Contacts of the helix formed by residues 89 - 109 (chain E) in PDB entry 2H4C
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 89 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E CYS* 5.6 0.4 - - - +
86E ASP* 3.3 1.4 - - + +
88E ASN* 1.3 78.2 - - - +
90E LEU* 1.3 69.6 + - - +
91E CYS* 3.4 16.5 - - - +
92E LEU* 3.1 51.3 + - + +
93E LYS* 2.9 26.4 + - - +
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Residues in contact with LEU 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E ASN 3.4 7.2 + - - +
89E ASN* 1.3 72.5 - - - +
91E CYS* 1.3 52.8 + - - +
93E LYS* 3.8 3.6 - - - +
94E THR* 2.3 40.7 + - - +
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Residues in contact with CYS 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E VAL* 3.4 13.9 - - - -
56E ASN* 4.7 2.0 - - - -
58E ASP* 3.7 12.6 - - + -
59E CYS* 2.0 73.6 - - + +
89E ASN* 3.3 12.3 - - - +
90E LEU* 1.3 75.7 - - - +
92E LEU* 1.3 70.8 + - - +
94E THR* 3.0 18.6 - - - -
95E VAL* 3.3 1.7 - - - +
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Residues in contact with LEU 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E CYS* 4.3 7.2 - - + -
71E ALA* 3.6 28.9 - - + -
72E THR 4.1 23.3 - - - +
73E TYR* 4.0 7.3 - - - +
86E ASP* 3.6 23.3 - - - +
89E ASN* 3.1 30.6 + - + +
91E CYS* 1.3 76.2 - - - +
93E LYS* 1.3 65.5 + - - +
95E VAL* 2.9 22.0 + - - +
96E CYS 3.6 2.1 + - - -
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Residues in contact with LYS 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84E CYS* 2.5 48.2 + - + +
86E ASP* 3.3 39.5 + - + +
89E ASN 2.9 14.1 + - - +
90E LEU* 4.0 2.9 - - - +
92E LEU* 1.3 76.1 - - - +
94E THR* 1.3 56.9 + - - +
96E CYS* 2.5 32.6 + - - +
97E GLU* 3.3 17.6 + - + +
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Residues in contact with THR 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E CYS* 4.6 4.5 - - - +
54E THR* 5.6 2.9 - - - +
55E VAL* 4.2 30.1 - - + +
90E LEU* 2.3 33.6 + - - +
91E CYS* 3.0 16.4 - - - -
93E LYS* 1.3 76.3 - - - +
95E VAL* 1.3 57.3 + - - +
96E CYS 3.4 0.2 + - - -
97E GLU* 3.9 5.2 + - - +
98E CYS* 3.4 22.6 + - - -
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Residues in contact with VAL 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1E ASN 5.3 0.2 - - - +
52E TYR* 4.1 16.8 - - + +
55E VAL* 4.4 5.6 - - + -
59E CYS* 3.5 18.8 - - + -
68E PRO* 3.8 42.0 - - + +
71E ALA* 4.7 6.3 - - + -
73E TYR* 3.6 19.8 - - + -
91E CYS 3.3 16.2 - - - +
92E LEU* 3.2 10.1 - - - +
93E LYS 2.9 0.8 - - - -
94E THR* 1.3 76.0 - - - +
96E CYS* 1.3 61.3 + - - +
98E CYS* 4.2 8.7 - - - +
99E ASP* 3.4 18.0 + - - +
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Residues in contact with CYS 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E MET* 3.9 10.7 - - - +
73E TYR* 4.0 22.2 - - + -
74E SER 4.1 1.3 - - - -
75E TYR* 3.7 23.1 - - - -
84E CYS* 2.0 47.8 - - + -
86E ASP* 4.6 0.7 - - - +
92E LEU 3.6 0.6 + - - -
93E LYS* 2.5 22.8 + - - +
95E VAL* 1.3 70.4 - - - +
97E GLU* 1.3 62.9 + - - +
98E CYS 2.9 5.5 + - - -
99E ASP* 3.0 9.9 + - - +
100E ARG* 2.9 16.5 + - - +
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Residues in contact with GLU 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E CYS* 5.1 0.4 - - - -
82E ILE 4.3 2.0 - - - +
84E CYS* 3.2 24.9 + - - +
93E LYS* 3.3 18.9 + - + +
94E THR* 4.5 4.7 - - - +
96E CYS* 1.3 74.4 - - - +
98E CYS* 1.3 67.3 + - - +
100E ARG* 2.9 49.7 + - + +
101E ALA* 2.9 19.8 + - - +
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Residues in contact with CYS 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E HIS* 3.3 22.1 - - + +
51E CYS* 2.0 62.1 - - - -
52E TYR* 3.9 15.7 - - + -
55E VAL* 5.4 1.1 - - - -
94E THR* 3.4 19.8 + - - -
95E VAL* 4.2 3.6 - - - +
96E CYS 2.9 1.0 + - - -
97E GLU* 1.3 72.4 - - - +
99E ASP* 1.3 58.3 + - - +
100E ARG 2.6 14.6 + - - -
101E ALA* 2.7 19.9 + - - +
102E ALA* 2.9 9.4 + - - +
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Residues in contact with ASP 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E ASN 3.9 1.9 - - - +
5E PHE* 3.0 32.4 + - + +
8E MET* 3.3 17.7 - - - -
48E HIS* 2.9 27.1 + - - -
52E TYR* 3.1 12.2 + - - -
73E TYR* 2.3 30.0 + - - +
95E VAL 3.4 12.2 - - - +
96E CYS 3.0 9.6 + - - +
98E CYS* 1.3 79.1 - - - +
100E ARG* 1.3 52.9 + - - +
102E ALA 3.6 0.6 - - - -
103E ALA* 2.7 39.5 + - - +
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Residues in contact with ARG 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E MET* 4.4 1.1 - - - +
81E ASP* 3.7 16.7 + - - +
82E ILE* 3.1 58.8 + - + +
96E CYS 2.9 6.9 + - - +
97E GLU* 2.9 43.6 + - + +
98E CYS 2.6 3.8 + - - -
99E ASP* 1.3 70.3 - - - +
101E ALA* 1.3 70.3 + - - +
103E ALA* 2.9 12.6 + - - +
104E ILE* 3.0 39.9 + - + +
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Residues in contact with ALA 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E VAL* 6.1 4.9 - - + -
51E CYS* 6.3 0.4 - - - -
97E GLU 2.9 6.8 + - - +
98E CYS* 2.7 14.5 + - - +
100E ARG* 1.3 78.9 - - - +
102E ALA* 1.3 50.6 + - - +
104E ILE* 3.7 6.6 - - - +
105E CYS* 2.7 39.5 + - + +
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Residues in contact with ALA 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E PHE* 3.4 31.4 - - + -
44E CYS* 4.7 13.0 - - + +
48E HIS* 3.7 24.7 - - + -
98E CYS 2.9 3.6 + - - -
99E ASP 3.7 1.8 - - - +
101E ALA* 1.3 74.8 - - - +
103E ALA* 1.3 57.5 + - - +
104E ILE 3.1 4.5 - - - -
105E CYS* 4.1 5.2 - - - -
106E LEU* 3.0 36.9 + - + +
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Residues in contact with ALA 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E PHE* 4.1 0.2 - - - -
8E MET* 3.3 38.6 - - + +
9E ILE* 3.5 19.9 - - + +
12E MET* 2.9 25.9 - - - +
13E THR* 5.6 0.5 - - - -
82E ILE* 4.0 7.9 - - + -
99E ASP 2.7 23.1 + - - +
100E ARG 3.6 3.6 - - - +
102E ALA* 1.3 72.2 - - - +
104E ILE* 1.3 58.7 + - - +
106E LEU* 4.6 1.3 - - - -
107E GLY* 4.6 6.0 + - - -
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Residues in contact with ILE 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E MET* 3.9 27.1 - - + -
82E ILE* 4.4 6.1 - - + +
100E ARG* 3.0 61.9 + - + +
101E ALA* 3.7 5.8 - - - +
103E ALA* 1.3 78.2 - - - +
105E CYS* 1.3 70.6 + - - +
106E LEU 3.3 0.7 - - - -
107E GLY* 3.1 10.6 + - - -
108E GLN* 3.1 41.5 + - + +
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Residues in contact with CYS 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E ALA 4.6 1.6 - - - -
43E ARG* 5.8 0.7 - - - -
44E CYS* 2.0 53.2 - - + -
101E ALA* 2.7 23.9 + - + +
102E ALA* 4.0 1.6 - - - +
104E ILE* 1.3 78.7 - - - +
106E LEU* 1.3 55.1 + - - +
107E GLY 2.9 4.0 + - - -
108E GLN* 3.0 15.5 + - - +
109E ASN* 2.7 31.2 + - - +
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Residues in contact with LEU 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E PHE* 4.5 7.6 - - + -
9E ILE* 4.0 25.8 - - + -
22E TYR* 3.3 48.4 + - + +
41E THR* 3.5 34.4 - - + +
44E CYS* 2.9 31.1 - - + -
45E CYS* 4.1 11.4 - - - -
102E ALA* 3.0 21.7 + - + +
103E ALA* 5.0 1.1 - - - -
105E CYS* 1.3 77.9 - - - +
107E GLY* 1.3 59.3 + - - +
109E ASN* 3.9 4.7 + - - +
110E VAL* 3.5 12.8 + - - +
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Residues in contact with GLY 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E MET 5.4 3.8 - - - -
13E THR* 4.9 15.7 - - - -
103E ALA 4.6 4.8 + - - -
104E ILE 3.1 8.2 + - - -
106E LEU* 1.3 74.6 - - - +
108E GLN* 1.3 58.6 + - - +
109E ASN 2.8 11.7 + - - -
110E VAL* 3.1 29.6 + - - +
111E ASN* 4.7 0.2 - - - +
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Residues in contact with GLN 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E ILE* 3.1 36.4 + - + +
105E CYS* 3.0 13.7 + - - +
107E GLY* 1.3 73.7 - - - +
109E ASN* 1.3 65.8 + - - +
110E VAL 3.8 0.4 - - - -
111E ASN* 3.4 12.0 + - - +
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Residues in contact with ASN 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E ALA* 3.5 31.1 - - + +
41E THR* 3.7 15.8 + - - +
44E CYS* 4.3 1.6 - - - -
105E CYS* 2.7 41.9 + - - +
106E LEU* 3.9 5.6 + - - +
107E GLY 2.8 1.2 + - - -
108E GLN* 1.3 90.5 + - - +
110E VAL* 1.3 60.5 + - - +
111E ASN* 2.9 19.0 + - - +
112E THR* 3.2 12.4 + - - +
113E TYR 3.6 5.7 + - - -
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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
------------------------------------------------------------
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