Contacts of the helix formed by residues 56 - 68 (chain A) in PDB entry 2E7Y
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 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A ALA 2.6 23.3 + - - -
27A GLY 3.6 12.1 - - - -
28A GLU* 3.5 10.6 - - - +
30A VAL* 4.0 8.4 - - - +
31A SER* 4.9 0.5 + - - -
55A ALA* 1.3 71.2 - - - +
57A LEU* 1.3 62.9 + - - +
58A TRP 3.3 1.6 - - - -
59A GLY* 3.3 5.2 + - - -
60A VAL* 3.3 22.5 + - - +
28B GLU* 3.8 10.5 - - - +
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Residues in contact with LEU 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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23A LEU* 5.8 0.2 - - + -
26A ALA* 3.5 12.7 + - + -
44A VAL* 4.5 20.9 - - + -
46A LEU* 4.7 9.4 - - + -
54A ILE* 2.9 16.8 + - + +
56A GLY* 1.3 77.4 - - - +
58A TRP* 1.3 63.4 + - - +
60A VAL* 3.2 12.0 + - + +
61A VAL* 3.1 32.3 + - + +
75A LEU* 4.8 0.9 - - + -
77A VAL* 4.2 34.5 - - + -
89A TYR* 4.0 8.1 - - + -
90A THR* 4.0 26.7 - - + -
93A ILE* 4.3 10.5 - - + -
104A PHE* 4.5 3.8 - - + -
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Residues in contact with TRP 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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55A ALA 4.5 2.0 - - - +
56A GLY 3.3 0.2 - - - -
57A LEU* 1.3 79.4 - - - +
59A GLY* 1.3 57.1 + - - +
61A VAL* 3.3 1.0 + - - +
62A ASN* 2.9 28.7 + - + +
89A TYR* 3.2 24.0 + + - +
92A PHE* 3.9 24.2 - + - -
93A ILE* 3.7 31.6 - - + +
96A ALA* 5.5 0.2 - - + -
97A ASN* 3.6 39.0 + - - +
100A LEU* 4.0 9.2 - - + +
49B GLY 5.0 1.8 - - - -
51B VAL* 3.4 38.4 - - + +
54B ILE* 3.9 29.2 - - + -
55B ALA* 4.0 12.8 - - + -
85B ALA* 5.7 1.8 - - + -
89B TYR* 3.8 30.1 - + + -
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Residues in contact with GLY 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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31A SER* 3.6 16.8 - - - -
55A ALA 4.9 0.8 + - - -
56A GLY* 3.3 7.0 + - - -
57A LEU 3.3 0.6 - - - -
58A TRP* 1.3 78.8 - - - +
60A VAL* 1.3 62.7 + - - +
62A ASN* 3.8 5.6 - - - +
63A ILE* 3.0 31.8 + - - +
11B PHE 6.2 0.2 - - - -
28B GLU* 5.0 6.2 + - - -
51B VAL* 4.4 12.1 - - - +
55B ALA* 5.8 1.2 - - - +
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Residues in contact with VAL 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 4.6 5.6 - - + -
26A ALA* 5.5 0.2 - - + -
30A VAL* 3.7 22.0 - - + -
31A SER* 3.8 12.3 - - - +
38A VAL* 4.4 4.8 - - + +
41A PHE* 3.8 29.8 - - + -
44A VAL* 5.4 0.9 - - + -
56A GLY 3.3 15.9 + - - +
57A LEU* 3.2 14.7 + - + +
59A GLY* 1.3 77.2 - - - +
61A VAL* 1.3 63.4 + - + +
63A ILE* 4.0 1.0 - - - +
64A ARG* 3.1 29.2 + - + +
75A LEU* 3.8 28.5 - - + -
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Residues in contact with VAL 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 LEU* 3.1 28.4 + - + +
58A TRP* 3.9 4.3 - - - +
60A VAL* 1.3 74.8 - - - +
62A ASN* 1.3 65.5 + - - +
64A ARG* 3.8 5.8 - - - +
65A ASN* 2.9 23.9 + - - +
75A LEU* 4.5 9.4 - - + -
93A ILE* 4.9 1.6 - - + -
100A LEU* 3.6 22.7 - - + -
103A SER* 3.7 13.6 - - - +
104A PHE* 3.4 53.6 - - + -
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Residues in contact with ASN 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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58A TRP* 2.9 20.7 + - + +
59A GLY* 3.8 4.3 - - - +
61A VAL* 1.3 79.2 - - - +
63A ILE* 1.3 68.4 + - + +
65A ASN* 3.7 0.9 - - - +
66A ASN* 3.0 56.2 + - - +
97A ASN* 5.6 2.6 - - - +
100A LEU* 4.1 25.5 - - + +
10B LEU* 4.5 2.9 - - - +
51B VAL* 3.5 31.5 - - + +
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Residues in contact with ILE 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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31A SER* 4.4 4.0 - - - +
35A GLY 4.8 1.6 - - - +
36A SER* 5.6 0.2 - - - -
38A VAL* 3.7 21.8 - - + -
39A TYR* 3.6 14.4 - - + +
59A GLY* 3.0 22.8 + - - +
60A VAL 4.1 2.2 - - - +
62A ASN* 1.3 80.8 - - + +
64A ARG* 1.3 68.2 + - - +
66A ASN* 3.8 4.8 - - + +
67A GLY* 2.9 22.9 + - - -
10B LEU* 3.5 32.1 - - + +
11B PHE* 3.7 46.9 - - + -
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Residues in contact with ARG 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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38A VAL* 3.1 27.1 + - + +
39A TYR* 2.7 33.0 + - - -
41A PHE* 2.3 32.9 + - - +
42A LYS* 5.7 0.2 - - - +
60A VAL* 3.1 23.5 + - + +
61A VAL* 3.8 5.4 - - + +
63A ILE* 1.3 75.5 - - - +
65A ASN* 1.3 60.1 + - - +
68A MET* 3.0 57.7 + - - +
72A GLU* 4.3 7.8 - - - +
73A LYS* 2.7 35.1 + - - +
74A PRO 4.1 0.8 + - - -
75A LEU* 3.8 37.7 - - - +
103A SER* 5.4 2.5 - - - -
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Residues in contact with ASN 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 VAL 2.9 19.1 + - - +
62A ASN 3.7 1.1 - - - +
64A ARG* 1.3 78.3 - - - +
66A ASN* 1.3 72.6 + - - +
69A GLY* 4.6 8.5 + - - +
72A GLU* 3.6 19.5 - - - +
99A ASP* 2.7 31.1 + - - +
100A LEU* 3.4 25.7 - - + +
103A SER* 2.9 19.8 + - - +
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Residues in contact with ASN 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 ASN* 3.0 49.5 + - - +
63A ILE* 4.2 5.8 - - + +
65A ASN* 1.3 88.8 + - - +
67A GLY* 1.3 59.7 + - - +
68A MET 3.7 0.4 - - - -
69A GLY* 4.7 3.8 + - - -
100A LEU* 5.4 0.2 - - - +
10B LEU* 6.4 1.8 - - + -
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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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39A TYR* 3.3 34.9 + - - -
63A ILE 2.9 11.5 + - - -
66A ASN* 1.3 78.5 - - - +
68A MET* 1.3 60.3 + - - +
69A GLY 3.5 2.0 - - - -
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Residues in contact with MET 68 (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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39A TYR* 3.3 50.0 - - + +
64A ARG* 3.0 55.6 + - - +
67A GLY* 1.3 77.8 - - - +
69A GLY* 1.3 62.0 + - - +
71A ARG* 2.8 42.7 + - + +
72A GLU* 3.5 26.2 - - + +
73A LYS* 4.1 17.9 - - + +
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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