Contacts of the helix formed by residues 394 - 405 (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 ALA 394 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393A GLY* 1.3 71.9 - - - +
395A LEU* 1.3 68.4 + - - +
397A TYR* 2.8 40.0 + - - -
398A LEU* 3.0 18.2 + - - +
421A MSE 3.4 23.3 - - + -
479A GLY 5.9 0.9 - - - +
480A ALA* 3.5 26.2 - - + +
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Residues in contact with LEU 395 (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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393A GLY 3.0 1.8 + - - +
394A ALA* 1.3 77.1 - - - +
396A THR* 1.3 63.7 + - - +
398A LEU* 3.3 6.5 + - + +
399A TRP* 3.0 37.0 + - + +
475A ASN* 3.9 18.4 - - - +
479A GLY* 3.6 26.7 - - - -
480A ALA* 3.4 16.1 - - + +
483A HIS* 3.6 22.4 - - + +
546A LEU* 4.1 5.6 - - + +
548A PRO 4.9 1.6 - - - +
550A PRO* 3.5 28.7 - - + -
553A GLU* 3.3 25.6 - - - +
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Residues in contact with THR 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A PRO* 6.4 0.7 - - - -
376A SER* 4.9 1.0 + - - -
392A ASP 3.5 13.5 - - - +
393A GLY 3.2 14.0 + - - -
395A LEU* 1.3 79.2 - - - +
397A TYR* 1.3 59.2 + - + +
399A TRP* 3.7 4.4 - - - +
400A LEU* 2.9 24.7 + - + +
445A VAL* 3.7 22.2 - - + +
446A THR 3.9 7.6 - - - +
447A GLY* 3.6 13.2 - - - -
473A MSE 3.4 44.4 + - + +
475A ASN* 5.7 2.8 + - - +
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Residues in contact with TYR 397 (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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239A TYR* 3.5 33.7 - + - -
282A LEU* 5.7 2.8 - - - +
391A ALA* 3.9 26.2 - - + -
392A ASP 4.0 4.9 - - - +
393A GLY 4.1 0.7 - - - -
394A ALA* 2.8 44.9 + - - -
396A THR* 1.3 74.2 - - - +
398A LEU* 1.3 80.3 + - + +
400A LEU* 3.9 7.4 - - + +
401A SER* 2.9 31.1 + - - -
412A PHE* 5.9 1.7 - - + -
414A CYS* 3.6 17.0 - - - -
415A HIS* 3.4 36.0 - + + +
419A GLY* 6.0 0.3 - - - -
421A MSE 4.5 4.0 - - + +
112B LEU* 5.0 11.6 - - - +
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Residues in contact with LEU 398 (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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239A TYR* 4.3 7.9 - - - +
394A ALA* 3.0 25.1 + - - +
395A LEU* 3.9 6.1 - - + +
397A TYR* 1.3 105.6 - - + +
399A TRP* 1.3 58.5 + - - +
401A SER* 2.8 21.0 + - - -
402A GLU* 3.9 10.9 - - - +
480A ALA* 5.5 4.3 - - + -
550A PRO* 3.8 23.4 - - + +
552A GLU* 3.8 23.8 - - + +
553A GLU* 4.2 31.0 - - + +
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Residues in contact with TRP 399 (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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360A ILE* 3.8 26.0 - - + -
363A LYS 5.9 0.4 - - - -
371A HIS* 3.4 20.0 - + - -
372A PRO* 3.4 36.2 - - + +
373A PHE* 3.9 21.5 - + + -
376A SER* 3.8 16.4 + - - +
395A LEU* 3.0 34.2 + - + +
396A THR* 3.7 4.3 - - - +
398A LEU* 1.3 73.7 - - - +
400A LEU* 1.3 66.0 + - - +
401A SER 3.1 1.6 - - - -
402A GLU* 3.1 22.0 + - + +
403A VAL 4.2 1.0 + - - -
548A PRO* 3.6 22.9 + - + -
549A ILE 3.4 11.0 - - - -
550A PRO* 3.3 48.0 - - + +
551A PRO* 4.1 8.3 - - + -
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Residues in contact with LEU 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A SER* 3.6 30.4 + - - +
379A ILE* 4.6 10.1 - - + -
389A VAL* 4.0 20.6 - - + -
391A ALA* 3.8 28.3 - - + -
396A THR* 2.9 19.5 + - + +
397A TYR* 3.4 5.8 + - - +
399A TRP* 1.3 73.9 - - - +
401A SER* 1.3 63.4 + - - +
402A GLU 3.0 1.6 + - - -
403A VAL* 3.0 30.2 + - + +
404A MSE 3.4 15.2 - - + +
412A PHE* 4.2 7.0 - - + -
445A VAL* 4.0 29.2 - - + -
473A MSE 6.4 0.2 - - + -
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Residues in contact with SER 401 (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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239A TYR* 4.3 12.2 + - - -
256A LEU* 3.5 25.2 - - - +
258A GLN* 3.0 28.4 + - - +
397A TYR 2.9 15.6 + - - -
398A LEU* 2.8 23.7 + - - -
400A LEU* 1.3 76.9 - - - +
402A GLU* 1.3 60.8 + - - +
404A MSE 3.3 18.6 + - - -
405A SER* 4.1 3.8 + - - -
412A PHE* 5.3 3.1 - - - -
552A GLU* 4.3 3.6 - - - +
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Residues in contact with GLU 402 (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* 4.1 5.4 - - - +
259A ASN* 5.8 0.3 + - - -
356A ARG* 2.5 49.2 + - - +
357A TYR* 3.4 22.5 - - + +
360A ILE* 4.7 9.0 - - + +
373A PHE* 4.0 16.6 - - + -
398A LEU 3.9 9.1 - - - +
399A TRP* 3.1 19.6 + - + +
400A LEU 3.0 0.6 + - - -
401A SER* 1.3 76.7 - - - +
403A VAL* 1.3 58.8 + - - +
404A MSE 3.5 0.2 - - - -
405A SER* 4.8 5.4 + - - -
406A ARG* 5.0 0.9 - - - -
551A PRO* 3.7 29.5 - - + +
552A GLU* 4.1 9.5 - - - +
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Residues in contact with VAL 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A TYR* 4.0 16.2 - - + +
373A PHE* 3.9 21.8 - - + -
376A SER* 3.7 38.4 - - - +
377A GLN* 4.0 15.9 - - + +
380A ALA* 3.9 16.4 - - + +
399A TRP 4.8 0.4 - - - +
400A LEU* 3.0 24.1 + - + +
402A GLU* 1.3 79.9 - - - +
404A MSE 1.3 68.9 + - - +
405A SER 3.4 2.2 + - - -
406A ARG* 3.9 13.0 - - - +
407A VAL* 3.4 17.0 - - - +
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Residues in contact with MSE 404 (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 LEU* 3.9 24.4 - - + +
256A LEU* 4.1 5.6 - - + -
379A ILE* 6.4 0.4 - - - -
380A ALA* 6.2 0.2 - - - -
383A VAL* 4.5 5.8 - - + -
389A VAL* 4.4 14.6 - - + -
400A LEU* 3.4 30.7 - - + +
401A SER* 3.3 12.2 + - - +
403A VAL* 1.3 82.2 - - - +
405A SER* 1.3 64.2 + - - +
406A ARG 3.4 0.2 - - - -
407A VAL* 3.4 29.9 - - + +
409A PRO* 3.6 35.4 - - + -
412A PHE* 3.5 48.0 - - + -
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Residues in contact with SER 405 (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 LEU* 4.9 2.9 - - - -
253A ARG* 2.9 28.8 + - - +
254A GLY 4.9 0.9 - - - -
255A GLY* 3.9 14.6 - - - -
256A LEU* 2.9 33.9 + - - +
259A ASN* 3.3 21.4 + - - -
353A ALA* 5.6 4.5 - - - -
401A SER 4.1 4.5 + - - -
402A GLU 4.8 4.0 + - - -
403A VAL 3.4 1.0 - - - +
404A MSE 1.3 79.0 - - - +
406A ARG* 1.3 59.5 + - - +
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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