Contacts of the helix formed by residues 61 - 76 (chain A) in PDB entry 2WH6
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 ASN 61 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ILE 2.8 25.1 + - - +
58A ILE 3.2 3.8 - - - -
60A ARG* 1.3 82.4 + - - +
62A SER* 1.3 66.0 + - - +
63A GLU 3.3 2.2 - - - -
64A THR* 3.1 10.3 + - - -
65A PHE* 2.8 28.8 + - + +
1166A BR 3.3 21.3 - - - +
65B ILE* 3.5 45.0 - - + +
68B GLU* 6.2 0.8 - - - +
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Residues in contact with SER 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ILE* 2.8 10.7 + - - -
59A GLU 3.3 15.7 + - - -
60A ARG 3.5 1.2 + - - -
61A ASN* 1.3 75.3 - - - +
63A GLU* 1.3 59.4 + - - +
65A PHE* 3.4 4.4 + - - +
66A THR* 3.0 30.7 + - - -
110A HIS* 5.2 1.2 - - - -
1161A BR 3.2 23.8 - - - +
1169A GOL 2.8 25.1 + - - -
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Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ASN 3.3 0.4 - - - -
62A SER* 1.3 77.4 - - - +
64A THR* 1.3 63.3 + - - +
66A THR* 3.2 3.2 + - - +
67A GLU* 2.8 62.8 + - - +
1169A GOL 2.6 45.5 + - - +
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Residues in contact with THR 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ASN* 3.1 12.3 + - - -
63A GLU* 1.3 79.7 - - - +
65A PHE* 1.3 53.8 + - + +
67A GLU* 3.9 7.1 + - - +
68A THR* 2.7 44.4 + - + +
57B TRP* 5.5 2.9 - - + -
61B GLU* 3.7 39.2 + - + +
62B LEU* 6.2 0.9 - - + -
65B ILE* 4.1 19.5 - - + -
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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
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57A ILE* 4.0 17.5 - - + -
58A ILE* 3.8 31.2 - - + +
61A ASN* 2.8 26.6 + - + +
62A SER* 3.7 5.6 - - - +
64A THR* 1.3 76.8 - - + +
66A THR* 1.3 65.8 + - - +
68A THR* 3.2 4.5 + - - -
69A TRP* 3.1 27.2 + - - +
103A ALA* 3.9 10.3 - - - -
106A ALA* 3.6 7.4 - - + -
107A TRP* 3.4 39.4 + + - -
110A HIS* 3.5 26.9 + + + +
62B LEU* 3.6 21.1 - - + -
65B ILE* 3.7 18.4 - - + -
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Residues in contact with THR 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 SER 3.0 8.7 + - - -
63A GLU* 3.6 8.3 - - - +
65A PHE* 1.3 75.9 - - - +
67A GLU* 1.3 58.9 + - + +
69A TRP* 4.0 1.0 - - - +
70A ASN* 2.9 48.6 + - - +
110A HIS* 3.9 17.3 + - - -
1169A GOL 2.9 45.2 + - - +
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Residues in contact with GLU 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 GLU* 2.8 53.2 + - - +
64A THR* 3.9 5.8 + - - +
66A THR* 1.3 72.3 - - + +
68A THR* 1.3 62.5 + - - +
70A ASN* 3.8 4.4 - - - +
71A ARG* 2.9 31.7 + - - +
57B TRP* 4.1 23.5 - - + -
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Residues in contact with THR 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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64A THR* 2.7 38.2 + - + +
65A PHE* 3.2 5.0 + - - -
67A GLU* 1.3 76.0 - - - +
69A TRP* 1.3 62.9 + - - +
71A ARG* 3.4 0.5 + - - +
72A PHE* 3.0 24.9 + - - +
107A TRP* 2.8 29.3 + - - -
57B TRP* 3.7 31.2 - - + -
58B ILE* 3.5 28.2 - - + +
61B GLU* 4.3 7.9 - - + -
62B LEU* 5.8 2.0 - - + +
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Residues in contact with TRP 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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65A PHE 3.1 19.7 + - - +
66A THR* 4.0 1.8 - - - +
68A THR* 1.3 77.8 + - - +
70A ASN* 1.3 76.9 + - - +
72A PHE* 3.1 20.9 + + - +
73A ILE* 3.0 58.2 + - + +
83A PHE* 3.5 29.4 - + - -
107A TRP* 3.8 20.8 - + + +
110A HIS* 4.2 11.4 - + + +
111A ALA* 3.5 24.4 + - + -
114A THR* 4.1 23.2 - - + +
115A LEU* 3.7 21.1 - - + -
129A SER* 3.9 7.0 - - - -
1162A BR 3.3 20.2 - - - +
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Residues in contact with ASN 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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66A THR* 2.9 41.2 + - - +
67A GLU* 4.0 4.6 - - - +
69A TRP* 1.3 86.3 - - - +
71A ARG* 1.3 60.4 + - - +
73A ILE* 4.2 7.0 - - - +
74A THR* 2.8 37.2 + - + +
114A THR* 5.2 4.9 - - - +
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Residues in contact with ARG 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 GLU 2.9 17.8 + - - +
68A THR 3.9 3.1 - - - +
70A ASN* 1.3 76.0 - - - +
72A PHE* 1.3 64.1 + - - +
74A THR* 4.0 4.5 - - - -
75A HIS* 2.8 52.6 + - - +
53B ARG* 4.1 13.1 + - - +
54B PRO* 3.5 53.4 - - + +
57B TRP* 4.2 34.2 - - + +
58B ILE* 5.3 0.7 - - + -
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Residues in contact with PHE 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 THR 3.0 18.7 + - - +
69A TRP* 3.4 31.2 - + + +
71A ARG* 1.3 78.5 - - - +
73A ILE* 1.3 61.9 + - + +
75A HIS* 3.2 1.7 + - - +
76A THR* 3.0 33.4 + - - -
79A VAL* 4.1 10.3 - - + -
82A ASP* 3.7 41.7 - - + -
83A PHE* 3.7 40.2 - + - -
86A VAL* 3.9 13.0 - - + -
107A TRP* 4.1 8.5 - + + -
54B PRO* 4.8 4.7 - - - -
55B GLU* 4.1 10.5 - - - -
58B ILE* 3.5 21.9 - - + +
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Residues in contact with ILE 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 TRP* 3.0 61.5 + - + +
70A ASN* 3.8 10.8 - - - +
72A PHE* 1.3 77.9 - - + +
74A THR* 1.3 68.8 + - + +
76A THR* 3.6 15.8 + - + +
79A VAL* 4.1 19.5 - - + -
115A LEU* 4.8 2.2 - - + -
125A VAL* 3.9 28.9 - - + -
129A SER* 4.0 7.2 - - - +
1162A BR 4.3 8.3 - - + -
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Residues in contact with THR 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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70A ASN* 2.8 27.0 + - + +
71A ARG* 3.6 0.9 + - - -
73A ILE* 1.3 85.7 - - + +
75A HIS* 1.3 79.2 + - - +
76A THR 3.7 1.1 - - - -
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Residues in contact with HIS 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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71A ARG* 2.8 51.1 + - + +
72A PHE 4.1 1.6 - - - +
74A THR* 1.3 95.3 + - - +
76A THR* 1.3 63.4 + - - +
77A GLU* 3.6 9.7 + - - +
51B ASP* 4.8 12.3 - - - +
54B PRO* 3.8 27.6 - - + -
55B GLU* 5.6 0.9 - - - +
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Residues in contact with THR 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 PHE* 3.0 22.0 + - + +
73A ILE* 3.6 21.6 - - + +
74A THR 5.1 0.7 - - - -
75A HIS* 1.3 78.7 - - - +
77A GLU* 1.3 61.4 + - - +
78A HIS 3.2 14.6 + - - -
79A VAL* 3.4 30.3 + - + +
82A ASP* 2.4 34.1 + - - -
55B GLU* 5.5 2.0 - - - -
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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