Contacts of the helix formed by residues 350 - 362 (chain A) in PDB entry 1QI9
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 350 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A LEU* 4.1 5.7 - - + +
141A VAL* 4.1 6.5 - - + -
349A ARG* 1.3 86.7 - - + +
351A GLU* 1.4 57.9 + - - +
353A LEU* 3.3 3.1 + - - +
354A GLY* 2.8 27.0 + - - -
400A LEU* 3.5 26.0 - - + +
413A SER* 3.7 1.8 - - - +
484A GLY 3.7 3.8 - - - +
485A ILE* 3.5 17.3 - - - +
486A HIS 3.6 28.7 - - - +
487A TYR* 3.3 37.7 - - + +
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Residues in contact with GLU 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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56A LYS* 2.8 28.5 + - - +
237A MET* 3.7 14.4 - - + +
243A TRP* 3.1 22.4 + - + +
247A GLN* 2.9 26.9 + - - +
349A ARG* 4.2 6.2 - - + +
350A PRO* 1.4 80.2 - - - +
352A ALA* 1.3 63.6 + - + +
354A GLY* 3.4 2.0 + - - +
355A GLY 3.1 11.1 + - - -
399A LEU* 5.1 0.2 - - - +
400A LEU* 4.1 8.4 + - - +
402A GLN* 3.7 27.2 - - + +
407A GLY* 3.4 4.5 - - - -
408A SER* 2.7 37.1 + - - -
484A GLY 4.2 2.7 + - - +
485A ILE* 4.3 0.7 - - - +
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Residues in contact with ALA 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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51A ALA 5.5 2.2 - - - +
53A LYS 5.6 1.8 - - - +
55A HIS* 5.8 7.4 - - + -
243A TRP* 4.3 7.9 - - - -
247A GLN* 4.3 14.8 - - - +
348A ALA* 4.4 13.9 - - + -
349A ARG* 3.0 16.2 + - + +
351A GLU* 1.3 79.1 - - + +
353A LEU* 1.3 65.9 + - - +
355A GLY* 3.1 11.8 + - - -
356A THR* 3.2 15.5 + - - -
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Residues in contact with LEU 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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51A ALA 3.5 24.2 - - - +
52A ALA* 4.4 2.0 - - - -
129A LEU* 3.9 19.7 - - + -
134A LEU* 3.6 38.4 - - + -
138A LEU* 3.8 16.8 - - + -
347A PHE* 4.2 8.1 - - + -
348A ALA* 3.8 11.7 - - + -
349A ARG 3.2 2.6 + - - -
350A PRO 3.8 5.2 - - - +
352A ALA* 1.3 78.9 - - - +
354A GLY* 1.3 56.6 + - - +
356A THR* 3.2 8.6 + - - +
357A LEU* 2.8 31.3 + - - +
369A PHE* 3.9 6.2 - - + -
487A TYR* 3.1 27.6 - - + +
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Residues in contact with GLY 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A LEU* 4.7 1.0 - - - +
142A TYR* 3.4 27.5 + - - -
350A PRO 2.8 16.9 + - - -
351A GLU 3.7 4.0 - - - -
352A ALA 3.2 0.4 - - - -
353A LEU* 1.3 77.0 - - - +
355A GLY* 1.3 54.3 + - - +
357A LEU* 3.7 2.3 - - - +
358A HIS* 2.9 30.1 + - - +
398A IYR 4.2 0.3 - - - +
399A LEU* 3.8 6.9 - - - +
400A LEU* 4.4 7.2 - - - -
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Residues in contact with GLY 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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63A LEU 5.9 0.2 - - - -
243A TRP* 3.5 30.1 - - - -
351A GLU 3.1 6.3 + - - -
352A ALA 3.1 4.4 + - - -
354A GLY* 1.3 73.1 - - - +
356A THR* 1.3 63.4 + - - +
358A HIS* 3.3 2.0 + - - +
359A LEU* 3.0 34.0 + - - +
399A LEU* 3.6 14.1 - - - +
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Residues in contact with THR 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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51A ALA* 4.4 27.1 + - + +
129A LEU* 5.0 2.2 - - + -
243A TRP* 5.1 0.2 - - - -
352A ALA 3.2 13.5 + - - -
353A LEU* 3.2 13.4 + - - -
355A GLY* 1.3 74.7 - - - +
357A LEU* 1.3 58.2 + - - +
359A LEU* 3.4 1.7 + - - +
360A THR* 2.9 33.4 + - - +
365A LEU* 4.3 19.6 - - + +
367A ALA* 3.4 28.5 - - + -
369A PHE* 3.9 8.7 - - + -
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Residues in contact with LEU 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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138A LEU* 4.7 1.8 - - + -
142A TYR* 3.6 35.0 - - + +
353A LEU 2.8 18.2 + - - +
354A GLY 3.7 3.6 - - - +
356A THR* 1.3 72.3 - - - +
358A HIS* 1.3 68.0 + - - +
360A THR* 2.9 4.8 + - - -
361A ILE* 2.8 37.7 + - + +
369A PHE* 3.6 17.6 - - + -
373A LEU* 4.0 37.7 - - + -
374A LEU* 4.0 27.4 - - + -
380A LEU* 4.2 13.0 - - + -
398A IYR 4.9 1.1 - - - +
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Residues in contact with HIS 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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240A PHE* 4.1 23.2 - + - +
354A GLY 2.9 19.4 + - - +
355A GLY 3.7 3.1 - - - +
357A LEU* 1.3 75.4 - - - +
359A LEU* 1.3 78.9 + - + +
361A ILE* 3.3 4.0 + - - +
362A LYS* 3.0 60.3 + - + +
364A GLU* 5.7 0.2 + - - -
395A GLU* 5.5 1.9 + - - -
397A THR* 3.5 28.8 - - + +
398A IYR 3.0 39.0 + - - +
399A LEU* 4.0 13.7 - - + -
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Residues in contact with LEU 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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63A LEU* 3.3 45.5 - - + +
240A PHE* 4.0 21.8 - - + -
243A TRP* 5.0 2.0 - - + -
355A GLY 3.0 22.5 + - - +
358A HIS* 1.3 92.6 - - + +
360A THR* 1.3 59.8 + - - +
362A LYS* 3.2 3.9 + - + +
363A GLY 2.9 8.7 + - - -
364A GLU* 2.9 55.2 + - + +
365A LEU* 3.7 26.9 - - + +
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Residues in contact with THR 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 THR 2.9 17.2 + - - -
357A LEU* 2.9 8.8 + - - -
359A LEU* 1.3 75.7 - - - +
361A ILE* 1.3 63.8 + - - +
363A GLY* 2.9 14.2 + - - -
365A LEU* 3.3 16.9 - - - +
366A ASN* 4.2 6.3 - - - +
367A ALA* 3.0 48.4 + - - +
369A PHE* 5.0 0.2 - - - -
374A LEU* 3.8 23.6 - - + -
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Residues in contact with ILE 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 LEU* 2.8 33.5 + - + +
358A HIS 3.7 6.1 - - - +
360A THR* 1.3 76.5 - - - +
362A LYS* 1.3 60.8 + - - +
363A GLY 3.4 0.9 + - - -
374A LEU* 4.4 13.5 - - + +
380A LEU* 3.7 40.8 - - + -
398A IYR 3.6 46.1 - - + +
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Residues in contact with LYS 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 HIS* 3.0 37.0 + - + +
359A LEU* 3.2 7.1 + - - +
361A ILE* 1.3 76.7 - - - +
363A GLY* 1.3 60.4 + - - +
364A GLU* 3.6 21.8 + - + +
395A GLU* 5.2 7.4 - - - +
396A VAL* 3.1 26.7 + - - +
398A IYR 2.9 37.3 - - + +
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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