Contacts of the helix formed by residues 55 - 73 (chain A) in PDB entry 1WCP
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 PHE 55 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ASP* 1.3 77.8 + - - +
56A ASN* 1.3 72.7 + - + +
57A THR 3.5 0.2 - - - -
58A ARG* 3.0 16.9 + - - +
59A THR* 2.9 59.8 + - + -
142A PRO* 5.1 13.0 - - + -
143A ASP* 5.3 0.4 - - - -
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Residues in contact with ASN 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 ASP* 3.0 6.3 + - - +
55A PHE* 1.3 90.5 - - + +
57A THR* 1.3 84.7 + - - +
59A THR* 3.8 1.0 + - - -
60A GLN* 3.0 46.1 + - - +
91A SER* 5.5 5.3 + - - -
93A ILE* 5.0 1.6 - - - +
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Residues in contact with THR 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU 3.6 16.4 - - - +
48A GLN* 3.7 13.8 + - + -
49A SER* 5.2 2.2 - - - +
54A ASP* 3.2 15.3 + - - -
56A ASN* 1.3 88.8 + - - +
58A ARG* 1.3 68.1 + - - +
61A VAL* 3.0 44.3 + - + +
92A SER 4.8 2.9 - - - +
93A ILE* 4.3 11.1 - - + +
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Residues in contact with ARG 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLN* 3.6 20.5 + - - +
53A LEU* 5.7 3.8 - - - +
54A ASP* 2.7 48.4 + - + +
55A PHE* 3.0 20.4 + - - +
57A THR* 1.3 82.9 - - - +
59A THR* 1.3 64.1 + - - +
61A VAL* 3.5 0.2 - - - -
62A THR* 2.7 35.5 + - - +
136A PHE* 3.6 51.2 - - + -
138A SER* 4.7 2.2 - - - +
143A ASP* 2.8 39.5 + - - -
151A VAL* 5.2 5.2 - - + -
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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
----------------------------------------------------------
55A PHE* 2.9 60.6 + - + +
56A ASN* 3.8 3.1 + - - -
58A ARG* 1.3 76.9 - - - +
60A GLN* 1.3 68.4 + - - +
62A THR* 3.4 4.6 + - - -
63A ARG* 3.1 26.2 + - - +
142A PRO* 3.7 18.4 - - + +
143A ASP* 3.1 33.6 + - - +
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Residues in contact with GLN 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 ASN* 3.0 47.2 + - - +
58A ARG 3.1 0.8 + - - -
59A THR* 1.3 87.1 + - - +
61A VAL* 1.3 58.2 + - - +
63A ARG* 3.0 22.6 + - - +
64A GLU* 3.2 13.7 + - - +
89A PRO* 5.2 6.7 - - + +
90A LEU* 5.4 4.7 + - - +
91A SER* 4.9 9.5 + - - -
93A ILE* 3.7 33.4 - - + +
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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
----------------------------------------------------------
46A VAL* 4.3 7.2 - - + -
47A LEU 3.9 7.0 - - - +
48A GLN* 3.2 29.5 - - + +
57A THR* 3.0 43.5 + - + +
58A ARG 2.9 5.4 + - - +
60A GLN* 1.3 71.7 - - - +
62A THR* 1.3 60.9 + - - +
64A GLU* 4.6 1.3 - - - -
65A ALA* 3.2 22.5 + - - +
93A ILE* 3.6 30.7 - - + -
94A LEU 3.2 24.5 - - - +
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Residues in contact with THR 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A GLN* 4.6 5.4 + - - +
58A ARG* 2.7 37.0 + - - +
59A THR* 3.4 8.6 - - - -
61A VAL* 1.3 71.4 - - - +
63A ARG* 1.3 62.0 + - - +
65A ALA* 3.9 3.4 - - - +
66A ILE* 3.3 30.7 + - + +
138A SER* 4.5 8.1 - - - +
143A ASP* 3.6 15.9 + - + +
144A THR* 3.5 31.2 - - + -
149A ALA* 4.2 13.7 - - + -
151A VAL* 5.8 3.4 - - + -
161A CYS* 5.1 8.3 - - - -
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Residues in contact with ARG 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 3.1 11.4 + - - +
60A GLN* 3.0 11.6 + - - +
62A THR* 1.3 71.4 - - - +
64A GLU* 1.3 55.2 + - - +
66A ILE* 3.3 6.1 + - - +
67A SER* 2.9 35.1 + - - -
141A ASP* 2.8 48.6 + - - -
142A PRO* 3.7 12.2 + - - +
143A ASP 3.3 15.8 + - - +
144A THR 4.5 3.1 - - - -
145A ALA* 3.7 19.8 - - - +
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Residues in contact with GLU 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 GLN 3.2 11.4 + - - +
61A VAL* 4.2 3.4 - - - +
63A ARG* 1.3 74.3 - - - +
65A ALA* 1.3 67.5 + - - +
67A SER* 3.1 13.6 + - - -
68A LEU* 3.0 31.6 + - - +
84A LYS* 5.7 9.0 - - - +
89A PRO* 4.7 16.5 - - + +
93A ILE* 4.2 15.7 - - + -
94A LEU* 4.1 13.7 - - - +
95A GLY 3.8 24.1 - - - +
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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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44A VAL* 3.5 30.0 - - + +
46A VAL* 4.7 4.7 - - + -
48A GLN* 5.6 0.2 - - - +
61A VAL 3.2 20.3 + - - +
62A THR* 3.9 5.8 - - - +
63A ARG 3.4 0.2 - - - -
64A GLU* 1.3 77.2 - - - +
66A ILE* 1.3 65.5 + - + +
68A LEU* 3.1 14.0 + - - +
69A VAL* 3.2 17.7 + - - +
95A GLY* 4.1 16.8 - - - +
161A CYS* 5.2 5.4 - - + -
163A ILE* 5.5 1.8 - - + -
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Residues in contact with ILE 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 THR* 3.3 20.9 + - + +
63A ARG* 3.8 3.1 - - - +
64A GLU 3.2 0.4 - - - -
65A ALA* 1.3 78.5 - - + +
67A SER* 1.3 56.9 + - - +
69A VAL* 3.3 6.9 + - + +
70A CYS* 3.0 38.0 + - - -
144A THR* 3.6 49.4 - - + +
146A GLU* 5.7 1.6 - - + -
147A TYR* 3.7 34.3 - - + -
149A ALA* 4.2 11.0 - - + -
161A CYS* 6.5 0.7 - - - -
163A ILE* 3.8 27.6 - - + -
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Residues in contact with SER 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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63A ARG 2.9 18.7 + - - -
64A GLU* 3.3 19.6 + - - -
66A ILE* 1.3 75.4 - - - +
68A LEU* 1.3 57.2 + - - +
70A CYS* 3.6 19.0 - - - +
71A GLU* 3.7 14.8 - - - +
82A ARG* 5.0 8.0 + - - +
84A LYS* 4.3 23.8 + - - +
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Residues in contact with LEU 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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44A VAL* 4.8 1.6 - - + -
64A GLU* 3.0 21.4 + - - +
65A ALA 3.1 10.1 + - - +
67A SER* 1.3 76.1 - - - +
69A VAL* 1.3 58.6 + - + +
70A CYS 3.3 0.2 - - - -
71A GLU* 3.0 23.8 + - + +
72A ALA* 3.0 21.4 + - + -
84A LYS* 4.9 5.6 - - - +
95A GLY 3.8 22.0 - - - +
96A ARG* 4.2 5.2 - - + -
97A SER* 3.3 34.8 - - - +
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Residues in contact with VAL 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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41A MET* 4.2 19.8 - - + +
42A GLY* 4.3 12.3 - - - -
43A CYS 4.2 10.8 - - - +
44A VAL* 3.5 31.4 - - + -
65A ALA 3.2 7.7 + - - +
66A ILE* 3.3 5.4 + - + +
68A LEU* 1.3 72.4 - - + +
70A CYS* 1.3 66.1 + - - +
71A GLU 3.0 1.1 - - - -
72A ALA* 3.5 11.2 - - + +
73A VAL* 3.1 42.1 + - + +
97A SER* 5.5 0.9 - - - +
99A LEU* 4.7 4.7 - - + -
163A ILE* 4.2 14.6 - - + -
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Residues in contact with CYS 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 MET* 5.9 1.3 - - - -
66A ILE* 3.0 33.4 + - - +
67A SER* 3.6 11.7 - - - +
69A VAL* 1.3 76.9 - - - +
71A GLU* 1.3 57.6 + - - +
73A VAL 3.9 8.2 - - - +
76A ALA* 4.2 18.9 - - + +
80A THR* 3.4 15.2 - - - +
82A ARG* 3.7 42.4 + - - +
146A GLU* 4.3 2.5 - - - -
147A TYR* 3.8 28.7 - - - -
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Residues in contact with GLU 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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67A SER 3.7 12.5 - - - +
68A LEU* 3.0 17.7 + - + +
69A VAL 3.0 0.2 - - - -
70A CYS* 1.3 80.1 - - - +
72A ALA* 1.3 56.7 + - - +
73A VAL 3.5 0.9 - - - -
80A THR* 3.5 25.7 - - - +
81A ARG* 4.3 16.6 + - + +
82A ARG* 3.2 29.3 + - + +
83A ARG* 2.9 30.8 + - - +
84A LYS* 2.4 29.4 + - - -
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Residues in contact with ALA 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 LEU* 3.0 14.2 + - + +
69A VAL* 3.2 12.4 + - + -
71A GLU* 1.3 75.6 - - - +
73A VAL* 1.3 62.7 + - - +
74A PRO* 3.7 7.2 - - - +
80A THR* 5.4 0.2 - - - -
97A SER* 3.7 23.3 - - - +
99A LEU* 4.0 27.2 - - + +
102A ALA* 4.6 1.6 - - - +
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Residues in contact with VAL 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A MET* 3.0 44.2 - - + +
69A VAL* 3.1 27.4 + - + +
70A CYS 3.9 11.1 - - - +
72A ALA* 1.3 77.5 - - - +
74A PRO* 1.4 76.4 - - + +
75A GLY 3.2 15.9 + - - +
76A ALA* 4.0 4.3 + - - +
80A THR* 3.7 8.8 - - - +
99A LEU* 4.2 7.2 - - + -
102A ALA* 4.2 3.1 - - + +
103A GLY* 3.6 25.8 - - - +
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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