Contacts of the helix formed by residues 84 - 101 (chain E) in PDB entry 1OUQ
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 ALA 84 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82E GLY 3.4 3.4 + - - +
83E LEU* 1.3 75.7 - - - +
85E VAL* 1.3 57.0 + - - +
86E LYS* 3.3 2.7 - - + +
87E THR* 2.7 33.6 + - - +
88E ILE* 3.3 3.7 + - - +
129E GLU* 3.5 22.4 - - + +
113H T 3.0 38.8 + - - +
114H A 5.5 2.2 - - - +
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Residues in contact with VAL 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B THR* 5.0 8.5 - - + +
83E LEU 3.9 1.4 + - - -
84E ALA* 1.3 70.1 - - - +
86E LYS* 1.3 56.0 + - - +
87E THR 2.6 12.6 + - - -
88E ILE* 2.8 23.8 + - + +
89E GLN* 3.1 20.9 + - - +
117E MET* 5.5 3.4 - - + -
120E ILE* 5.1 6.1 - - + -
121E ARG* 4.3 33.7 - - + +
124E ASN* 3.5 24.4 - - + +
125E VAL* 5.1 2.7 - - + +
129E GLU* 2.9 29.5 + - + +
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Residues in contact with LYS 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B THR* 5.5 6.4 + - - +
84E ALA* 3.2 2.7 + - + +
85E VAL* 1.3 78.2 - - - +
87E THR* 1.3 57.5 + - - +
89E GLN* 4.1 11.6 - - + +
90E GLN* 3.8 14.9 + - - +
129E GLU* 4.5 2.4 + - - +
113H T 4.3 10.2 - - + +
114H A 3.7 45.4 + - + +
115H G 3.0 49.2 + - - -
116H C 4.7 3.0 - - - +
121Y G 5.0 4.3 - - - -
122Y C 5.3 1.8 - - - +
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Residues in contact with THR 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E LEU* 4.4 11.4 - - + -
84E ALA* 2.7 17.4 + - - +
85E VAL 2.6 5.1 + - - -
86E LYS* 1.3 71.2 - - - +
88E ILE* 1.3 65.1 + - - +
89E GLN 2.9 1.6 - - - -
90E GLN* 2.8 12.8 + - - +
91E HIS* 2.9 37.3 + - + +
112H A 3.7 12.8 - - + +
113H T 2.6 61.4 + - + +
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Residues in contact with ILE 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75E LEU* 3.8 25.4 - - + +
78E LEU* 4.2 12.3 - - + -
79E GLN* 4.0 28.0 - - + +
83E LEU* 4.2 13.5 - - + +
84E ALA 3.7 11.4 - - - +
85E VAL* 2.8 11.6 + - - +
87E THR* 1.3 75.5 - - - +
89E GLN* 1.3 57.2 + - - +
91E HIS* 3.3 11.3 + - - +
92E LEU* 3.0 27.2 + - - +
117E MET* 3.8 24.0 - - + -
120E ILE* 3.9 28.7 - - + -
124E ASN* 5.7 1.6 - - - +
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Residues in contact with GLN 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E VAL* 3.1 18.7 + - - +
86E LYS* 4.2 13.7 - - + +
87E THR 2.9 0.2 - - - -
88E ILE* 1.3 80.0 - - - +
90E GLN* 1.3 54.3 + - - +
92E LEU* 4.3 10.4 - - + +
93E GLY* 2.5 34.8 + - - -
117E MET* 4.3 25.1 + - - +
121E ARG* 5.2 14.1 - - - +
121Y G 6.2 1.8 - - - +
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Residues in contact with GLN 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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44E MET* 4.3 16.8 - - + -
48E VAL* 6.0 1.3 - - + -
86E LYS 3.8 11.7 + - - +
87E THR 2.8 13.8 + - - +
89E GLN* 1.3 72.2 - - - +
91E HIS* 1.3 63.3 + - + +
93E GLY* 4.3 1.9 - - - +
94E GLN* 2.9 75.9 + - + +
113H T 3.5 25.1 - - + +
114H A 3.3 13.1 + - - +
122Y C 4.4 10.8 + - - +
123Y T 2.6 33.9 + - - +
124Y A 4.1 0.9 + - - -
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Residues in contact with HIS 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E SER 5.6 0.7 - - - -
48E VAL* 2.9 35.2 - - + +
51E SER* 4.4 11.2 - - - -
74E TYR* 3.1 25.6 + - + +
75E LEU* 4.9 1.3 - - + -
78E LEU* 3.1 28.3 - - + +
81E ARG* 5.0 1.6 - - - -
83E LEU* 4.5 4.2 - - + +
87E THR* 2.9 44.6 + - + +
88E ILE 3.3 7.4 - - - +
90E GLN* 1.3 79.5 - - + +
92E LEU* 1.3 66.3 + - - +
94E GLN* 3.3 2.8 + - - +
95E LEU* 2.9 26.5 + - - +
112H A 4.2 18.3 + - - -
113H T 5.4 1.3 - - + +
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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
----------------------------------------------------------
71E VAL* 4.9 3.8 - - + -
75E LEU* 3.5 23.0 - - + +
88E ILE 3.0 13.0 + - - +
89E GLN* 3.6 12.6 - - + +
91E HIS* 1.3 76.1 - - - +
93E GLY* 1.3 70.0 + - - +
95E LEU* 3.2 8.4 + - + +
96E ASN* 3.0 27.3 + - - +
107E PRO* 4.5 9.0 - - + -
108E SER* 3.0 28.5 - - - +
113E VAL* 3.9 14.1 - - + -
114E SER* 6.2 0.2 - - - -
117E MET* 3.2 41.3 - - + -
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Residues in contact with GLY 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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89E GLN* 2.5 23.4 + - - -
90E GLN* 3.8 3.4 - - - -
92E LEU* 1.3 75.8 - - - +
94E GLN* 1.3 64.4 + - - +
96E ASN* 2.9 24.9 + - - +
97E MET* 3.2 6.0 + - - +
121Y G 6.4 2.7 - - - -
122Y C 5.6 0.9 + - - -
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Residues in contact with GLN 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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41E THR* 3.9 16.4 - - - +
44E MET* 3.9 18.1 - - + +
45E LEU* 3.5 40.7 - - + +
48E VAL* 3.5 22.2 - - + -
90E GLN* 2.9 51.1 + - + +
93E GLY* 1.3 70.6 - - - +
95E LEU* 1.3 67.4 + - - +
97E MET* 3.3 25.0 + - - +
98E LEU* 3.1 18.0 + - - +
122Y C 5.7 0.5 - - - -
123Y T 4.0 4.5 - - - +
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Residues in contact with LEU 95 (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 VAL* 4.5 12.6 - - + -
49E CYS* 4.9 9.2 - - - -
52E TRP* 3.8 50.7 - - + +
66E ALA* 5.1 0.7 - - + -
71E VAL* 4.5 20.2 - - + -
74E TYR* 4.3 18.4 - - + -
75E LEU* 6.0 0.4 - - + -
91E HIS 2.9 14.1 + - - +
92E LEU* 3.4 12.6 - - - +
94E GLN* 1.3 72.9 - - - +
96E ASN* 1.3 65.7 + - - +
98E LEU* 2.8 18.5 + - + +
99E HIS* 2.9 32.7 + - + -
107E PRO* 4.6 7.9 - - + -
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Residues in contact with ASN 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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92E LEU* 3.0 26.4 + - - +
93E GLY* 2.9 12.0 + - - +
95E LEU* 1.3 74.8 - - - +
97E MET* 1.3 64.9 + - - +
99E HIS* 2.8 14.4 + - - +
100E ARG* 2.9 14.1 + - - +
106E ARG* 3.0 44.0 - - + +
107E PRO* 3.3 6.5 - - - +
108E SER* 2.6 39.0 + - - -
121Y G 5.3 4.4 + - - +
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Residues in contact with MET 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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30E MET* 5.1 4.5 - - + -
37E PHE* 3.3 31.2 - - + -
41E THR* 4.0 13.5 - - + -
42E TRP* 6.5 0.2 - - - -
45E LEU* 4.7 15.7 - - - -
93E GLY 3.2 6.9 + - - +
94E GLN* 3.3 31.8 + - - +
96E ASN* 1.3 77.8 - - - +
98E LEU* 1.3 63.2 + - - +
100E ARG* 4.5 8.3 - - - +
101E ARG* 3.0 42.5 + - + +
106E ARG* 5.9 0.2 - - - +
122Y C 3.5 43.6 + - + +
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Residues in contact with LEU 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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27E LEU* 4.7 13.8 - - + +
30E MET* 4.2 21.0 - - + +
31E PHE* 6.5 0.4 - - + -
45E LEU* 4.3 15.0 - - + +
49E CYS* 3.5 26.9 - - - -
63E TRP* 3.7 26.7 - - + -
64E PHE* 4.3 19.5 - - + -
94E GLN 3.1 10.4 + - - +
95E LEU* 2.8 22.8 + - + +
97E MET* 1.3 73.8 - - - +
99E HIS* 1.3 63.1 + - + +
101E ARG* 4.2 4.2 + - - +
102E SER* 3.2 15.1 + - - -
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Residues in contact with HIS 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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52E TRP* 6.0 0.2 - + - -
63E TRP* 5.4 2.7 - + - -
64E PHE* 4.9 8.7 - + - -
65E PRO* 4.4 2.8 - - + +
66E ALA* 3.0 50.3 + - + +
95E LEU* 2.9 34.8 + - + -
96E ASN 2.8 6.0 + - - +
98E LEU* 1.3 86.9 - - + +
100E ARG* 1.3 63.2 + - - +
101E ARG 3.2 0.7 - - - -
102E SER* 2.5 23.0 + - - -
104E LEU* 3.3 37.4 - - + +
105E PRO 3.9 20.6 - - - +
106E ARG* 4.1 4.3 - - - -
107E PRO* 4.0 11.4 - - + +
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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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96E ASN 2.9 14.3 + - - +
97E MET* 4.0 7.4 - - - +
99E HIS* 1.3 77.2 - - - +
101E ARG* 1.3 84.8 + - - +
102E SER 2.5 13.9 + - - -
103E GLY* 3.7 7.3 + - - -
104E LEU 3.9 9.2 + - - +
106E ARG* 3.5 44.6 - - - +
111F ASN* 4.2 6.7 + - - +
118F ARG* 5.9 0.6 - - - +
121Y G 4.1 19.2 + - - -
122Y C 2.9 34.8 + - - -
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Residues in contact with ARG 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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26E ASN* 4.0 3.3 - - - +
27E LEU* 4.2 4.3 - - - +
30E MET* 3.9 41.5 - - + +
37E PHE* 4.2 10.3 - - + -
97E MET* 3.0 29.0 + - - +
98E LEU 4.3 1.2 - - - +
99E HIS 3.2 0.2 - - - -
100E ARG* 1.3 108.4 - - - +
102E SER* 1.4 62.3 + - - -
111F ASN* 3.1 46.2 + - - +
114F SER* 3.7 21.2 + - - -
115F LEU* 3.4 35.8 - - + +
118F ARG* 4.4 14.3 - - - +
122Y C 4.5 5.1 + - - -
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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