Contacts of the helix formed by residues 97 - 114 (chain B) in PDB entry 3OX4
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 GLY 97 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39B ASP* 5.3 0.4 + - - -
96B GLY* 1.3 72.1 - - - -
98B GLY* 1.3 64.2 - - - -
100B PRO* 3.0 12.6 - - - +
101B HIS* 2.9 25.2 + - - -
137B ASN* 4.2 0.9 - - - -
138B THR* 3.5 1.8 + - - -
139B THR* 3.7 16.2 - - - -
1385B NAD 3.1 32.5 + - - -
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Residues in contact with GLY 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B GLY* 1.3 71.4 - - - -
99B SER* 1.3 62.0 + - - +
101B HIS* 3.3 1.1 + - - -
102B ASP* 2.5 30.1 + - - +
142B THR* 3.5 8.3 - - - +
144B SER* 3.1 20.3 + - - -
1385B NAD 3.0 35.2 + - - -
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Residues in contact with SER 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B ASP* 5.9 0.4 - - - -
68B VAL* 3.6 8.4 - - - +
69B MET 3.7 18.8 - - - -
70B PRO* 3.4 16.9 - - - +
71B ASN 3.4 5.7 + - - -
72B PRO* 3.7 15.2 - - - +
98B GLY* 1.3 76.4 - - - +
100B PRO* 1.3 71.1 - - - +
102B ASP 3.5 0.2 + - - -
103B CYS* 3.0 24.8 + - - +
1385B NAD 3.0 29.6 + - - -
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Residues in contact with PRO 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B VAL* 3.8 15.1 - - + +
38B SER* 4.2 7.6 - - - -
39B ASP* 4.2 15.3 - - - +
68B VAL* 3.9 16.8 - - + -
94B SER* 3.8 2.6 - - - -
95B LEU 3.6 30.7 - - - +
96B GLY* 4.0 1.3 - - - -
97B GLY 3.0 28.9 - - - +
99B SER* 1.3 88.4 - - - +
101B HIS* 1.3 56.2 + - - +
103B CYS* 3.3 2.6 + - + +
104B ALA* 2.8 32.2 + - - +
1385B NAD 3.6 4.9 - - - +
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Residues in contact with HIS 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B SER* 2.7 31.1 + - - +
96B GLY 3.2 25.9 + - - -
97B GLY 2.9 21.4 + - - -
98B GLY 3.7 0.4 - - - +
99B SER 3.3 0.8 - - - -
100B PRO* 1.3 77.1 - - - +
102B ASP* 1.3 58.4 + - - +
104B ALA* 3.3 2.4 + - - +
105B LYS* 2.8 36.0 + - - +
133B LEU* 4.9 0.3 - - - +
135B SER* 3.9 4.8 - - - +
136B ILE 3.4 24.0 - - - -
137B ASN* 3.3 19.3 + - - +
142B THR* 4.6 0.2 - - + -
144B SER* 2.9 37.9 - - - +
145B GLU* 3.8 17.2 - - + +
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Residues in contact with ASP 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B PRO* 3.8 9.4 - - + -
98B GLY 2.5 25.2 + - - +
101B HIS* 1.3 72.5 - - - +
103B CYS* 1.3 68.5 - - - +
105B LYS* 3.1 8.2 + - - -
106B ALA* 3.1 19.2 + - - +
144B SER* 3.7 7.2 - - - -
149B PHE 4.7 1.1 - - - -
150B CYS* 3.4 13.1 - - - -
151B ILE* 2.8 44.3 + - - +
152B ILE* 5.2 1.1 - - - -
1385B NAD 3.4 41.7 - - - +
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Residues in contact with CYS 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B VAL* 4.2 0.7 - - + -
65B TYR* 4.3 0.9 - - - -
68B VAL* 3.8 26.5 - - + -
72B PRO* 3.9 14.2 - - + +
76B ALA* 4.1 12.6 - - - -
77B VAL* 4.1 28.7 - - - -
99B SER 3.0 18.4 + - - +
100B PRO 3.7 3.6 - - - +
102B ASP* 1.3 77.1 - - - +
104B ALA* 1.3 57.2 + - - +
106B ALA* 3.3 2.9 + - - +
107B ILE* 3.0 49.8 + - - +
152B ILE* 5.5 0.9 - - - -
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Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B VAL* 4.0 16.3 - - + +
92B VAL* 3.8 20.0 - - + +
94B SER* 3.5 24.5 - - - -
100B PRO 2.8 21.9 + - - +
101B HIS 3.5 2.2 - - - +
103B CYS* 1.3 72.4 - - - +
105B LYS* 1.3 59.2 + - - +
107B ILE* 3.4 3.6 + - - +
108B ALA* 2.9 32.1 + - - +
133B LEU* 3.9 6.3 - - + -
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Residues in contact with LYS 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B HIS* 2.8 24.3 + - - +
102B ASP* 3.5 8.7 + - - +
104B ALA* 1.3 77.1 - - - +
106B ALA* 1.3 58.4 + - - +
108B ALA* 3.8 2.3 - - - +
109B LEU* 2.9 31.6 + - - +
130B ALA* 4.7 1.2 - - - +
133B LEU* 3.8 15.7 - - + -
135B SER* 5.6 0.2 - - - +
144B SER* 2.6 36.4 + - - -
147B THR* 2.8 28.7 + - - -
149B PHE 2.8 29.9 + - - +
150B CYS* 4.0 10.3 - - + -
168B VAL* 3.6 35.3 - - + +
170B PRO* 4.0 8.5 - - - -
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Residues in contact with ALA 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B VAL* 3.6 13.5 - - + -
102B ASP 3.1 9.0 + - - +
103B CYS 3.5 8.1 - - - +
104B ALA 3.2 0.2 - - - -
105B LYS* 1.3 73.6 - - - +
107B ILE* 1.3 65.5 + - - +
109B LEU* 3.2 5.6 + - - +
110B VAL* 2.9 30.9 + - - +
117B VAL* 4.5 3.8 - - + -
150B CYS* 3.8 5.8 - - - -
152B ILE* 3.0 36.6 - - + -
163B ILE* 5.3 3.8 - - + -
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Residues in contact with ILE 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B LEU* 4.0 11.2 - - + -
37B VAL* 3.9 22.7 - - + -
65B TYR* 4.6 0.7 - - + -
77B VAL* 3.7 20.9 - - + +
80B GLY* 3.7 23.8 - - - +
81B LEU* 3.5 21.8 - - + +
84B LEU* 3.7 24.7 - - + -
92B VAL* 4.8 2.7 - - + -
103B CYS* 3.0 33.7 + - - +
104B ALA* 3.7 4.7 - - - +
106B ALA* 1.3 75.0 - - - +
108B ALA* 1.3 59.2 + - - +
111B ALA* 2.9 29.1 + - - +
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Residues in contact with ALA 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B VAL* 4.1 15.9 - - + +
104B ALA 2.9 18.3 + - - +
105B LYS* 3.8 6.1 - - - +
107B ILE* 1.3 78.2 - - - +
109B LEU* 1.3 60.6 + - - +
111B ALA* 3.5 9.9 + - - +
112B THR 3.6 5.5 + - - -
130B ALA* 3.6 7.7 - - + -
131B LEU* 3.0 48.7 + - + +
133B LEU* 4.6 6.7 - - + -
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Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B LYS 2.9 19.4 + - - +
106B ALA* 3.2 5.1 + - - +
108B ALA* 1.3 75.5 - - - +
110B VAL* 1.3 59.7 + - + +
112B THR* 3.4 0.7 + - - -
113B ASN* 2.9 57.7 + - - +
120B TYR* 3.9 37.5 - - + -
126B SER* 3.6 20.9 - - - +
128B LYS 4.0 4.5 - - - +
130B ALA* 3.6 12.3 - - + +
163B ILE* 4.3 12.8 - - + -
165B ASP* 4.6 1.6 - - - +
167B HIS* 4.1 12.8 - - + -
168B VAL* 3.9 19.3 - - + -
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Residues in contact with VAL 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B LEU* 3.8 31.2 - - + -
106B ALA* 2.9 22.6 + - - +
109B LEU* 1.3 74.6 - - + +
111B ALA* 1.3 62.3 + - - +
112B THR 3.2 0.7 - - - -
113B ASN* 4.7 0.4 - - - -
114B GLY* 2.6 38.5 + - - +
115B GLY 3.7 21.3 - - - +
116B GLU* 5.3 0.4 - - - -
117B VAL* 4.4 28.9 - - + +
120B TYR* 4.5 13.7 - - + -
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Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B LEU* 3.9 7.8 - - + +
84B LEU* 3.7 29.2 - - + -
107B ILE 2.9 17.5 + - - +
108B ALA 3.6 7.0 - - - +
109B LEU 3.3 0.4 - - - -
110B VAL* 1.3 78.4 - - - +
112B THR* 1.3 59.9 + - + +
114B GLY 4.7 0.7 + - - -
131B LEU* 4.1 15.5 - - + -
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Residues in contact with THR 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ALA 3.6 1.0 + - - -
109B LEU 3.4 2.8 + - - -
110B VAL 3.2 0.2 - - - -
111B ALA* 1.3 80.0 - - - +
113B ASN* 1.3 75.5 + - - +
114B GLY 3.6 0.2 - - - -
128B LYS* 4.8 10.6 - - - +
129B PRO 2.9 23.4 + - - +
130B ALA* 3.5 4.4 - - - -
131B LEU* 3.4 42.0 - - + +
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Residues in contact with ASN 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B LEU* 2.9 39.9 + - + +
112B THR* 1.3 88.8 + - - +
114B GLY* 1.3 64.8 + - - +
120B TYR* 3.2 24.6 + - + +
126B SER* 3.9 7.9 - - - -
127B LYS* 3.4 8.5 + - - +
128B LYS* 2.8 50.3 + - - +
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Residues in contact with GLY 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B VAL* 2.6 31.3 + - - +
111B ALA 4.5 1.0 + - - -
112B THR 3.6 1.0 - - - -
113B ASN* 1.3 74.4 - - - +
115B GLY* 1.3 65.9 + - - -
120B TYR* 2.8 23.4 + - - -
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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