Contacts of the helix formed by residues 342 - 362 (chain A) in PDB entry 2AG1
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 ARG 342 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201A LEU 3.2 22.0 + - - -
202A ARG 3.4 13.3 + - - -
204A ALA 2.8 30.3 + - - -
205A GLU* 4.0 9.6 + - - +
207A PRO* 3.6 29.1 - - + +
231A THR 3.9 13.5 + - - +
232A GLY 3.5 21.8 - - - +
233A VAL* 4.1 7.4 - - + +
339A TRP* 4.9 5.1 - - - -
340A PRO* 3.7 25.3 + - - +
341A ASP* 1.3 77.0 - - - +
343A GLY* 1.3 57.6 + - - +
344A ASP 3.3 2.7 - - - +
345A TRP* 3.3 15.1 + - + +
346A CYS* 2.9 34.1 + - - -
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Residues in contact with GLY 343 (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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341A ASP* 2.8 22.4 + - - -
342A ARG* 1.3 77.5 - - - +
344A ASP* 1.3 56.5 + - - +
346A CYS* 3.5 7.0 + - - +
347A ALA* 3.0 28.8 + - - +
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Residues in contact with ASP 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A ASP* 4.5 1.0 + - - -
342A ARG* 3.3 0.9 - - - -
343A GLY* 1.3 75.9 - - - +
345A TRP* 1.3 57.2 + - - +
347A ALA* 3.3 8.0 + - - +
348A LYS* 3.0 28.0 + - - +
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Residues in contact with TRP 345 (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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205A GLU 4.3 9.2 - - - +
206A ARG* 3.5 46.3 - - + -
207A PRO* 2.7 37.1 + - + -
208A VAL* 3.7 17.9 - - + -
234A PRO* 3.4 19.9 - - + +
263A PHE* 3.7 19.3 - + - -
268A ALA* 3.2 38.1 - - + -
270A PRO* 4.6 2.9 - - + -
342A ARG* 3.3 19.7 + - - +
344A ASP* 1.3 79.2 - - - +
346A CYS* 1.3 57.3 + - - +
348A LYS* 3.2 13.3 + - + -
349A VAL* 3.0 33.1 + - + +
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Residues in contact with CYS 346 (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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232A GLY* 3.3 26.0 - - - -
234A PRO* 4.1 15.5 - - - -
251A ALA* 3.1 34.2 - - + +
252A MSE 4.5 6.3 - - - -
342A ARG 2.9 25.6 + - - +
343A GLY* 3.6 7.2 - - - +
345A TRP* 1.3 74.0 - - - +
347A ALA* 1.3 60.5 + - - +
349A VAL* 3.4 10.2 + - - +
350A THR* 2.9 30.5 + - - -
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Residues in contact with ALA 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A GLY 3.0 18.0 + - - +
344A ASP* 3.3 8.0 + - - +
346A CYS* 1.3 75.0 - - - +
348A LYS* 1.3 57.9 + - - +
350A THR* 3.3 8.6 + - + -
351A ASP* 2.8 42.5 + - - +
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Residues in contact with LYS 348 (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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266A ALA* 4.4 14.9 + - - +
268A ALA* 4.3 20.6 - - + -
344A ASP 3.0 14.2 + - - +
345A TRP* 3.5 20.2 - - + +
346A CYS 3.2 0.2 - - - -
347A ALA* 1.3 75.7 - - - +
349A VAL* 1.3 62.5 + - - +
351A ASP* 3.2 10.3 + - + +
352A LEU* 3.0 60.5 + - + +
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Residues in contact with VAL 349 (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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234A PRO* 3.9 18.8 - - + -
236A PHE* 3.6 29.6 - - + -
251A ALA 5.8 0.9 - - - +
253A ARG 5.0 1.1 - - - +
254A GLY* 3.8 18.4 - - - +
263A PHE* 3.9 17.1 - - + -
345A TRP* 3.0 48.1 + - + +
346A CYS* 3.5 8.5 - - - +
348A LYS* 1.3 75.1 - - - +
350A THR* 1.3 64.4 + - - +
352A LEU* 3.2 4.3 + - - +
353A ALA* 3.1 22.3 + - + +
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Residues in contact with THR 350 (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 ASP 4.4 9.7 + - - -
251A ALA* 4.4 12.8 + - - -
253A ARG 4.8 7.7 + - - -
346A CYS 2.9 18.4 + - - -
347A ALA* 3.4 7.6 - - - +
349A VAL* 1.3 77.7 - - - +
351A ASP* 1.3 72.7 + - - +
353A ALA* 3.4 6.2 + - - +
354A GLN* 2.9 32.9 + - + +
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Residues in contact with ASP 351 (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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347A ALA* 2.8 30.8 + - - +
348A LYS* 3.7 10.9 - - + +
350A THR* 1.3 83.0 - - - +
352A LEU* 1.3 60.3 + - + +
354A GLN* 3.4 9.3 + - - +
355A GLU* 2.9 30.2 + - - +
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Residues in contact with LEU 352 (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 ASN* 5.5 1.6 - - - -
262A SER* 4.8 13.9 + - - +
263A PHE* 3.6 49.1 - - + -
266A ALA* 3.9 23.6 - - + -
268A ALA* 4.2 5.6 - - + -
348A LYS* 3.0 44.5 + - + +
349A VAL 3.2 4.2 + - - +
351A ASP* 1.3 74.6 - - + +
353A ALA* 1.3 66.2 + - - +
355A GLU* 3.1 25.3 + - - +
356A ARG* 3.1 22.0 + - - +
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Residues in contact with ALA 353 (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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253A ARG 5.9 1.6 - - - +
254A GLY 4.3 10.5 - - - +
259A ASN* 4.1 32.1 + - - +
263A PHE* 5.2 2.7 - - + -
349A VAL* 3.1 10.3 + - + +
350A THR* 3.6 10.5 - - - +
352A LEU* 1.3 76.7 - - - +
354A GLN* 1.3 62.8 + - - +
355A GLU 3.3 0.2 + - - -
356A ARG* 3.3 5.4 + - - +
357A TYR* 3.2 20.8 + - - +
405A SER* 5.6 4.5 - - - -
406A ARG* 5.6 0.9 - - - -
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Residues in contact with GLN 354 (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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350A THR* 2.9 21.1 + - + +
351A ASP* 3.7 10.5 - - - +
353A ALA* 1.3 75.8 - - - +
355A GLU* 1.3 57.7 + - - +
357A TYR* 3.4 6.3 + - - +
358A ALA* 3.0 36.4 + - + +
406A ARG* 2.8 47.1 + - - +
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Residues in contact with GLU 355 (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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262A SER* 5.4 2.8 + - - -
351A ASP 2.9 18.8 + - - +
352A LEU* 3.1 26.2 + - - +
354A GLN* 1.3 76.7 - - - +
356A ARG* 1.3 59.4 + - - +
358A ALA* 3.5 5.3 + - - +
359A SER* 2.9 30.6 + - - -
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Residues in contact with ARG 356 (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 GLN* 3.6 27.3 + - - +
259A ASN* 3.7 27.6 - - + +
261A TYR* 4.2 13.3 - - - +
262A SER* 5.8 2.0 + - - -
352A LEU 3.1 10.8 + - - +
353A ALA* 3.3 10.3 + - - +
355A GLU* 1.3 74.4 + - - +
357A TYR* 1.3 60.0 + - - +
359A SER* 3.2 7.4 - - - -
360A ILE* 3.0 42.5 + - + +
402A GLU* 2.5 53.2 + - - +
551A PRO* 4.3 9.9 - - + +
552A GLU* 3.2 25.9 + - - -
555A ILE* 6.0 0.8 - - - +
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Residues in contact with TYR 357 (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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353A ALA 3.2 10.2 + - - +
354A GLN* 3.4 13.0 - - - +
355A GLU 3.3 0.2 - - - -
356A ARG* 1.3 80.3 - - - +
358A ALA* 1.3 61.8 + - - +
360A ILE* 3.3 8.2 + - - +
361A ALA* 2.9 30.6 + - + +
373A PHE* 3.8 17.2 - + - -
377A GLN* 3.0 37.6 + - - +
380A ALA* 5.9 1.4 - - - +
402A GLU* 3.4 28.3 - - - +
403A VAL* 4.0 10.9 - - + +
406A ARG* 3.3 52.6 + - - +
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Residues in contact with ALA 358 (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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354A GLN* 3.0 26.5 + - - +
355A GLU* 4.0 5.8 - - - +
357A TYR* 1.3 76.9 - - + +
359A SER* 1.3 65.2 + - - +
361A ALA* 3.3 8.9 + - - +
362A ALA* 3.0 25.5 + - - +
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Residues in contact with SER 359 (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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355A GLU* 2.9 21.1 + - - -
356A ARG* 3.2 9.9 - - - -
358A ALA* 1.3 75.4 - - - +
360A ILE* 1.3 66.0 + - - +
362A ALA* 3.2 14.5 + - - +
363A LYS* 3.2 32.2 + - - +
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Residues in contact with ILE 360 (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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356A ARG* 3.0 30.4 + - + +
357A TYR* 3.6 7.4 - - - +
359A SER* 1.3 77.3 - - - +
361A ALA* 1.3 63.3 + - - +
363A LYS* 3.0 33.5 + - - +
364A SER* 3.1 14.3 + - - +
373A PHE* 3.5 35.2 - - + -
399A TRP* 3.8 19.3 - - + -
402A GLU* 4.7 10.3 - - + +
551A PRO* 3.4 30.5 - - + -
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Residues in contact with ALA 361 (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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357A TYR* 2.9 22.3 + - + +
358A ALA* 3.6 10.8 - - - +
359A SER 3.3 0.2 - - - -
360A ILE* 1.3 76.2 - - - +
362A ALA* 1.3 59.1 - - - +
363A LYS 3.1 1.4 + - - -
364A SER* 3.8 12.8 + - - +
373A PHE* 3.6 23.1 - - + -
374A HIS* 4.8 5.9 - - + -
377A GLN* 4.7 6.5 - - - +
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Residues in contact with ALA 362 (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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358A ALA 3.0 12.8 + - - +
359A SER* 3.5 12.8 - - - +
360A ILE 3.2 0.6 + - - -
361A ALA* 1.3 75.4 - - - +
363A LYS* 1.3 66.0 + - + +
364A SER 3.8 1.3 + - - -
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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