Contacts of the helix formed by residues 69 - 88 (chain A) in PDB entry 1WVA
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 69 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LYS* 3.4 50.2 + - + +
19A GLN 5.1 3.8 + - - -
61A ASP* 2.6 34.7 + - - +
63A PRO* 4.8 2.2 - - - +
68A LYS* 1.3 83.8 - - - +
70A PRO* 1.3 67.9 - - - +
72A SER* 3.2 3.2 + - - +
73A VAL* 3.0 21.5 + - - +
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Residues in contact with PRO 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ASP* 3.7 2.7 - - - +
62A SER 3.5 25.6 - - - +
63A PRO* 4.0 0.4 - - + -
64A PHE* 4.0 15.5 - - + +
67A VAL* 3.5 12.1 - - + +
68A LYS* 3.1 5.8 - - - -
69A ASN* 1.3 90.6 - - - +
71A ARG* 1.3 62.9 + - - +
73A VAL 3.6 0.2 + - - -
74A GLY* 2.9 24.1 + - - -
140A LEU* 3.8 14.4 - - + -
159A VAL* 3.6 20.9 - - + -
160A PRO* 3.4 17.7 - - + +
162A PHE* 3.3 11.7 - - + -
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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
----------------------------------------------------------
58A ILE* 4.1 21.5 - - + +
60A ASN 4.3 13.1 + - - -
61A ASP* 2.8 28.1 + - - +
62A SER* 2.7 42.9 + - - +
63A PRO 5.5 1.4 + - - -
70A PRO* 1.3 74.4 - - - +
72A SER* 1.3 59.7 + - - +
75A LYS* 3.1 29.8 + - - +
160A PRO* 3.5 41.2 - - + +
161A GLY* 4.3 7.7 - - - +
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Residues in contact with SER 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A PHE* 3.5 10.8 - - - -
17A LYS* 3.9 26.9 + - - +
57A ASP* 3.9 16.7 + - - -
58A ILE* 4.1 10.3 - - - +
61A ASP* 3.0 20.1 + - - +
69A ASN* 3.2 6.9 + - - -
71A ARG* 1.3 75.7 - - - +
73A VAL* 1.3 66.0 + - - +
75A LYS* 3.5 2.9 + - - +
76A ALA* 3.0 26.0 + - - +
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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
----------------------------------------------------------
15A PHE* 3.4 8.5 - - + -
17A LYS 3.1 32.5 - - - +
18A GLY* 3.4 12.3 - - - -
69A ASN 3.0 11.5 + - - +
72A SER* 1.3 75.6 - - - +
74A GLY* 1.3 59.9 + - - +
76A ALA* 3.6 2.6 - - - +
77A SER* 3.4 22.5 + - - -
102A SER* 3.5 29.9 + - - +
105A ILE* 5.1 0.9 - - + -
140A LEU* 3.4 33.4 - - + -
162A PHE* 3.9 9.8 - - + -
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Residues in contact with GLY 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A PRO 2.9 14.1 + - - -
71A ARG 4.1 0.7 - - - -
72A SER 3.2 0.2 - - - -
73A VAL* 1.3 74.9 - - - +
75A LYS* 1.3 59.8 + - - +
76A ALA 3.2 1.3 - - - -
77A SER 3.4 0.9 + - - -
78A GLU 3.0 21.0 + - - -
161A GLY 3.7 16.4 - - - -
162A PHE* 3.4 24.8 - - - -
164A TRP* 3.4 13.5 + - - -
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Residues in contact with LYS 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ALA 6.0 2.7 - - - +
58A ILE* 5.2 14.1 - - + -
71A ARG 3.1 19.2 + - - +
72A SER* 4.3 3.1 - - - +
74A GLY* 1.3 72.8 - - - +
76A ALA* 1.3 61.2 + - - +
78A GLU* 3.0 33.7 + - - +
79A GLN* 2.9 59.3 + - - +
161A GLY* 4.4 4.0 + - - +
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Residues in contact with ALA 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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15A PHE* 3.8 33.4 - - + -
55A PHE* 3.5 25.3 - - + -
72A SER 3.0 19.3 + - - +
73A VAL 3.6 6.7 - - - +
74A GLY 3.2 0.2 - - - -
75A LYS* 1.3 79.2 - - - +
77A SER* 1.3 60.2 + - - +
79A GLN* 4.0 0.9 - - - +
80A LEU* 3.2 22.3 + - - +
103A LEU* 4.0 10.1 - - + +
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Residues in contact with SER 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A VAL 3.4 13.2 + - - -
74A GLY* 3.8 1.8 - - - -
75A LYS 3.3 0.2 - - - -
76A ALA* 1.3 76.9 - - - +
78A GLU* 1.3 57.8 + - - +
80A LEU* 3.1 2.6 + - - -
81A ALA* 2.6 33.8 + - - +
102A SER 3.2 19.2 + - - -
103A LEU* 3.8 7.3 - - - +
105A ILE* 3.5 7.2 - - - +
106A GLY* 3.1 36.5 + - - -
162A PHE* 5.2 0.4 - - - -
164A TRP* 3.7 13.9 - - - -
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Residues in contact with GLU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLY 3.0 17.2 + - - +
75A LYS* 3.0 44.3 + - - +
77A SER* 1.3 77.4 - - - +
79A GLN* 1.3 64.4 + - - +
81A ALA* 3.3 2.3 + - - +
82A GLY* 3.2 17.0 + - - -
113A ARG* 4.7 4.5 + - - +
164A TRP* 3.3 50.6 - - + +
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Residues in contact with GLN 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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53A LEU* 4.6 1.7 - - + +
54A PRO* 3.1 26.1 - - - +
55A PHE* 3.2 38.9 - - + +
56A ALA 4.6 5.8 + - - +
75A LYS* 2.9 47.2 + - - +
76A ALA* 4.0 3.7 - - - +
78A GLU* 1.3 74.5 - - - +
80A LEU* 1.3 56.4 + - - +
82A GLY* 3.2 4.2 + - - -
83A LYS* 2.6 59.2 + - + +
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Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ILE* 3.7 20.9 - - + -
13A ALA* 4.6 2.2 - - + -
53A LEU* 3.7 25.3 - - + +
55A PHE* 5.1 0.4 - - + -
76A ALA 3.2 15.2 + - - +
77A SER 3.1 5.7 + - - +
79A GLN* 1.3 80.2 - - - +
81A ALA* 1.3 51.8 + - - +
83A LYS* 3.1 1.3 + - + +
84A VAL* 2.7 43.7 + - + +
96A VAL* 4.0 27.4 - - + -
103A LEU* 3.4 48.0 - - + +
106A GLY 4.2 0.2 - - - -
107A SER* 3.8 13.7 - - - +
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Residues in contact with ALA 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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77A SER 2.6 19.1 + - - +
78A GLU 3.6 5.4 - - - +
80A LEU* 1.3 72.2 - - - +
82A GLY* 1.3 63.6 + - - +
84A VAL* 3.3 0.4 + - - -
85A ALA* 3.0 12.5 + - - +
106A GLY 3.1 22.8 + - - +
110A GLY* 3.0 29.3 - - - +
113A ARG* 3.7 20.6 - - - +
164A TRP* 3.8 11.2 - - + -
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Residues in contact with GLY 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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78A GLU 3.2 6.6 + - - -
79A GLN* 3.2 6.7 + - - -
81A ALA* 1.3 79.9 - - - +
83A LYS* 1.3 64.2 + - - +
85A ALA* 3.5 5.6 + - - +
86A GLU* 3.4 19.9 + - - +
113A ARG* 3.9 14.3 - - - +
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Residues in contact with LYS 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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11A ILE* 4.0 14.1 - - + -
50A TYR* 5.5 1.4 - - + -
53A LEU* 3.2 39.9 - - + -
54A PRO* 5.9 0.7 - - - -
79A GLN* 2.6 49.0 + - - +
80A LEU* 3.1 12.1 + - + +
82A GLY* 1.3 79.2 - - - +
84A VAL* 1.3 60.0 + - - +
86A GLU* 3.2 14.7 + - - +
87A VAL* 3.4 18.4 + - - +
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Residues in contact with VAL 84 (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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11A ILE* 3.8 22.2 - - + -
80A LEU* 2.7 24.4 + - + +
81A ALA* 3.8 3.8 - - - +
83A LYS* 1.3 70.0 - - - +
85A ALA* 1.3 65.2 + - - +
87A VAL* 3.1 2.7 - - - +
88A LYS* 3.0 30.7 + - + +
94A SER* 3.7 19.7 - - - +
96A VAL* 4.0 19.5 - - + -
107A SER* 3.4 33.4 - - - +
110A GLY* 4.2 1.3 - - - -
111A HIS* 3.5 19.3 - - + +
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Residues in contact with ALA 85 (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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81A ALA 3.0 15.4 + - - +
82A GLY* 3.8 8.7 - - - +
83A LYS 3.3 0.2 - - - -
84A VAL* 1.3 77.5 - - - +
86A GLU* 1.3 54.5 + - - +
89A LYS* 2.6 41.8 + - - +
110A GLY* 3.4 22.4 + - - +
113A ARG* 4.7 13.0 - - + +
114A VAL* 3.5 16.0 - - + +
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Residues in contact with GLU 86 (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 TYR* 4.6 9.6 - - + -
82A GLY 3.4 9.6 + - - +
83A LYS* 3.2 11.1 + - - +
84A VAL 3.2 0.6 - - - -
85A ALA* 1.3 77.2 - - - +
87A VAL* 1.3 61.5 + - + +
89A LYS* 2.9 27.7 + - - +
90A ASN* 2.9 60.8 + - - +
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Residues in contact with VAL 87 (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 GLY* 4.4 9.4 - - - +
11A ILE* 3.6 17.5 - - + -
50A TYR* 3.6 46.2 - - + -
83A LYS 3.4 13.0 - - - +
84A VAL* 3.1 14.4 - - - +
86A GLU* 1.3 75.1 - - - +
88A LYS* 1.3 67.7 + - + +
90A ASN* 3.1 11.3 + - - +
91A GLY 3.5 0.2 + - - -
92A ARG* 3.1 22.7 + - + +
93A ILE 4.7 0.4 - - - -
94A SER* 3.3 34.8 - - - +
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Residues in contact with LYS 88 (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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84A VAL* 3.0 28.6 + - + +
85A ALA 3.8 0.4 - - - -
87A VAL* 1.3 81.9 - - + +
89A LYS* 1.3 59.3 + - - +
91A GLY* 3.5 10.0 + - - -
92A ARG 2.5 29.5 + - - +
93A ILE* 3.9 2.4 - - - +
94A SER* 3.8 11.9 - - - +
111A HIS* 3.7 25.1 - - + -
114A VAL* 3.8 30.1 - - + +
115A HIS* 3.7 26.7 - - - -
271A SER* 2.7 40.8 + - - +
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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