Contacts of the helix formed by residues 435 - 447 (chain B) in PDB entry 2G9Y
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 GLN 435 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84B TYR* 3.1 40.3 + - + +
85B THR 2.8 21.3 + - - +
86B HIS* 3.3 16.8 - - - +
105B SER* 3.0 39.7 - - - +
108B ALA* 3.7 10.9 - - + +
109B TRP* 3.5 26.9 - - + -
114B LYS* 4.7 0.7 - - - +
369B ASP* 3.1 24.2 + - - +
434B ASP* 1.3 75.2 - - - +
436B THR* 1.3 61.0 + - - +
438B LEU* 3.1 20.1 + - - +
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Residues in contact with THR 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A GLY* 5.9 0.2 - - - -
22A ALA* 3.6 22.2 + - + +
23A ARG* 3.7 5.4 + - - +
108B ALA* 3.5 32.5 - - + +
112B GLY 3.7 24.9 - - - +
114B LYS* 4.0 23.3 - - + +
434B ASP* 2.7 23.8 + - - +
435B GLN* 1.3 74.3 - - - +
437B ASP* 1.3 64.4 + - - +
439B PHE* 3.2 13.3 + - - +
440B TYR* 3.4 17.2 - - - -
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Residues in contact with ASP 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ARG* 3.3 17.6 + - - +
24A ARG* 2.9 22.9 + - - +
25A LEU* 3.0 42.3 + - + +
428B ASN 5.6 0.7 - - - +
433B THR* 4.2 9.0 - - - +
434B ASP* 2.6 39.0 + - - +
436B THR* 1.3 79.5 + - - +
438B LEU* 1.3 56.0 + - - +
440B TYR* 3.3 5.1 + - - +
441B THR* 2.9 34.1 + - - +
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Residues in contact with LEU 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B LEU* 4.3 20.0 - - + -
84B TYR* 4.2 22.4 - - + +
109B TRP* 3.9 21.5 - - + -
365B ILE* 3.5 32.1 - - + -
367B THR* 4.4 6.7 - - + -
419B ILE* 4.3 17.7 - - + -
429B VAL* 5.0 2.2 - - + -
434B ASP 3.7 2.0 + - - +
435B GLN 3.1 13.8 + - - +
436B THR 3.1 0.6 - - - -
437B ASP* 1.3 80.4 - - - +
439B PHE* 1.3 60.7 + - - +
441B THR* 3.3 8.5 + - + -
442B MET* 3.0 44.4 + - + +
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Residues in contact with PHE 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ALA 4.0 0.4 - - - +
109B TRP 3.3 20.0 + - - +
110B SER 3.2 31.2 - - - -
111B THR* 3.5 15.5 - - - -
112B GLY* 3.3 22.7 - - - +
130B PRO 4.3 2.9 - - - -
132B ILE* 3.8 21.8 - - + +
135B MET* 3.6 27.1 - - + -
435B GLN 4.0 0.6 + - - -
436B THR 3.2 11.6 + - - +
438B LEU* 1.3 79.4 - - - +
440B TYR* 1.3 77.1 + + - +
442B MET* 3.3 4.9 + - - +
443B LYS* 2.9 49.8 + - + +
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Residues in contact with TYR 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PRO* 3.7 10.0 - - - +
20A GLY* 3.2 24.7 + - - -
23A ARG* 3.6 52.5 - - + +
111B THR 4.8 1.0 + - - -
112B GLY* 3.8 18.5 + - - -
436B THR 3.4 14.4 - - - -
437B ASP* 3.3 6.8 + - - +
439B PHE* 1.3 96.6 - + - +
441B THR* 1.3 61.2 + - - +
443B LYS* 3.8 30.9 + - - +
444B ALA* 2.9 32.9 + - - +
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Residues in contact with THR 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 4.6 5.4 - - - +
363B LEU* 4.6 13.7 - - + -
365B ILE* 4.9 10.1 - - + -
425B HIS* 4.4 7.8 - - + +
428B ASN* 3.4 49.8 + - + +
429B VAL* 5.2 3.8 - - + -
437B ASP 2.9 21.1 + - - -
438B LEU* 3.6 9.4 - - + +
440B TYR* 1.3 77.0 - - - +
442B MET* 1.3 58.2 + - - +
444B ALA* 4.1 2.7 - - - +
445B ALA* 3.0 28.4 + - - +
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Residues in contact with MET 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ILE* 3.5 34.2 - - + +
47B LEU* 4.0 28.7 - - + -
109B TRP* 3.5 27.1 - - + +
132B ILE* 4.1 25.8 - - + -
318B PHE* 4.1 14.4 - - - -
363B LEU* 5.1 0.4 - - - -
365B ILE* 4.4 9.4 - - + -
438B LEU* 3.0 42.8 + - + +
439B PHE* 3.8 4.3 - - - +
441B THR* 1.3 76.7 - - - +
443B LYS* 1.3 65.6 + - - +
445B ALA* 4.3 0.2 - - - -
446B LEU* 3.2 23.2 + - - +
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Residues in contact with LYS 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ILE* 3.9 12.2 - - + +
135B MET* 3.7 26.0 - - + -
439B PHE* 2.9 33.4 + - + +
440B TYR* 3.8 33.8 + - - +
442B MET* 1.3 77.6 - - - +
444B ALA* 1.3 63.1 + - - +
446B LEU 3.5 0.2 + - - -
447B GLY 2.9 21.3 + - - -
448B LEU* 3.0 44.9 + - + +
449B LYS* 6.4 0.2 - - + -
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Residues in contact with ALA 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425B HIS* 5.0 7.2 + - + +
428B ASN* 6.3 1.3 - - - +
440B TYR 2.9 17.3 + - - +
441B THR* 4.2 3.6 - - - +
443B LYS* 1.3 78.8 - - - +
445B ALA* 1.3 66.9 + - - +
447B GLY* 2.9 16.3 + - - +
448B LEU 5.0 0.2 - - - +
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Residues in contact with ALA 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B PRO* 3.9 7.1 - - - +
42B ALA* 3.0 40.3 + - + -
45B ILE* 4.0 2.2 - - + -
363B LEU* 3.9 19.3 - - + -
425B HIS* 3.9 23.9 + - + -
441B THR 3.0 21.6 + - - +
442B MET 3.7 4.3 - - - +
444B ALA* 1.3 77.3 - - - +
446B LEU* 1.3 60.7 + - - +
447B GLY* 4.5 0.2 - - - -
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Residues in contact with LEU 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PRO* 5.8 2.9 - - - +
42B ALA 3.2 22.5 - - - +
43B LYS 3.6 17.7 - - - +
44B ASN* 4.2 2.5 - - - +
45B ILE* 3.4 35.7 - - + +
132B ILE* 5.0 3.4 - - + -
136B ALA* 5.0 2.0 - - + -
141B LEU* 4.0 24.2 - - + +
317B PHE 4.7 0.9 - - - +
318B PHE* 4.6 20.6 - - + -
442B MET 3.2 9.8 + - - +
443B LYS 3.9 0.7 - - - +
445B ALA* 1.3 79.3 - - - +
447B GLY* 1.3 63.3 + - - +
448B LEU* 3.9 25.5 - - + +
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Residues in contact with GLY 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443B LYS 2.9 5.9 + - - -
444B ALA* 2.9 17.6 + - - -
445B ALA 4.5 0.2 - - - -
446B LEU* 1.3 81.0 - - - +
448B LEU* 1.3 66.2 + - - +
449B LYS* 3.5 6.9 + - - +
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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