Contacts of the helix formed by residues 61 - 80 (chain A) in PDB entry 2W7W
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 THR 61 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A PHE* 5.3 0.4 - - - -
60A SER* 1.3 73.6 - - - +
62A GLY* 1.3 77.5 + - - +
63A GLY 3.6 0.3 + - - -
64A VAL* 3.7 6.9 + - - +
65A PHE* 3.3 17.0 + - - -
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Residues in contact with GLY 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A THR* 1.3 85.7 + - - +
63A GLY* 1.3 57.9 + - - -
65A PHE* 3.0 14.6 + - - +
66A ASN* 3.0 23.8 + - - +
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Residues in contact with GLY 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 3.6 11.9 - - - -
61A THR 3.6 0.2 + - - -
62A GLY* 1.3 68.0 - - - -
64A VAL* 1.3 64.2 + - - +
66A ASN* 4.3 9.8 - - - +
67A ASN* 2.8 33.4 + - - +
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Residues in contact with VAL 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 3.8 11.7 - - + +
42A LEU* 3.7 33.3 - - + +
43A ILE* 4.8 1.6 - - + -
46A THR* 6.0 2.0 - - + -
48A PHE* 4.0 24.7 - - + -
56A ILE* 3.5 28.3 - - + -
60A SER* 3.6 12.3 - - - -
61A THR 3.7 7.6 + - - +
62A GLY 3.3 0.6 - - - -
63A GLY* 1.3 76.2 - - - +
65A PHE* 1.3 63.1 + - - +
68A ALA* 3.0 23.4 + - - +
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Residues in contact with PHE 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ILE* 3.3 39.5 - - + -
60A SER* 3.3 25.3 + - - +
61A THR* 3.3 18.1 + - - -
62A GLY 3.0 10.9 + - - +
64A VAL* 1.3 79.1 - - - +
66A ASN* 1.3 68.4 + - - +
68A ALA* 4.0 1.5 - - - +
69A ALA* 2.7 57.3 + - + +
142A ALA* 4.0 19.3 - - + -
143A ALA* 4.2 12.3 - - + -
144A THR* 4.5 3.1 - - + -
147A THR* 4.0 15.9 - - + -
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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
----------------------------------------------------------
62A GLY* 3.0 20.1 + - - +
63A GLY* 3.8 10.8 - - - +
64A VAL 3.3 0.2 - - - -
65A PHE* 1.3 89.1 - - - +
67A ASN* 1.3 64.7 + - - +
70A GLN* 3.1 31.9 + - - +
142A ALA* 3.7 10.2 - - - +
119B PHE* 3.5 53.9 - - + +
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Residues in contact with ASN 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A TYR* 3.3 42.9 - - - +
38A LYS* 3.4 37.1 - - - +
39A LEU* 4.0 11.7 - - + +
42A LEU* 3.6 12.3 - - - +
63A GLY* 2.8 23.7 + - - +
64A VAL 4.2 1.1 - - - +
66A ASN* 1.3 77.6 - - - +
68A ALA* 1.3 64.7 + - - +
70A GLN 3.3 1.2 + - - -
71A ILE* 3.0 29.3 + - - +
119B PHE* 5.6 1.6 - - - -
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Residues in contact with ALA 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 LEU* 3.8 26.2 - - + +
53A LEU* 3.7 8.3 - - + +
56A ILE* 3.8 20.9 - - + -
57A ILE* 3.5 21.4 - - + +
64A VAL 3.0 19.5 + - - +
65A PHE* 4.0 2.0 - - - +
67A ASN* 1.3 75.3 - - - +
69A ALA* 1.3 64.3 + - - +
71A ILE* 3.3 5.0 + - - +
72A TRP 3.3 16.6 + - - -
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Residues in contact with ALA 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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57A ILE* 3.8 15.2 - - + +
65A PHE* 2.7 41.4 + - + +
68A ALA* 1.3 73.3 - - - +
70A GLN* 1.3 58.9 + - - +
72A TRP* 3.3 3.7 + - - +
73A ASN* 2.9 34.1 + - - -
142A ALA* 3.4 24.5 - - + +
144A THR* 4.2 9.2 - - + -
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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
----------------------------------------------------------
35A TYR* 3.3 50.3 + - + +
66A ASN 3.1 22.8 + - - +
67A ASN 3.3 0.6 + - - +
69A ALA* 1.3 73.8 - - - +
71A ILE* 1.3 64.9 + - - +
73A ASN* 3.1 18.2 + - - +
74A HIS* 2.6 46.1 + - - -
123A TRP* 3.0 26.1 + - - -
141A ASN 3.9 4.9 - - - -
142A ALA* 3.4 12.8 - - + -
160A TRP* 3.4 25.4 - - - +
119B PHE* 4.1 3.6 - - + -
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Residues in contact with ILE 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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3A PHE* 5.3 5.8 - - + -
4A GLU 5.1 5.6 - - - +
6A PRO* 5.4 2.0 - - + -
32A HIS* 3.2 29.7 + - - +
35A TYR* 3.5 34.5 - - + +
36A VAL* 3.7 28.0 - - + +
39A LEU* 3.6 26.9 - - + -
53A LEU* 3.8 19.5 - - + -
67A ASN 3.0 20.0 + - - +
68A ALA* 3.6 6.1 - - - +
69A ALA 3.3 0.4 - - - -
70A GLN* 1.3 77.5 - - - +
72A TRP* 1.3 63.0 + - - +
75A THR* 3.2 15.9 + - - +
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Residues in contact with TRP 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LEU* 4.2 15.2 - - + +
54A GLU* 3.2 36.3 + - + +
57A ILE* 3.5 25.4 - - + -
68A ALA 3.3 2.8 + - - +
69A ALA 3.3 3.6 + - - +
71A ILE* 1.3 77.9 - - - +
73A ASN* 1.3 79.0 + - - +
75A THR* 3.4 5.3 + - - -
76A PHE* 3.1 58.3 + + + +
125A TRP* 4.1 9.9 - + - -
144A THR* 4.1 16.4 - - + -
146A LEU* 3.9 24.7 - - + -
153A PRO* 3.9 20.9 - - + -
194A LYS* 5.9 4.5 - - - -
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Residues in contact with ASN 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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69A ALA 2.9 22.8 + - - +
70A GLN* 3.1 17.0 + - - +
72A TRP* 1.3 83.3 - - - +
74A HIS* 1.3 57.9 - - - +
76A PHE* 3.5 3.1 + - - +
77A TYR* 2.9 27.4 + - - +
123A TRP* 3.5 31.3 - - + +
125A TRP* 3.3 16.8 - - - -
142A ALA 3.0 28.3 + - - -
143A ALA 4.0 3.4 + - - -
144A THR* 3.2 24.6 + - - -
156A THR* 4.6 2.1 - - - +
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Residues in contact with HIS 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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27A HIS* 3.1 22.4 + + - -
31A HIS* 5.1 1.0 - - - +
32A HIS* 3.4 32.1 - + + +
35A TYR* 3.6 18.4 - + - -
70A GLN* 2.6 54.7 + - - +
72A TRP 3.2 0.2 - - - -
73A ASN* 1.3 73.5 - - - +
75A THR* 1.3 59.6 + - - +
77A TYR* 3.2 8.1 + + - +
78A TRP* 2.9 40.5 + + - +
123A TRP* 3.6 8.9 - + - -
158A ASP* 3.2 3.3 + - - -
162A HIS* 3.8 1.4 + - - -
1195A FE 2.2 31.6 - - - -
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Residues in contact with THR 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 PRO* 3.8 27.7 - - + +
32A HIS* 3.3 20.7 + - - -
71A ILE* 3.2 14.7 + - - +
72A TRP* 4.0 5.2 - - - -
74A HIS* 1.3 77.3 - - - +
76A PHE* 1.3 65.3 + - - +
78A TRP* 3.4 7.5 + - - +
79A ASN* 3.0 38.0 + - - +
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Residues in contact with PHE 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 TRP* 3.1 51.3 + + + +
73A ASN* 3.6 3.8 - - - +
75A THR* 1.3 77.0 - - - +
77A TYR* 1.3 63.7 + - - +
79A ASN* 3.2 10.4 + - - +
80A CYS* 3.2 38.5 + - - -
125A TRP* 3.9 12.3 - + - -
153A PRO* 3.5 32.3 - - + -
154A LEU 3.7 9.2 - - - -
155A LEU 3.8 16.4 - - - -
156A THR* 3.7 14.8 - - + -
187A PHE* 3.7 21.9 - + - -
191A ASN* 3.7 11.7 - - - -
194A LYS* 6.2 1.3 - - - -
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Residues in contact with TYR 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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19A ILE* 4.2 7.1 - - - +
27A HIS* 3.6 20.7 + + - -
73A ASN 2.9 15.5 + - - +
74A HIS* 3.2 10.1 + + - +
76A PHE* 1.3 76.2 - - - +
78A TRP* 1.3 95.7 + + - +
80A CYS* 2.7 29.4 + - - +
81A LEU* 3.5 30.0 + - + +
123A TRP* 4.0 9.0 - + + -
156A THR* 3.9 20.9 - - + -
157A VAL* 4.2 6.5 - - + -
158A ASP* 3.6 33.2 - - + -
163A ALA* 4.3 5.9 + - - +
175A TYR* 2.9 29.5 + - - -
179A PHE* 4.8 1.6 - + - -
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Residues in contact with TRP 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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6A PRO 5.8 0.4 - - - -
8A LEU* 3.5 21.5 - - + -
9A PRO* 3.8 19.8 - - + +
10A PHE* 3.3 16.1 - + + -
19A ILE* 6.0 1.6 - - + -
23A THR* 6.2 0.2 - - + -
24A LEU* 3.6 24.9 - - + -
27A HIS* 3.3 42.6 - + + -
28A HIS* 3.6 30.6 - + + -
32A HIS* 3.0 31.2 + + - -
74A HIS* 2.9 31.3 + + - +
75A THR* 3.8 7.2 - - - +
76A PHE 3.4 0.4 - - - -
77A TYR* 1.3 94.6 - + - +
79A ASN* 1.3 56.5 - - - +
81A LEU* 3.1 37.6 + - + +
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Residues in contact with ASN 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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9A PRO* 3.6 26.1 - - - +
75A THR* 3.0 26.4 + - - +
76A PHE* 3.5 9.3 - - - +
77A TYR 3.2 0.8 - - - -
78A TRP* 1.3 78.4 - - - +
80A CYS* 1.3 57.0 + - - +
81A LEU 3.2 0.7 - - - -
184A ASN* 3.2 15.8 + - - +
187A PHE* 3.2 52.0 - - + +
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Residues in contact with CYS 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 PHE* 3.2 33.7 + - - -
77A TYR* 2.7 12.4 + - - +
79A ASN* 1.3 75.9 - - - +
81A LEU* 1.3 62.2 + - + +
155A LEU* 3.8 21.8 - - + +
156A THR 3.6 34.3 - - - +
179A PHE* 5.0 3.1 - - + -
183A VAL* 3.5 9.2 - - - +
184A ASN* 2.9 26.3 + - - -
187A PHE* 3.9 12.1 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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