 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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37A MET* 5.5 0.9 - - - +
64A MET* 3.8 9.0 - - + +
91A GLY* 3.4 28.3 - - - +
93A GLU* 3.8 12.6 - - - +
94A GLY* 3.8 26.5 - - - +
255A GLY 5.2 0.2 - - - +
256A ASN* 3.4 38.3 - - - +
258A VAL* 5.1 3.2 + - + +
288A ILE* 5.5 0.2 - - + -
313A ASP 4.4 0.2 - - - +
314A HIS* 1.3 96.2 - - + +
316A ILE* 1.3 61.3 + - - +
318A ARG* 3.6 1.8 + - + +
319A LEU* 3.1 24.1 + - - +
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Residues in contact with ILE 316 (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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61A TYR* 3.8 7.0 - - + -
64A MET* 3.8 49.1 - - + +
65A THR* 3.7 16.2 - - + -
68A ASN* 4.1 13.7 - - + +
93A GLU* 3.9 16.4 - - - +
314A HIS* 3.0 28.4 + - + +
315A PRO* 1.3 74.3 - - - +
317A SER* 1.3 62.3 + - - +
319A LEU* 3.4 3.5 + - - +
320A ARG* 2.8 53.0 + - - +
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Residues in contact with SER 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ASP 4.9 2.9 + - - -
311A LYS 6.2 0.4 - - - -
314A HIS* 3.3 26.2 + - - +
316A ILE* 1.3 80.2 - - - +
318A ARG* 1.3 56.4 + - - +
320A ARG* 3.3 22.6 + - - +
321A HIS* 2.9 46.2 + - - -
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Residues in contact with ARG 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ARG* 4.3 3.4 - - - +
37A MET* 2.6 42.1 + - + +
38A ASP* 3.4 15.8 + - - +
39A ARG* 3.7 29.4 - - + +
41A GLY* 3.7 8.6 - - - +
254A ASP* 3.1 35.7 + - - -
256A ASN* 3.3 26.5 + - - +
257A ASP* 3.7 11.4 + - - +
313A ASP* 3.1 31.4 + - - -
314A HIS 3.1 17.1 + - - +
315A PRO 3.9 4.0 - - - +
317A SER* 1.3 77.0 - - - +
319A LEU* 1.3 61.8 + - - +
321A HIS* 3.3 11.1 + - - +
322A TYR* 3.2 18.7 + - - +
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Residues in contact with LEU 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A MET* 4.3 3.7 - - + +
57A VAL* 3.8 28.5 - - + -
60A LEU* 4.0 8.3 - - + -
61A TYR* 3.7 33.0 - - + +
64A MET* 3.4 32.5 - - + -
258A VAL* 3.9 24.5 - - + -
259A PHE* 4.5 7.9 - - + -
315A PRO 3.1 17.2 + - - +
316A ILE 3.8 3.4 - - - +
318A ARG* 1.3 73.5 - - - +
320A ARG* 1.3 67.8 + - - +
322A TYR* 3.2 9.9 + - + +
323A LEU* 3.0 26.2 + - + +
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Residues in contact with ARG 320 (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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61A TYR* 2.9 38.6 + - + +
65A THR* 4.5 4.0 - - - +
316A ILE* 2.8 35.6 + - - +
317A SER* 3.5 28.9 + - - +
319A LEU* 1.3 76.8 - - - +
321A HIS* 1.3 65.6 + - - +
323A LEU* 3.2 8.2 + - - +
324A LEU* 3.0 40.8 + - + +
329A TRP* 4.6 10.8 - - + -
334A GLU* 3.5 22.2 + - - -
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Residues in contact with HIS 321 (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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39A ARG 3.8 19.5 + - - -
40A GLN* 3.4 42.8 + - - +
41A GLY* 4.4 2.0 - - - -
42A GLN* 4.9 0.9 + - - -
317A SER* 2.9 38.5 + - - -
318A ARG 3.5 5.2 - - - +
319A LEU 3.3 0.2 - - - -
320A ARG* 1.3 80.3 - - - +
322A TYR* 1.3 62.3 + - - +
324A LEU* 3.5 19.1 + - + +
325A SER* 3.2 21.1 + - - -
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Residues in contact with TYR 322 (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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37A MET* 4.0 10.1 - - - -
41A GLY* 3.5 23.4 - - - +
43A ILE* 4.2 19.7 - - + -
49A ASP* 4.5 12.6 + - - -
51A HIS* 5.6 4.3 + - - -
52A LEU 5.3 2.3 + - - -
57A VAL* 4.1 12.1 - - + -
259A PHE* 3.7 39.2 - + + -
318A ARG 3.2 12.2 + - - +
319A LEU* 3.4 9.9 - - + +
321A HIS* 1.3 73.0 - - - +
323A LEU* 1.3 70.4 + - - +
325A SER* 2.6 25.6 + - - -
326A GLN* 3.2 43.0 + - + +
328A TRP* 3.9 21.6 - + - -
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Residues in contact with LEU 323 (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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57A VAL* 3.6 31.6 - - + +
58A LEU* 3.8 23.8 - - + -
61A TYR* 3.6 41.3 - - + -
319A LEU* 3.0 18.9 + - + +
320A ARG* 3.2 8.5 + - - +
322A TYR* 1.3 76.6 - - - +
324A LEU* 1.3 65.5 + - - +
326A GLN 3.2 6.6 + - - -
328A TRP* 2.9 42.4 + - + +
329A TRP* 3.7 25.4 - - + -
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Residues in contact with LEU 324 (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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320A ARG* 3.0 36.6 + - + +
321A HIS* 3.7 19.5 - - + +
323A LEU* 1.3 80.4 - - - +
325A SER* 1.3 60.6 + - - +
327A GLY* 3.1 13.5 + - - -
329A TRP* 3.4 42.2 - - + +
330A ASP* 3.9 12.6 - - - +
331A GLU* 5.1 2.0 - - + +
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Residues in contact with SER 325 (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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41A GLY 4.3 1.6 + - - -
42A GLN* 4.5 19.7 - - - -
321A HIS 3.2 11.8 + - - -
322A TYR* 2.6 30.2 + - - -
324A LEU* 1.3 75.4 - - - +
326A GLN* 1.3 77.9 + - - +
327A GLY 3.5 0.2 + - - -
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Residues in contact with GLN 326 (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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322A TYR* 3.2 46.6 + - + +
323A LEU 3.2 3.8 + - - +
325A SER* 1.3 98.2 + - - +
327A GLY* 1.3 58.5 + - - +
328A TRP* 3.2 46.8 + - + -
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Residues in contact with GLY 327 (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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54A LYS* 4.6 4.5 + - - -
324A LEU 3.1 14.6 + - - -
325A SER 3.3 1.2 + - - -
326A GLN* 1.3 79.5 - - - +
328A TRP* 1.3 63.4 + - - +
329A TRP 3.4 6.2 + - - -
333A GLN* 5.7 0.5 + - - -
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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