Contacts of the helix formed by residues 67 - 83 (chain A) in PDB entry 2GWU
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 TRP 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A PHE* 3.1 24.9 - + + -
38A GLU 3.5 6.6 + - - +
39A ASN* 5.1 3.1 - - + -
47A ALA* 4.6 2.0 - - + -
66A GLY* 1.4 73.5 - - - -
68A CYS* 1.4 95.6 + - + +
69A LEU* 3.4 10.4 - - + +
70A GLN* 3.1 15.4 + - + +
71A VAL* 2.9 23.2 + - - +
106A ILE* 3.2 24.2 - - + -
108A LEU* 6.2 0.7 - - + -
205A MET* 5.0 1.3 - - + -
206A ASN* 3.0 49.7 + - - +
209A LEU* 3.2 47.1 - - + -
210A GLN* 3.7 12.8 - - - +
217A PHE* 4.4 21.3 - + + -
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Residues in contact with CYS 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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37A PHE* 3.3 5.8 - - + -
67A TRP* 1.4 115.1 - - + +
69A LEU* 1.3 76.7 + - - +
71A VAL* 2.9 22.9 - - - +
72A ASN* 3.0 18.1 + - - +
106A ILE 3.7 3.4 - - - -
107A HIS* 3.5 34.1 - - + +
108A LEU* 3.7 14.6 - - - +
124A GLY* 3.5 14.1 - - - +
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Residues in contact with LEU 69 (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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49A ASP 5.2 1.1 - - - +
50A LEU* 2.9 44.9 - - + -
55A ILE* 5.3 0.4 - - + -
67A TRP* 3.4 12.5 - - + +
68A CYS* 1.3 84.4 - - - +
70A GLN* 1.3 64.6 + - + +
73A HIS* 2.8 59.4 + - + +
108A LEU* 3.5 17.0 - - + -
202A PHE 3.3 8.1 - - - +
205A MET* 5.7 0.2 - - + -
206A ASN* 2.9 47.3 - - + +
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Residues in contact with GLN 70 (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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41A ASN* 4.4 10.4 + - - +
47A ALA* 4.6 12.0 - - + +
49A ASP 6.0 0.7 - - - +
55A ILE* 2.7 34.9 - - + +
58A GLN* 2.8 42.8 + - - +
59A VAL* 5.1 6.2 - - + +
65A GLY 3.1 11.0 + - - +
66A GLY* 2.9 29.6 - - - +
67A TRP* 3.1 22.3 + - + +
69A LEU* 1.3 85.0 - - + +
71A VAL* 1.3 59.0 + - + +
74A LEU* 2.9 11.3 + - - +
206A ASN* 5.1 3.4 - - - +
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Residues in contact with VAL 71 (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 GLN* 5.2 9.0 - - + +
35A VAL* 5.1 11.4 - - + +
36A PRO 4.9 5.8 - - - +
37A PHE* 5.2 3.8 - - + -
59A VAL* 5.9 3.6 - - + -
66A GLY* 4.1 19.5 - - - +
67A TRP 2.9 21.2 + - - +
68A CYS 2.9 14.4 - - - +
70A GLN* 1.3 71.8 - - + +
72A ASN* 1.3 57.9 - - - +
74A LEU* 3.2 9.3 + - + +
75A LEU* 3.0 29.4 + - - +
123A ALA* 4.4 14.4 - - + +
124A GLY* 2.9 36.1 - - - +
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Residues in contact with ASN 72 (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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68A CYS* 3.0 21.7 + - - +
71A VAL* 1.3 75.2 - - - +
73A HIS* 1.3 60.4 + - - +
75A LEU* 4.5 3.8 - - - +
76A TYR* 2.8 31.9 + - - +
88A MET* 3.5 19.1 - - + -
108A LEU 2.7 27.6 + - - +
109A LEU* 4.3 4.0 - - - -
110A LEU* 3.6 14.1 - - + +
121A VAL 3.8 4.7 - - - +
122A ASP* 2.8 24.1 + - - +
123A ALA* 3.4 20.6 + - - +
124A GLY* 3.5 11.1 - - - -
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Residues in contact with HIS 73 (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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50A LEU* 2.9 64.3 - - + +
55A ILE* 2.9 18.2 - - + -
69A LEU* 2.8 38.4 + - + +
72A ASN* 1.3 78.2 - - - +
74A LEU* 1.3 60.5 + - - +
76A TYR* 3.2 7.3 - + + +
77A TRP* 3.1 35.8 + + - +
88A MET* 3.5 24.1 - - + +
199A ILE* 3.6 11.8 - - + +
202A PHE* 3.5 14.8 - + + +
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Residues in contact with LEU 74 (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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6A TYR* 3.3 33.0 - - + +
31A GLN* 4.8 6.3 - - - +
55A ILE* 2.8 24.6 - - + +
56A PHE* 3.8 37.0 - - + -
59A VAL* 3.1 48.0 - - + -
60A VAL* 4.1 0.7 - - + -
70A GLN 2.9 13.8 + - - +
71A VAL* 3.2 7.2 + - - +
73A HIS* 1.3 74.2 - - - +
75A LEU* 1.3 62.9 + - - +
77A TRP* 3.1 6.8 + - - +
78A ALA* 3.0 20.1 + - - +
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Residues in contact with LEU 75 (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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6A TYR* 4.1 12.8 - - - +
27A ILE* 3.5 31.0 - - + -
28A LEU* 4.1 12.8 - - + -
31A GLN* 5.5 4.3 - - + -
71A VAL 3.0 13.8 + - - +
72A ASN* 4.0 4.9 - - - +
74A LEU* 1.3 81.0 - - + +
76A TYR* 1.3 52.8 + - - +
78A ALA* 3.1 9.6 + - + -
79A LEU* 2.8 54.0 + - + +
110A LEU* 3.8 8.3 - - + -
121A VAL* 3.3 34.1 - - + -
123A ALA* 4.7 12.6 - - + -
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Residues in contact with TYR 76 (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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72A ASN 2.8 19.3 + - - +
73A HIS* 3.2 9.6 - + - +
75A LEU* 1.3 75.9 - - - +
77A TRP* 1.3 99.7 + + - +
79A LEU* 3.4 1.5 + - - +
80A THR* 3.1 23.5 + - + +
85A GLU* 5.5 0.5 + - - -
86A THR* 3.0 63.2 + - + +
87A THR* 4.8 0.3 - - - -
88A MET* 3.9 21.5 - - + -
110A LEU* 3.6 23.0 - - + +
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Residues in contact with TRP 77 (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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1A MET* 3.7 17.3 - - - -
50A LEU 3.8 12.1 + - - -
51A GLY* 5.3 2.0 - - - -
52A LEU* 3.5 54.0 - - + +
55A ILE* 4.1 7.2 - - + -
56A PHE* 4.3 2.0 - - + -
73A HIS* 3.1 30.5 + + - -
74A LEU 3.1 6.7 + - - +
76A TYR* 1.3 107.2 - + - +
78A ALA* 1.3 59.6 + - - +
80A THR* 2.7 32.0 - - + +
81A THR* 3.1 11.8 + - - +
199A ILE* 5.5 9.0 - - + -
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Residues in contact with ALA 78 (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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1A MET* 3.7 14.8 - - + +
3A ILE* 5.9 2.0 - - + -
6A TYR* 4.3 32.1 - - + -
7A LEU* 6.0 2.0 - - + -
27A ILE* 5.8 2.7 - - + -
56A PHE* 5.1 2.2 - - + -
74A LEU 3.0 12.2 + - - +
75A LEU* 3.1 13.4 + - + +
77A TRP* 1.3 77.5 - - - +
79A LEU* 1.3 61.7 + - + +
81A THR* 2.6 20.5 + - - -
82A ILE* 2.9 17.9 - - + +
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Residues in contact with LEU 79 (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 LEU* 3.9 27.4 - - + -
27A ILE* 3.9 25.6 - - + -
75A LEU* 2.8 45.7 + - + +
76A TYR* 3.9 4.5 - - - +
78A ALA* 1.3 72.7 - - - +
80A THR* 1.3 62.9 + - - +
82A ILE* 3.1 11.9 + - - +
83A GLY 3.2 0.3 + - - -
84A PHE* 3.0 44.4 + - + -
86A THR* 4.9 4.5 - - + +
110A LEU* 4.1 8.7 - - + -
112A VAL* 3.7 31.0 - - + -
121A VAL* 4.9 0.4 - - + -
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Residues in contact with THR 80 (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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76A TYR* 3.1 19.4 + - + +
77A TRP* 2.7 45.5 - - + +
79A LEU* 1.3 77.2 - - - +
81A THR* 1.3 65.5 + - + +
83A GLY* 3.1 13.0 + - - -
84A PHE 3.4 15.5 + - - +
85A GLU* 5.7 1.2 + - - -
86A THR* 4.2 12.3 - - - +
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Residues in contact with THR 81 (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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1A MET* 2.9 41.0 - - + +
3A ILE* 3.3 25.5 - - + +
52A LEU* 5.7 1.1 - - + -
77A TRP 3.1 6.1 + - - +
78A ALA 2.6 20.6 + - - -
80A THR* 1.3 81.0 - - + +
82A ILE* 1.3 61.9 + - - +
83A GLY* 3.4 1.0 + - - -
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Residues in contact with ILE 82 (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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3A ILE* 5.0 11.0 - - + -
7A LEU* 5.3 10.1 - - + -
16A ARG* 5.7 8.3 - - - +
17A ASN* 3.7 33.2 - - - +
19A LEU* 2.8 36.0 - - + +
27A ILE* 4.8 12.1 - - + -
78A ALA* 2.9 26.9 - - + +
79A LEU* 3.1 13.0 + - - +
81A THR* 1.3 81.5 - - - +
83A GLY* 1.3 54.9 + - - +
84A PHE* 3.4 25.6 - - + -
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Residues in contact with GLY 83 (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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19A LEU* 3.8 15.3 - - - +
80A THR 3.1 11.2 + - - -
81A THR 3.3 1.7 - - - -
82A ILE* 1.3 79.6 - - - +
84A PHE* 1.3 64.7 + - - +
85A GLU 3.9 0.9 + - - -
113A THR 5.1 0.2 - - - +
115A ASP* 4.2 13.7 - - - +
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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