Contacts of the helix formed by residues 97 - 114 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D ASP* 4.3 1.0 + - - -
96D GLY* 1.3 73.1 - - - -
98D GLY* 1.3 60.4 + - - -
99D SER 3.3 0.2 - - - -
100D PRO* 3.0 17.7 - - - +
101D HIS* 2.9 20.7 + - - -
137D ASN* 4.4 1.1 - - - -
138D THR* 3.5 2.6 + - - -
139D THR* 3.8 15.7 - - - -
1385D NAD 3.1 32.4 + - - -
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Residues in contact with GLY 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D GLY* 1.3 72.3 - - - -
99D SER* 1.3 55.7 + - - +
101D HIS* 3.5 6.9 - - - +
102D ASP* 2.4 39.5 + - - +
142D THR* 3.5 19.7 + - - -
144D SER* 3.9 3.8 - - - -
1385D NAD 2.9 30.5 + - - -
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Residues in contact with SER 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D ASP* 4.9 2.0 - - - -
68D VAL* 4.1 4.9 - - - -
69D MET 3.7 20.0 - - - -
70D PRO* 3.1 9.0 - - - +
71D ASN 3.1 22.7 + - - -
72D PRO* 3.8 15.5 - - - +
98D GLY* 1.3 75.0 - - - +
100D PRO* 1.3 71.9 - - - +
102D ASP* 3.3 2.1 + - - +
103D CYS* 2.9 25.3 + - - +
1385D NAD 3.1 21.9 + - - -
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Residues in contact with PRO 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D VAL* 3.7 18.9 - - + +
38D SER* 4.2 7.0 - - - -
39D ASP* 3.4 31.0 - - - +
68D VAL* 4.1 10.5 - - + -
94D SER* 4.0 2.2 - - - -
95D LEU 3.6 24.9 - - - +
97D GLY 3.0 23.1 - - - +
99D SER* 1.3 90.4 - - - +
101D HIS* 1.3 57.0 + - - +
104D ALA* 2.8 32.9 + - - +
1385D NAD 3.5 7.2 - - - +
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Residues in contact with HIS 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94D SER* 2.7 34.0 + - - +
96D GLY 3.1 27.2 + - - -
97D GLY 2.9 19.7 - - - -
98D GLY* 3.5 9.6 - - - +
99D SER 3.2 0.8 - - - -
100D PRO* 1.3 76.3 - - - +
102D ASP* 1.3 63.5 + - - +
104D ALA* 3.3 2.3 + - - +
105D LYS* 2.9 31.0 + - - +
135D SER* 3.7 11.8 + - - +
136D ILE 3.4 21.5 - - - -
137D ASN* 3.3 18.8 + - - +
142D THR* 4.5 0.7 - - - -
144D SER* 3.8 19.7 - - - +
145D GLU* 3.8 19.0 - - + +
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Residues in contact with ASP 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D PRO* 3.7 10.5 - - + -
98D GLY 2.4 32.8 + - - +
101D HIS* 1.3 76.2 - - - +
103D CYS* 1.3 62.3 + - - +
105D LYS* 3.2 7.0 + - - -
106D ALA* 3.1 19.1 + - - +
144D SER* 3.7 17.4 + - - -
149D PHE 4.6 3.7 - - - +
150D CYS* 3.3 15.0 - - - -
151D ILE* 2.6 57.2 + - - +
152D ILE* 4.1 2.2 - - - -
1385D NAD 4.0 9.6 - - - +
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Residues in contact with CYS 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D VAL* 4.2 4.9 - - + -
65D TYR* 4.2 9.4 - - - -
68D VAL* 4.2 11.0 - - + -
72D PRO* 3.9 14.2 - - + +
76D ALA* 4.0 30.1 - - - -
77D VAL* 4.0 11.7 - - - -
99D SER 2.9 17.2 + - - +
100D PRO 3.8 3.6 - - - +
102D ASP* 1.3 76.4 - - - +
104D ALA* 1.3 57.0 + - - +
106D ALA* 3.4 3.2 + - - +
107D ILE* 3.0 48.9 + - - +
152D ILE* 4.2 5.8 - - - -
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Residues in contact with ALA 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D VAL* 4.0 23.9 - - + +
92D VAL* 4.1 6.0 - - + +
94D SER* 3.5 23.3 - - - -
100D PRO 2.8 22.2 + - - +
101D HIS 3.6 2.0 - - - +
103D CYS* 1.3 69.1 - - - +
105D LYS* 1.3 60.5 + - - +
107D ILE* 3.5 3.6 + - - +
108D ALA* 3.0 31.4 + - - +
133D LEU* 3.9 15.6 - - + +
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Residues in contact with LYS 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D HIS* 2.9 30.7 + - - +
102D ASP* 3.2 6.7 + - - +
104D ALA* 1.3 76.8 - - - +
106D ALA* 1.3 59.3 + - - +
108D ALA* 3.8 1.8 - - - +
109D LEU* 2.9 30.9 + - - +
130D ALA* 5.0 0.9 - - - +
133D LEU* 3.9 15.9 - - + -
135D SER* 5.3 0.2 - - - -
144D SER* 2.6 33.4 + - - +
147D THR* 2.8 25.9 + - - -
149D PHE 2.8 30.1 + - - +
150D CYS* 4.0 10.1 - - + -
168D VAL* 3.6 38.1 - - + +
170D PRO* 4.1 9.0 - - - -
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Residues in contact with ALA 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D VAL* 3.6 33.2 - - + -
102D ASP 3.1 9.3 + - - +
103D CYS 3.6 4.0 - - - +
105D LYS* 1.3 76.6 - - - +
107D ILE* 1.3 65.1 + - - +
109D LEU* 3.2 6.3 + - - +
110D VAL* 2.9 30.6 + - + +
117D VAL* 4.8 8.1 - - + -
150D CYS* 3.8 15.2 - - - -
152D ILE* 3.9 7.2 - - + -
163D ILE* 5.6 1.8 - - + -
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Residues in contact with ILE 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D LEU* 4.0 10.5 - - + -
37D VAL* 4.0 23.8 - - + -
65D TYR* 4.5 1.6 - - + -
77D VAL* 3.8 25.3 - - + +
80D GLY* 3.9 23.3 - - - -
81D LEU* 3.6 22.9 - - + +
84D LEU* 3.8 19.3 - - + -
92D VAL* 5.0 3.6 - - + -
103D CYS* 3.0 31.6 + - - +
104D ALA* 3.7 4.9 - - - +
106D ALA* 1.3 76.4 - - - +
108D ALA* 1.3 62.3 + - - +
110D VAL* 5.0 0.4 - - - -
111D ALA* 3.0 24.1 + - - +
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Residues in contact with ALA 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92D VAL* 4.1 17.3 - - + -
104D ALA 3.0 18.2 + - - +
105D LYS* 3.8 5.6 - - - +
107D ILE* 1.3 79.1 - - - +
109D LEU* 1.3 62.8 + - - +
111D ALA* 3.5 11.3 + - - +
112D THR* 3.7 2.9 + - - -
130D ALA* 3.8 7.2 - - + -
131D LEU* 3.1 45.6 + - - +
133D LEU* 4.5 7.9 - - + -
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Residues in contact with LEU 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D LYS 2.9 18.3 + - - +
106D ALA* 3.7 5.8 - - - +
108D ALA* 1.3 74.3 - - - +
110D VAL* 1.3 66.8 + - + +
112D THR 3.2 2.9 + - - -
113D ASN* 3.0 50.1 + - - +
120D TYR* 4.0 35.2 - - + -
126D SER* 3.5 19.5 - - - +
128D LYS 4.3 0.9 - - - +
130D ALA* 3.9 9.6 - - + +
150D CYS* 6.3 0.2 - - + -
163D ILE* 4.3 13.5 - - + -
165D ASP* 4.8 2.5 - - - +
167D HIS* 4.0 16.6 - - + -
168D VAL* 3.8 22.0 - - + -
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Residues in contact with VAL 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D VAL* 4.9 2.2 - - + -
81D LEU* 3.5 28.7 - - + -
106D ALA* 2.9 23.1 + - + +
107D ILE 4.1 0.7 - - - +
109D LEU* 1.3 74.9 - - + +
111D ALA* 1.3 58.8 + - - +
114D GLY* 2.7 37.1 + - - +
115D GLY 3.5 22.4 - - - +
116D GLU* 4.5 0.9 - - - +
117D VAL* 4.3 25.8 - - + +
120D TYR* 4.3 19.1 - - + -
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Residues in contact with ALA 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D LEU* 4.4 9.4 - - + +
84D LEU* 4.3 24.9 - - + -
107D ILE 3.0 19.5 + - - +
108D ALA 3.6 8.5 - - - +
109D LEU 3.2 0.4 - - - -
110D VAL* 1.3 77.5 - - - +
112D THR* 1.3 60.0 + - + +
114D GLY* 4.7 1.0 + - - -
131D LEU* 4.3 13.9 - - + -
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Residues in contact with THR 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108D ALA 3.7 0.2 + - - -
109D LEU 3.2 8.7 + - - -
110D VAL 3.2 0.2 - - - -
111D ALA* 1.3 79.1 - - - +
113D ASN* 1.3 64.1 + - - +
114D GLY 3.6 0.7 - - - -
128D LYS* 3.1 26.6 - - - +
129D PRO 2.7 25.4 + - - +
130D ALA* 3.5 5.8 - - - -
131D LEU* 3.8 37.2 - - + +
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Residues in contact with ASN 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D LEU* 3.0 41.4 + - - +
112D THR* 1.3 83.0 + - - +
114D GLY* 1.3 60.7 + - - +
115D GLY 3.7 0.5 + - - -
120D TYR* 2.7 34.1 + - + +
126D SER* 3.7 7.8 - - - -
127D LYS* 3.5 6.3 + - - +
128D LYS* 2.8 53.8 + - - +
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Residues in contact with GLY 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110D VAL* 2.7 28.8 + - - +
111D ALA 4.5 1.4 + - - -
112D THR 3.6 2.0 - - - -
113D ASN* 1.3 74.2 - - - +
115D GLY* 1.3 66.3 + - - +
120D TYR* 2.7 24.3 + - - -
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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