Contacts of the helix formed by residues 97 - 113 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A ASP* 5.2 1.2 + - - -
96A GLY* 1.3 71.8 - - - -
98A GLY* 1.3 64.5 + - - -
100A PRO* 3.0 13.4 - - - +
101A HIS* 2.8 21.9 + - - -
137A ASN* 4.1 2.0 - - - -
138A THR* 3.4 2.6 + - - -
139A THR* 3.9 12.8 - - - -
1385A NAD 3.1 34.2 + - - -
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Residues in contact with GLY 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A GLY* 1.3 70.6 - - - -
99A SER* 1.3 61.1 + - - -
101A HIS* 3.1 11.3 + - - +
102A ASP* 3.0 19.9 + - - +
142A THR* 3.8 5.7 - - - +
144A SER* 3.0 20.4 + - - -
1385A NAD 2.9 39.1 + - - -
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Residues in contact with SER 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A VAL* 3.8 8.2 - - - +
69A MET 3.7 18.8 - - - -
70A PRO* 3.3 8.3 - - - +
71A ASN 3.1 20.1 + - - -
72A PRO* 3.9 15.6 - - - +
98A GLY* 1.3 75.3 - - - +
100A PRO* 1.3 69.6 - - - +
102A ASP* 3.4 2.4 + - - +
103A CYS* 3.2 23.4 + - - +
1385A NAD 3.3 23.4 + - - -
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Residues in contact with PRO 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A VAL* 3.9 15.2 - - - +
38A SER* 4.1 9.0 - - - -
39A ASP* 4.2 14.8 - - + +
68A VAL* 3.8 18.4 - - + -
94A SER* 3.8 2.6 - - - -
95A LEU 3.6 30.3 - - - +
97A GLY 3.0 28.0 - - - +
99A SER* 1.3 92.0 - - - +
101A HIS* 1.3 55.6 + - - +
103A CYS* 3.4 1.9 + - - +
104A ALA* 2.8 31.4 + - - +
1385A NAD 3.8 3.8 - - - +
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Residues in contact with HIS 101 (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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94A SER* 2.5 38.1 + - - +
95A LEU 4.4 0.2 - - - -
96A GLY 3.1 20.0 + - - -
97A GLY 2.8 20.4 + - - -
98A GLY 3.1 4.6 + - - +
100A PRO* 1.3 74.3 - - - +
102A ASP* 1.3 55.7 + - - +
104A ALA* 3.6 1.0 - - - +
105A LYS* 2.7 43.8 + - - +
133A LEU* 5.1 0.2 - - - +
135A SER* 3.7 8.9 - - - +
136A ILE 3.3 31.2 - - - -
137A ASN* 3.7 13.1 + - - +
144A SER* 3.0 35.9 - - - +
145A GLU* 4.0 11.4 - - + +
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Residues in contact with ASP 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PRO* 3.8 21.5 - - + +
98A GLY 3.0 15.6 + - - +
99A SER 3.9 2.0 - - - +
101A HIS* 1.3 73.7 - - - +
103A CYS* 1.3 63.4 + - - +
105A LYS* 3.4 7.6 + - - -
106A ALA 3.1 18.2 + - - -
144A SER* 3.8 16.5 - - - -
149A PHE 4.5 5.4 - - - +
150A CYS* 3.3 16.9 - - - -
151A ILE* 3.0 39.9 + - - +
152A ILE* 3.5 4.9 - - + +
1385A NAD 4.8 16.5 + - - -
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Residues in contact with CYS 103 (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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37A VAL* 4.3 4.0 - - + -
65A TYR* 4.3 4.0 - - - -
68A VAL* 3.8 26.9 - - + -
72A PRO* 4.2 9.1 - - + +
76A ALA* 3.9 28.3 - - - -
77A VAL* 4.0 15.5 - - - -
99A SER 3.2 15.1 + - - +
100A PRO 3.7 3.8 - - - +
102A ASP* 1.3 78.5 - - - +
104A ALA* 1.3 58.9 + - - +
106A ALA* 3.2 3.9 + - - +
107A ILE* 2.9 37.5 + - - +
152A ILE* 4.2 10.1 - - - +
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Residues in contact with ALA 104 (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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37A VAL* 4.1 9.1 - - + +
92A VAL* 4.0 10.6 - - + +
94A SER* 3.4 24.5 - - - -
100A PRO 2.8 19.7 + - - +
101A HIS 3.6 2.5 - - - +
103A CYS* 1.3 74.8 - - - +
105A LYS* 1.3 66.1 + - - +
107A ILE* 3.1 9.7 + - - +
108A ALA* 2.9 26.7 + - - +
133A LEU* 4.0 14.1 - - + +
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Residues in contact with LYS 105 (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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101A HIS* 2.7 33.9 + - - +
102A ASP* 3.7 5.8 + - - +
104A ALA* 1.3 72.8 - - - +
106A ALA* 1.3 58.4 + - - +
108A ALA* 3.5 1.6 + - - +
109A LEU* 3.0 30.9 + - - +
130A ALA* 4.9 1.2 - - - +
133A LEU* 3.8 17.7 - - + +
144A SER* 2.7 33.5 + - - +
147A THR* 2.8 24.7 + - - -
149A PHE 2.7 31.1 + - - +
150A CYS* 4.0 8.7 - - + -
168A VAL* 3.4 42.4 - - + +
170A PRO* 4.1 8.7 - - + -
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Residues in contact with ALA 106 (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 VAL* 3.5 26.7 - - + -
102A ASP 3.1 12.4 + - - +
103A CYS 3.4 9.0 - - - +
104A ALA 3.2 0.2 - - - -
105A LYS* 1.3 75.6 - - - +
107A ILE* 1.3 67.0 + - - +
109A LEU* 3.9 5.7 - - - +
110A VAL* 3.1 28.9 + - - +
117A VAL* 4.9 7.6 - - + -
150A CYS* 3.8 6.7 - - - -
152A ILE* 3.7 16.2 - - + -
163A ILE* 5.5 2.0 - - + -
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Residues in contact with ILE 107 (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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35A LEU* 3.9 15.0 - - + -
37A VAL* 4.5 10.3 - - + -
77A VAL* 3.0 46.4 - - + +
80A GLY* 4.2 6.7 - - - -
81A LEU* 3.4 20.5 - - + +
84A LEU* 3.7 26.0 - - + -
92A VAL* 4.7 3.8 - - + -
103A CYS* 2.9 36.5 + - - +
104A ALA* 3.1 9.8 + - - +
106A ALA* 1.3 77.1 - - - +
108A ALA* 1.3 59.4 + - - +
111A ALA* 2.8 30.5 + - - +
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Residues in contact with ALA 108 (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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92A VAL* 4.2 15.2 - - + +
104A ALA 2.9 16.5 + - - +
105A LYS 3.9 2.9 - - - +
107A ILE* 1.3 78.0 - - - +
109A LEU* 1.3 60.4 + - - +
111A ALA* 3.6 13.2 - - - +
112A THR* 3.5 3.1 + - - -
130A ALA* 3.2 8.8 - - + +
131A LEU* 2.9 45.7 + - + +
133A LEU* 4.4 12.8 - - + -
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Residues in contact with LEU 109 (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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105A LYS 3.0 18.8 + - - +
106A ALA* 3.9 5.2 - - - +
107A ILE 3.3 0.4 - - - -
108A ALA* 1.3 73.1 - - - +
110A VAL* 1.3 64.3 + - + +
112A THR 3.4 1.6 + - - -
113A ASN* 2.8 54.5 + - - +
120A TYR* 3.9 35.4 - - + -
126A SER* 3.5 19.5 - - - +
128A LYS 4.2 0.2 - - - +
130A ALA* 3.5 11.6 - - + +
163A ILE* 4.1 13.2 - - + -
165A ASP* 4.7 2.2 - - - +
167A HIS* 3.9 18.4 - - + -
168A VAL* 3.8 20.9 - - + -
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Residues in contact with VAL 110 (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 VAL* 4.8 4.3 - - + -
78A LEU* 6.6 0.2 - - + -
81A LEU* 4.2 18.8 - - + -
106A ALA* 3.1 18.5 + - - +
107A ILE 3.9 2.0 - - - +
109A LEU* 1.3 75.7 - - + +
111A ALA* 1.3 66.9 + - - +
112A THR 3.0 1.4 + - - -
113A ASN* 3.0 21.5 + - - +
114A GLY 3.4 9.0 - - - +
115A GLY* 3.4 30.5 - - - +
116A GLU* 4.8 0.4 - - - -
117A VAL* 4.7 21.8 - - + +
120A TYR* 4.7 9.6 - - + -
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Residues in contact with ALA 111 (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 LEU* 3.9 7.3 - - + +
84A LEU* 3.8 29.8 - - + +
107A ILE 2.8 19.7 + - - +
108A ALA* 3.6 10.8 - - - +
109A LEU 3.3 0.2 - - - -
110A VAL* 1.3 77.7 - - - +
112A THR* 1.3 60.8 + - - +
113A ASN 5.0 0.5 - - - +
131A LEU* 4.2 14.8 - - + +
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Residues in contact with THR 112 (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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108A ALA 3.5 0.7 + - - -
109A LEU 3.4 2.8 + - - -
110A VAL 3.1 0.4 - - - -
111A ALA* 1.3 78.2 - - - +
113A ASN* 1.3 63.1 + - - +
128A LYS* 3.8 21.9 - - - +
129A PRO 2.6 26.1 + - - +
130A ALA* 3.1 12.3 - - - -
131A LEU* 3.4 46.0 - - + +
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Residues in contact with ASN 113 (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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109A LEU* 2.8 41.0 + - - +
110A VAL 3.0 7.2 + - - +
111A ALA 4.9 0.3 - - - +
112A THR* 1.3 86.6 + - - +
114A GLY* 1.3 72.3 + - - +
120A TYR* 2.8 17.7 + - + +
126A SER* 3.8 6.5 - - - -
127A LYS* 3.9 4.2 + - - +
128A LYS* 2.8 55.5 + - - +
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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