Contacts of the helix formed by residues 349 - 364 (chain A) in PDB entry 1D9Z
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 GLY 349 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345A PRO 3.5 4.8 + - - -
346A GLN 3.4 9.5 + - - -
348A ARG* 1.3 78.4 - - - +
350A MET* 1.3 59.7 + - - +
351A TYR 3.5 2.0 - - - -
352A ASN* 4.0 16.4 - - - +
353A GLY* 3.6 15.1 + - - -
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Residues in contact with MET 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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93A TYR* 4.5 13.0 - - + -
142A VAL* 3.4 41.3 - - + +
145A ILE* 4.2 19.5 - - + -
146A TYR* 4.7 19.1 - - - +
346A GLN* 3.3 26.9 - - + +
347A LEU* 3.6 15.5 - - - +
348A ARG 3.3 2.0 - - - -
349A GLY* 1.3 75.7 - - - +
351A TYR* 1.3 65.3 + - - +
353A GLY* 3.5 1.1 + - - -
354A ASP* 3.2 23.4 + - - +
376A PRO* 3.7 10.0 - - + +
377A LEU 5.3 0.4 - - - +
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Residues in contact with TYR 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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348A ARG 4.3 5.5 + - - +
349A GLY 3.5 0.4 - - - -
350A MET* 1.3 81.0 - - - +
352A ASN* 1.3 78.9 + - - +
353A GLY 3.3 0.2 + - - -
354A ASP* 3.3 1.0 + - - +
355A ARG* 3.0 67.8 + - + +
375A ARG* 3.3 45.3 - - + -
376A PRO* 3.7 11.5 - - + +
377A LEU 3.5 17.4 + - - +
378A THR* 3.7 27.4 - - + -
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Residues in contact with ASN 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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348A ARG 5.2 0.2 + - - -
349A GLY* 3.9 18.2 + - - +
350A MET 3.3 0.2 - - - -
351A TYR* 1.3 95.9 - - - +
353A GLY* 1.3 55.6 + - - +
355A ARG* 3.9 5.6 - - - +
356A ALA* 3.0 28.2 + - - +
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Residues in contact with GLY 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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349A GLY 3.6 8.5 + - - -
350A MET* 3.5 5.0 + - - -
351A TYR 3.3 0.6 - - - -
352A ASN* 1.3 76.1 - - - +
354A ASP* 1.3 67.3 + - - +
356A ALA* 3.6 6.4 - - - +
357A ARG* 3.2 35.2 + - - +
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Residues in contact with ASP 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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146A TYR* 4.5 13.0 + - - -
350A MET 3.2 13.9 + - - +
351A TYR 3.6 7.0 - - - +
353A GLY* 1.3 71.3 - - - +
355A ARG* 1.3 70.7 + - - +
356A ALA 2.7 2.8 + - - -
357A ARG* 2.8 34.6 + - - +
358A LYS* 3.1 30.3 + - - +
374A ASN 4.1 7.6 - - - +
375A ARG* 4.0 10.3 - - + +
376A PRO* 3.7 26.5 - - + +
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Residues in contact with ARG 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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351A TYR* 3.0 55.8 + - + +
352A ASN* 3.9 6.7 - - - +
354A ASP* 1.3 79.8 + - - +
356A ALA* 1.3 66.2 + - - +
358A LYS* 3.9 4.4 - - - +
359A GLN* 3.1 44.5 + - - +
372A LEU* 3.9 54.5 + - - +
373A ASP* 5.7 1.6 + - - -
375A ARG* 4.8 5.7 - - + +
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Residues in contact with ALA 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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352A ASN 3.0 19.3 + - - +
353A GLY* 3.6 9.2 - - - +
354A ASP 2.7 4.6 + - - -
355A ARG* 1.3 79.5 - - - +
357A ARG* 1.3 59.2 + - + +
358A LYS 3.1 3.8 + - - -
359A GLN* 3.4 11.0 + - - +
360A VAL* 3.7 10.7 + - - +
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Residues in contact with ARG 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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98A PRO* 3.6 48.4 - - - +
99A GLU 5.3 0.7 - - - +
100A ALA* 4.1 19.9 - - + +
146A TYR* 5.5 4.8 + - - -
350A MET 5.8 0.4 + - - -
353A GLY* 3.2 30.1 + - - +
354A ASP* 2.8 25.0 + - - +
356A ALA* 1.3 74.7 - - + +
358A LYS* 1.3 59.4 + - + +
360A VAL* 3.5 20.4 - - + +
361A LEU* 3.9 10.8 - - + +
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Residues in contact with LYS 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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99A GLU* 5.7 5.4 - - - -
308A ASN* 3.5 26.9 + - - +
354A ASP* 3.1 30.8 + - - +
355A ARG* 4.4 2.2 - - - +
356A ALA 3.1 0.2 + - - -
357A ARG* 1.3 78.7 - - + +
359A GLN* 1.3 65.7 + - - +
360A VAL 3.1 2.4 + - - -
361A LEU* 3.3 21.9 + - + +
362A VAL* 2.9 29.0 + - + +
367A ARG* 5.7 2.7 - - + -
371A ALA* 3.8 24.9 + - + +
372A LEU* 4.5 13.0 - - + -
374A ASN* 3.8 26.0 + - - +
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Residues in contact with GLN 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 ARG* 3.1 45.4 + - - +
356A ALA* 3.4 5.2 + - - +
358A LYS* 1.3 78.1 - - - +
360A VAL* 1.3 63.0 + - - +
362A VAL* 3.2 11.4 + - + +
363A ASP* 3.1 37.9 + - - +
372A LEU* 4.2 15.8 - - + +
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Residues in contact with VAL 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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100A ALA* 5.6 0.4 - - + -
101A TYR* 4.2 20.4 - - + +
103A PRO* 4.1 25.8 - - + -
356A ALA 3.7 7.4 + - - +
357A ARG* 3.5 24.0 - - + +
359A GLN* 1.3 78.5 - - - +
361A LEU* 1.3 75.1 + - + +
363A ASP* 3.0 13.2 + - - +
364A HIS* 2.9 36.9 + - + +
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Residues in contact with LEU 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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99A GLU* 3.0 42.8 - - - +
100A ALA* 4.0 9.4 - - - +
101A TYR* 3.8 27.1 - - + -
108A TYR* 4.9 3.6 - - + -
357A ARG 3.9 16.6 - - - +
358A LYS* 3.3 24.5 + - + +
360A VAL* 1.3 82.1 - - + +
362A VAL* 1.3 52.9 + - + +
364A HIS* 3.6 5.5 - - - -
365A GLY 2.7 11.0 + - - -
366A PHE* 2.5 51.5 + - + +
367A ARG* 4.7 10.5 - - + +
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Residues in contact with VAL 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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270A ARG* 3.5 23.8 + - - +
358A LYS* 2.9 23.6 - - + +
359A GLN* 3.4 12.8 - - + +
360A VAL 3.1 0.8 - - - -
361A LEU* 1.3 74.5 - - + +
363A ASP* 1.3 68.5 + - - +
365A GLY* 3.3 9.7 + - - -
367A ARG* 3.8 19.2 - - + +
368A LEU 4.5 9.2 - - - +
369A PRO* 3.9 33.0 - - + -
371A ALA* 5.4 1.3 - - + -
372A LEU* 4.7 13.9 - - + -
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Residues in contact with ASP 363 (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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270A ARG* 5.4 1.5 + - - +
274A LEU* 5.4 5.0 - - - +
280A LEU* 4.1 23.5 - - + +
359A GLN* 3.1 23.7 + - - +
360A VAL* 3.0 13.8 + - + +
362A VAL* 1.3 80.1 - - - +
364A HIS* 1.3 72.9 + - + +
365A GLY* 3.0 2.1 + - - -
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Residues in contact with HIS 364 (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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101A TYR* 3.0 30.9 - + + -
103A PRO* 3.3 38.2 - - + +
106A ASP* 5.4 2.5 - - - -
280A LEU* 5.4 9.9 - - + -
283A ALA 5.5 1.6 - - - +
285A ARG* 2.9 43.8 + - - +
360A VAL* 2.9 22.2 + - + +
361A LEU* 4.5 1.6 - - - -
363A ASP* 1.3 85.0 - - + +
365A GLY* 1.3 56.8 + - - +
366A PHE* 2.9 19.0 - - + -
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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