Contacts of the helix formed by residues 251 - 263 (chain A) in PDB entry 1A35
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 PRO 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231A TYR* 3.9 16.8 - - + -
233A PRO* 5.9 5.4 - - + -
249A LEU 3.5 1.9 - - - +
250A SER* 1.3 85.3 - - - +
252A LYS* 1.3 58.4 + - + +
254A GLU* 3.6 9.7 - - + +
255A GLU* 2.9 29.6 + - - +
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Residues in contact with LYS 252 (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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250A SER* 3.2 3.5 + - - +
251A PRO* 1.3 79.6 - - + +
253A ALA* 1.3 62.4 + - - +
255A GLU* 3.5 20.0 + - - +
256A VAL* 3.1 35.2 + - + +
285A GLU* 2.9 52.7 + - + +
373A LEU* 4.8 8.4 - - - +
375A ARG* 5.7 6.7 - - - +
376A ARG* 5.8 5.5 - - - +
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Residues in contact with ALA 253 (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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249A LEU* 3.7 8.8 - - + +
250A SER* 3.0 22.3 + - - +
252A LYS* 1.3 75.5 - - - +
254A GLU* 1.3 65.5 + - - +
255A GLU 3.3 0.2 - - - -
256A VAL* 4.0 0.9 - - - -
257A ALA* 3.2 11.3 + - - +
282A TRP* 2.8 37.9 + - + +
285A GLU* 4.7 3.7 + - - -
286A MET* 4.1 16.4 - - + -
290A GLU* 3.6 17.0 - - - +
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Residues in contact with GLU 254 (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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231A TYR* 2.5 23.2 + - - +
233A PRO* 3.7 5.1 - - - +
234A LEU* 2.7 49.1 + - + +
248A LYS* 5.5 0.5 - - - -
249A LEU* 3.5 31.6 + - + +
250A SER 2.6 20.4 + - - +
251A PRO* 3.6 8.8 - - - +
253A ALA* 1.3 72.5 - - - +
255A GLU* 1.3 65.4 + - - +
257A ALA* 3.3 3.7 + - - +
258A THR* 2.9 25.1 + - - +
305A MET* 5.6 1.6 - - + -
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Residues in contact with GLU 255 (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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231A TYR* 3.6 45.6 + - + +
251A PRO 2.9 18.7 + - - +
252A LYS* 3.7 22.2 + - + +
253A ALA 3.3 0.2 - - - -
254A GLU* 1.3 76.5 - - - +
256A VAL* 1.3 64.9 + - + +
258A THR* 2.5 22.9 + - - -
259A PHE* 3.3 32.3 + - + -
358A PRO* 3.9 4.7 - - - +
376A ARG* 3.5 26.8 + - - -
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Residues in contact with VAL 256 (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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252A LYS* 3.1 21.3 + - - +
254A GLU 3.4 0.2 - - - -
255A GLU* 1.3 77.0 - - + +
257A ALA* 1.3 62.1 + - - +
259A PHE* 3.1 29.9 + - + +
260A PHE 3.3 4.5 + - - -
278A PHE* 3.7 19.0 - - + -
281A ASP* 5.3 0.9 - - + -
282A TRP* 3.4 34.3 - - + +
285A GLU* 3.9 22.7 - - + -
360A LEU* 4.6 9.2 - - + -
373A LEU* 4.2 19.3 - - + -
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Residues in contact with ALA 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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249A LEU* 3.9 9.9 - - + -
253A ALA 3.2 17.4 + - - +
254A GLU 3.5 4.9 - - - +
255A GLU 3.2 0.2 - - - -
256A VAL* 1.3 78.3 - - - +
258A THR* 1.3 57.8 + - - +
260A PHE* 3.1 8.5 + - - +
261A ALA* 2.8 26.5 + - - +
278A PHE* 4.6 1.1 - - - -
282A TRP* 3.8 22.9 - - + +
302A PHE* 3.8 19.8 - - + -
305A MET* 4.1 9.9 - - - -
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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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231A TYR* 3.9 23.5 - - + +
234A LEU* 4.5 7.0 - - + -
254A GLU* 2.9 19.5 - - + +
255A GLU* 2.5 18.7 + - - -
257A ALA* 1.3 73.4 - - - +
259A PHE* 1.3 73.4 + - - +
261A ALA* 3.0 8.6 + - - +
262A LYS* 2.9 34.7 + - - +
305A MET* 4.3 10.3 - - - -
309A PHE* 3.7 27.1 - - + -
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Residues in contact with PHE 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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231A TYR* 6.1 0.7 - + - -
255A GLU* 3.7 34.1 - - + -
256A VAL* 3.1 25.0 + - + +
258A THR* 1.3 87.0 + - - +
260A PHE* 1.3 63.3 + - - +
262A LYS* 3.6 13.0 + - + +
263A MET* 3.3 24.2 - - - +
358A PRO* 3.1 35.0 - - + -
359A GLY* 3.8 12.3 - - - -
360A LEU* 3.7 19.7 - - + +
373A LEU* 3.4 33.9 - - + -
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Residues in contact with PHE 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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256A VAL 3.3 1.0 + - - -
257A ALA 3.1 9.6 + - - +
258A THR 3.1 0.2 - - - -
259A PHE* 1.3 82.7 - - - +
261A ALA* 1.3 62.3 + - - +
263A MET* 3.0 14.2 + - - +
264A LEU* 3.3 29.5 + - + +
269A THR* 3.6 29.6 - - + +
274A PHE* 3.9 15.0 - + - -
275A ARG* 4.7 10.1 - - + -
278A PHE* 3.4 51.6 - + + -
297A LEU* 4.5 17.3 - - + -
302A PHE* 3.5 35.2 - + + -
360A LEU* 3.7 11.4 - - + +
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Residues in contact with ALA 261 (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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257A ALA 2.8 13.6 + - - +
258A THR* 3.0 7.4 + - - +
260A PHE* 1.3 73.2 - - - +
262A LYS* 1.3 58.8 + - - +
263A MET 2.9 10.5 + - - -
264A LEU* 3.1 26.4 + - - +
265A ASP* 4.9 0.3 + - - -
302A PHE* 4.2 8.7 - - + +
305A MET* 3.6 29.2 - - + -
306A SER* 4.1 23.6 + - - +
309A PHE* 4.2 3.8 - - + -
310A LYS* 5.4 0.9 + - - -
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Residues in contact with LYS 262 (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 THR* 2.9 27.1 + - - +
259A PHE* 4.1 11.2 - - + +
260A PHE 3.3 0.4 - - - -
261A ALA* 1.3 70.9 - - - +
263A MET* 1.3 61.4 + - + +
264A LEU 3.6 0.2 - - - -
265A ASP* 3.6 13.2 - - - +
306A SER* 5.9 0.9 - - - +
309A PHE* 3.4 56.2 - - + -
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Residues in contact with MET 263 (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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259A PHE* 3.3 16.6 - - - +
260A PHE 3.0 10.0 + - - +
261A ALA 2.9 1.4 - - - -
262A LYS* 1.3 85.4 - - + +
264A LEU* 1.3 53.0 + - - +
265A ASP* 3.0 8.7 - - - -
266A HIS* 2.7 33.9 + - + +
268A TYR* 3.9 14.8 - - + -
269A THR* 3.2 17.4 + - + +
274A PHE* 3.6 31.0 - - + -
360A LEU* 4.3 16.2 - - - +
362A ARG* 3.5 46.0 - - - +
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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