Contacts of the helix formed by residues 54 - 66 (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 GLY 54 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B GLY 3.0 5.5 + - - -
53B MET* 1.3 78.9 - - - +
55B ASP* 1.3 66.1 + - - -
56B SER 3.1 3.6 - - - -
57B GLU* 2.9 18.3 + - - -
58B ILE* 3.1 19.8 + - - +
370B HIS 4.4 0.6 + - - -
371B ALA* 4.4 9.6 - - - -
417B LEU* 4.1 20.6 - - - -
418B ARG 5.7 0.4 - - - -
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Residues in contact with ASP 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ASP* 4.6 13.3 - - + +
83A GLN* 3.2 21.0 + - - +
415A SER* 3.3 11.9 - - - +
416A GLN* 3.1 38.0 + - + +
54B GLY* 1.3 72.3 - - - -
56B SER* 1.3 57.0 + - - +
58B ILE* 3.4 4.9 + - - +
59B THR* 2.8 33.8 + - - -
83B GLN* 5.6 0.7 - - - +
416B GLN 4.4 2.4 - - - +
417B LEU* 3.5 10.3 - - - +
418B ARG* 3.0 31.4 + - - +
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Residues in contact with SER 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A SER* 3.2 27.8 + - - -
54B GLY 3.1 0.4 - - - -
55B ASP* 1.3 77.6 - - - +
57B GLU* 1.3 62.5 + - - +
59B THR* 3.3 3.1 + - - -
60B ALA* 3.0 29.7 + - - +
372B HIS 6.0 0.9 - - - -
374B SER* 2.7 31.0 + - - -
375B GLN* 3.8 9.6 - - - +
376B ILE* 3.8 5.9 + - - +
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Residues in contact with GLU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B GLY 3.3 18.7 - - - +
53B MET* 3.9 11.4 - - + -
54B GLY* 2.9 29.7 + - - +
56B SER* 1.3 80.5 - - - +
58B ILE* 1.3 64.5 + - - +
60B ALA* 3.4 2.4 + - - +
61B ALA* 3.0 26.0 + - - +
326B ILE* 4.4 8.7 - - + -
330B ASP* 2.7 27.3 - - - +
338B GLN* 3.7 20.5 + - - +
342B THR* 4.6 4.0 + - - +
371B ALA* 5.4 0.2 - - - +
372B HIS* 3.4 17.0 + - - +
374B SER* 2.8 19.8 + - - +
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Residues in contact with ILE 58 (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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416A GLN* 4.0 9.2 - - - +
53B MET* 3.6 39.3 - - + +
54B GLY 3.1 14.6 + - - +
55B ASP* 3.7 9.0 - - - +
57B GLU* 1.3 76.8 - - - +
59B THR* 1.3 58.0 + - - +
61B ALA* 3.5 2.9 + - - -
62B ARG* 3.0 53.5 + - - +
72B PHE* 3.7 7.8 - - + -
75B ILE* 4.3 9.6 - - + -
76B ASP* 4.2 7.2 - - - +
342B THR* 4.8 3.4 - - + -
418B ARG* 3.9 36.1 - - + +
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Residues in contact with THR 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A THR* 5.2 5.2 - - + -
414A GLY 3.5 23.1 - - - +
415A SER* 3.9 0.9 - - - -
416A GLN* 2.8 31.7 + - + +
55B ASP 2.8 21.7 + - - -
56B SER 3.6 4.5 - - - -
58B ILE* 1.3 76.3 - - - +
60B ALA* 1.3 57.6 + - - +
62B ARG* 3.3 16.2 + - - +
63B ASN* 2.8 47.3 + - - +
376B ILE* 3.6 11.9 - - + -
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Residues in contact with ALA 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B SER* 3.0 18.4 + - - +
57B GLU* 3.9 5.6 - - - +
58B ILE 3.4 0.2 - - - -
59B THR* 1.3 75.7 - - - +
61B ALA* 1.3 63.9 + - - +
63B ASN 3.4 0.2 + - - -
64B TYR* 3.0 21.7 + - - +
338B GLN* 4.7 1.8 - - - +
339B ILE* 4.5 2.2 - - + -
374B SER* 5.5 0.4 - - - +
376B ILE* 3.4 18.3 - - + +
398B MET* 3.5 14.8 - - + +
400B MET* 3.7 35.9 - - + -
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Residues in contact with ALA 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLU 3.0 17.7 + - - +
58B ILE 3.9 1.1 - - - +
60B ALA* 1.3 74.0 - - - +
62B ARG* 1.3 61.9 + - - +
64B TYR* 4.1 0.3 - - - +
65B ALA* 3.0 34.3 + - - +
72B PHE* 3.6 9.7 - - + -
338B GLN* 6.4 0.2 - - - +
339B ILE* 3.7 23.2 - - + +
342B THR* 3.4 35.7 - - + +
343B VAL* 5.2 0.4 - - + +
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Residues in contact with ARG 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A THR* 3.6 19.4 - - - +
416A GLN* 2.8 31.5 + - - +
432A LEU* 3.7 13.8 - - - +
24B ARG* 4.5 2.5 - - - +
58B ILE* 3.0 29.7 + - - +
59B THR* 3.7 16.4 - - - +
61B ALA* 1.3 72.5 - - - +
63B ASN* 1.3 63.7 + - - +
66B GLU* 2.8 36.2 + - + +
67B GLY 2.8 17.4 + - - +
68B ALA 4.3 11.7 - - - -
70B GLY 3.6 23.8 - - - +
71B PHE 4.5 0.4 - - - +
72B PHE* 3.5 16.9 - - + -
76B ASP* 2.8 41.1 + - - +
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Residues in contact with ASN 63 (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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85A THR* 6.1 0.9 - - - +
87A TYR* 5.6 1.0 - - - +
98A TYR* 3.5 32.0 + - + +
414A GLY 5.3 0.8 + - - -
59B THR* 2.8 42.7 + - - +
60B ALA 3.6 4.3 - - - +
62B ARG* 1.3 78.6 + - - +
64B TYR* 1.3 58.3 + - - +
67B GLY* 3.1 28.7 + - - -
68B ALA* 3.4 21.5 + - - +
376B ILE* 3.7 6.9 - - - +
392B THR* 3.4 14.1 - - - +
394B ASP* 4.1 0.7 - - - +
398B MET* 3.6 22.7 - - - -
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Residues in contact with TYR 64 (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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60B ALA 3.0 16.6 + - - +
61B ALA 4.1 1.3 - - - +
63B ASN* 1.3 78.0 - - - +
65B ALA* 1.3 64.4 + - - +
268B TRP* 3.6 33.9 - + - -
284B VAL 4.3 0.9 - - - -
285B THR* 3.6 11.3 - - - +
286B CYS* 2.8 41.8 + - + +
339B ILE* 3.7 18.6 - - + -
390B LEU* 3.9 30.1 - - + -
391B ASN 3.1 30.2 + - - -
392B THR* 3.8 8.4 - - + +
393B LYS* 3.0 24.4 + - - +
398B MET* 4.1 4.0 - - + -
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Residues in contact with ALA 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ALA 3.0 16.4 + - - +
64B TYR* 1.3 81.8 - - + +
66B GLU* 1.3 74.0 + - + +
72B PHE* 4.9 1.1 - - + -
268B TRP* 4.3 12.1 - - + -
339B ILE* 4.8 0.4 - - + -
343B VAL* 3.7 28.3 - - + -
393B LYS* 3.2 16.9 + - - +
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Residues in contact with GLU 66 (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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62B ARG* 2.8 16.2 + - + +
65B ALA* 1.3 84.1 - - - +
67B GLY* 1.3 62.4 + - - +
70B GLY* 3.4 24.8 + - - -
71B PHE 3.9 21.6 + - - +
72B PHE* 4.0 33.5 - - + -
73B LYS* 6.1 0.5 - - - -
343B VAL* 6.2 0.2 - - - +
346B ASP* 5.3 2.1 - - - +
393B LYS* 3.6 22.5 - - - +
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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