Contacts of the helix formed by residues 54 - 67 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A GLY 2.9 12.7 + - - -
53A MET* 1.3 77.0 - - - +
55A ASP* 1.3 66.7 + - - -
56A SER 3.1 2.9 - - - -
57A GLU* 3.1 12.7 + - - -
58A ILE* 3.1 19.9 + - - +
370A HIS 4.4 0.4 + - - -
371A ALA* 4.5 8.5 - - - -
417A LEU* 4.2 23.1 - - - -
418A ARG* 5.7 0.9 - - - -
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Residues in contact with ASP 55 (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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54A GLY* 1.3 73.0 - - - -
56A SER* 1.3 57.6 + - - +
58A ILE* 3.4 4.1 + - - +
59A THR* 2.7 34.3 + - - -
83A GLN* 5.6 1.0 - - - +
416A GLN 4.4 2.4 - - - +
417A LEU* 3.5 9.1 - - - +
418A ARG* 3.0 31.7 + - - +
55B ASP* 4.6 13.3 - - + +
83B GLN* 3.2 20.3 - - - +
415B SER* 3.3 11.9 - - - +
416B GLN* 3.1 37.6 + - + +
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Residues in contact with SER 56 (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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54A GLY 3.1 0.6 - - - -
55A ASP* 1.3 77.2 - - - +
57A GLU* 1.3 64.9 + - - +
59A THR* 3.8 1.2 - - - -
60A ALA* 2.9 30.7 + - - +
372A HIS 6.1 0.4 - - - -
374A SER* 2.7 32.3 + - - -
375A GLN* 3.8 9.2 - - - +
376A ILE* 3.9 6.9 + - - +
415B SER* 3.1 26.5 + - - +
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Residues in contact with GLU 57 (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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52A GLY 3.4 16.9 - - - +
53A MET* 3.9 11.2 - - + -
54A GLY* 3.1 30.0 + - - +
56A SER* 1.3 80.6 - - - +
58A ILE* 1.3 66.2 + - - +
60A ALA* 3.5 2.2 + - - +
61A ALA* 3.0 25.3 + - - +
326A ILE* 4.4 9.0 - - + -
330A ASP* 2.7 28.9 - - - +
338A GLN* 3.6 20.1 + - - +
342A THR* 4.5 4.0 + - - +
372A HIS* 3.3 16.9 + - - +
374A SER* 2.8 20.1 + - - +
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Residues in contact with ILE 58 (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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53A MET* 3.7 38.6 - - + +
54A GLY 3.1 15.0 + - - +
55A ASP* 3.7 8.7 - - - +
56A SER 3.4 0.2 - - - -
57A GLU* 1.3 76.8 - - - +
59A THR* 1.3 58.0 + - - +
61A ALA* 3.3 2.8 + - - -
62A ARG* 2.9 53.5 + - - +
72A PHE* 3.7 9.6 - - + -
75A ILE* 4.2 14.1 - - + -
76A ASP* 4.1 8.1 - - - +
342A THR* 4.7 4.7 - - + -
418A ARG* 3.9 31.4 - - + +
416B GLN* 4.1 8.1 - - - +
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Residues in contact with THR 59 (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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55A ASP 2.7 22.2 + - - -
56A SER 3.8 3.6 - - - -
58A ILE* 1.3 74.2 - - - +
60A ALA* 1.3 60.3 + - - +
62A ARG* 3.1 20.2 + - - +
63A ASN* 2.8 54.4 + - - +
376A ILE* 3.8 5.4 - - + -
85B THR* 5.1 4.9 - - + -
414B GLY 3.6 22.0 - - - +
415B SER* 4.1 0.9 - - - -
416B GLN* 2.9 30.7 + - + +
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Residues in contact with ALA 60 (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 SER* 2.9 19.5 + - - +
57A GLU* 3.8 5.4 - - - +
59A THR* 1.3 75.8 - - - +
61A ALA* 1.3 63.5 + - - +
63A ASN* 3.4 0.6 + - - +
64A TYR* 3.1 20.4 + - - +
338A GLN* 4.9 1.1 - - - +
339A ILE* 4.5 2.7 - - + -
374A SER* 5.3 0.7 - - - +
376A ILE* 3.4 20.3 - - + +
398A MET* 3.4 14.8 - - - +
400A MET* 3.7 33.2 - - + -
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Residues in contact with ALA 61 (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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57A GLU 3.0 18.1 + - - +
58A ILE 3.7 2.5 - - - +
60A ALA* 1.3 74.1 - - - +
62A ARG* 1.3 59.0 + - - +
64A TYR* 4.0 0.3 - - - +
65A ALA* 2.8 35.3 + - - +
72A PHE* 3.7 8.5 - - + -
339A ILE* 3.7 24.8 - - + +
342A THR* 3.5 35.0 - - + +
343A VAL* 5.2 0.4 - - + +
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Residues in contact with ARG 62 (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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24A ARG* 4.5 2.7 - - - +
58A ILE* 2.9 29.5 + - - +
59A THR* 3.1 17.3 + - - +
61A ALA* 1.3 76.4 - - - +
63A ASN* 1.3 60.6 + - - +
66A GLU* 2.7 41.0 + - + +
67A GLY 2.8 13.4 + - - +
68A ALA 4.3 11.6 + - - -
70A GLY 3.6 21.5 - - - -
71A PHE 4.5 0.4 - - - +
72A PHE* 3.5 15.8 - - + -
76A ASP* 2.8 41.4 + - - +
85B THR* 3.6 20.8 - - - +
416B GLN* 2.7 31.1 + - - +
432B LEU* 3.8 14.1 - - - +
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Residues in contact with ASN 63 (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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59A THR* 2.8 37.0 + - - +
60A ALA 3.6 0.2 - - - +
62A ARG* 1.3 73.8 + - - +
64A TYR* 1.3 62.1 + - - +
67A GLY* 3.1 26.5 + - - -
68A ALA* 3.5 19.7 + - - +
376A ILE* 3.7 15.6 - - - +
392A THR* 3.5 12.8 - - - -
394A ASP* 4.1 0.9 - - - +
398A MET* 3.4 31.2 - - - -
87B TYR* 5.6 1.2 - - - +
98B TYR* 3.5 28.4 + - + +
414B GLY 5.2 1.0 + - - -
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Residues in contact with TYR 64 (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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60A ALA 3.1 14.2 + - - +
61A ALA 4.0 1.8 - - - +
63A ASN* 1.3 79.8 - - - +
65A ALA* 1.3 64.1 + - - +
268A TRP* 3.6 35.2 - + - -
284A VAL 4.5 0.7 - - - -
285A THR* 3.7 12.0 - - - +
286A CYS* 2.8 41.6 + - + +
339A ILE* 3.9 18.4 - - + -
390A LEU* 4.0 27.4 - - + -
391A ASN 3.1 28.3 + - - -
392A THR* 3.9 10.3 - - + +
393A LYS* 3.0 25.6 + - - +
398A MET* 4.2 4.3 - - + -
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Residues in contact with ALA 65 (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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61A ALA 2.8 20.5 + - - +
64A TYR* 1.3 80.5 - - + +
66A GLU* 1.3 72.7 + - + +
72A PHE* 4.7 2.5 - - + -
268A TRP* 4.4 10.1 - - + -
339A ILE* 4.8 0.4 - - + -
343A VAL* 3.7 29.6 - - + -
393A LYS* 3.5 16.8 + - - +
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Residues in contact with GLU 66 (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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62A ARG* 2.7 19.1 + - + +
65A ALA* 1.3 82.5 - - + +
67A GLY* 1.3 56.1 + - - +
70A GLY* 3.2 15.5 + - - -
71A PHE 3.8 36.4 + - - +
72A PHE* 3.9 31.1 - - + -
73A LYS 5.8 0.2 + - - -
346A ASP* 5.3 2.3 - - - +
393A LYS* 3.8 26.4 + - - +
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Residues in contact with GLY 67 (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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62A ARG* 2.8 15.7 + - - +
63A ASN* 3.1 17.5 + - - -
65A ALA 3.7 1.0 - - - -
66A GLU* 1.3 78.3 - - - +
68A ALA* 1.3 62.6 + - - +
69A GLY 3.2 2.9 - - - -
70A GLY* 2.8 17.0 + - - -
393A LYS* 4.0 7.2 - - - +
394A ASP* 3.2 20.4 - - - -
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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