Contacts of the helix formed by residues 256 - 260 (chain A) in PDB entry 1EJI
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 256 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A SER 4.8 0.7 - - - -
119A SER* 4.2 1.8 - - - -
233A SER* 4.1 2.1 + - - -
254A THR* 3.4 32.5 + - + +
255A THR* 1.3 85.3 + - - +
257A LYS* 1.3 81.9 + - + +
259A LEU* 3.5 8.1 + - - +
260A ARG* 4.2 0.7 - - - +
261A GLY 3.8 20.4 - - - +
262A CYS 4.3 4.0 - - - +
263A ARG* 3.5 46.4 + - + +
264A ALA 3.9 8.1 - - - -
500A PLG 3.7 10.8 + - - -
70B ASN* 5.8 1.8 - - - +
73B TYR* 3.4 37.1 + + - -
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Residues in contact with LYS 257 (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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52A ALA 5.3 2.2 - - - +
53A SER* 3.1 33.5 + - - +
54A GLU* 4.7 1.9 - - - +
55A ASN* 3.0 31.0 + - - +
230A ALA* 3.4 24.0 - - - +
231A HIS* 3.4 19.0 + - + +
254A THR* 3.5 19.2 + - - +
256A HIS* 1.3 82.8 - - + +
258A THR* 1.3 63.9 + - + +
259A LEU 2.9 10.0 + - - -
260A ARG* 3.0 9.9 + - - +
406A PRO* 5.2 1.3 - - - -
500A PLG 2.8 55.8 + - - -
73B TYR* 3.7 16.4 - - - -
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Residues in contact with THR 258 (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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52A ALA 5.5 0.9 - - - +
55A ASN* 4.4 7.2 - - - +
231A HIS 2.9 22.7 + - - +
232A ILE 3.4 0.7 - - - -
233A SER* 3.2 14.0 + - - -
234A GLY* 2.7 40.4 + - - -
235A LEU* 4.1 14.1 - - + -
257A LYS* 1.3 79.4 - - + +
259A LEU* 1.3 56.6 + - - +
260A ARG* 3.4 0.7 - - - -
324A PHE* 3.8 3.5 - - - -
327A TYR* 4.7 2.5 - - - -
328A GLN* 3.4 18.9 + - - +
357A HIS* 3.9 24.7 - - + -
406A PRO* 3.9 12.3 - - + -
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Residues in contact with LEU 259 (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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104A TYR* 3.6 23.8 - - + +
233A SER* 3.5 18.6 - - - +
234A GLY* 3.9 17.5 - - - -
237A ALA* 4.6 2.7 - - + -
254A THR 4.4 0.2 - - - +
255A THR* 3.4 29.8 - - + +
256A HIS 3.5 2.6 + - - +
257A LYS 2.9 1.0 - - - -
258A THR* 1.3 79.0 + - - +
260A ARG* 1.3 71.4 + - - +
261A GLY* 3.3 1.6 + - - -
266A MSE 4.3 17.0 - - + -
312A VAL* 6.5 0.2 - - + -
315A ALA* 4.3 14.3 - - + +
316A LEU* 4.8 10.1 - - + -
319A ALA* 4.0 25.1 - - + -
324A PHE* 4.1 9.9 - - + -
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Residues in contact with ARG 260 (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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55A ASN* 3.2 30.3 - - - +
56A PHE 3.1 26.0 - - - +
57A ALA* 4.0 12.9 - - - +
58A SER* 4.3 5.0 + - - +
61A VAL* 4.4 2.9 - - - +
255A THR 4.0 0.8 + - - -
256A HIS 4.2 1.3 - - - -
257A LYS 3.0 12.8 + - - +
258A THR 5.0 1.6 - - - +
259A LEU* 1.3 80.3 - - - +
261A GLY* 1.3 59.3 - - - +
315A ALA* 4.2 5.9 - - - +
318A GLN* 4.7 8.0 + - - +
324A PHE* 3.6 21.5 - - + -
327A TYR* 3.5 16.1 - - - -
410A SER* 3.1 20.8 + - - -
18B HIS* 2.9 29.1 + - - -
21B MSE 3.6 28.7 - - - +
22B LEU* 3.6 21.0 - - - +
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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