Contacts of the helix formed by residues 94 - 108 (chain D) in PDB entry 1OJ7
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 94 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D GLY* 1.3 72.7 - - - -
95D GLY* 1.3 66.0 + - - -
96D SER* 3.3 3.1 - - - -
97D VAL* 3.1 8.8 + - - +
98D LEU* 3.0 27.0 + - - +
137D LEU* 4.4 4.0 - - - -
138D THR* 3.6 2.0 + - - -
139D LEU* 4.0 26.5 - - - -
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Residues in contact with GLY 95 (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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94D GLY* 1.3 71.4 - - - -
96D SER* 1.3 56.2 + - - +
98D LEU* 4.4 7.4 - - - -
99D ASP* 2.8 39.0 + - - +
137D LEU* 4.6 4.0 - - - +
139D LEU* 4.7 6.3 + - - +
141D ALA* 6.3 0.2 - - - +
142D THR* 3.8 33.8 + - - +
144D SER* 4.7 1.8 - - - -
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Residues in contact with SER 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D ILE* 3.5 8.7 - - - +
66D GLU 3.8 6.3 - - - -
67D PRO* 3.2 21.1 - - - +
68D ASN* 3.0 21.8 + - - -
69D PRO* 3.4 23.6 - - - +
94D GLY 3.3 1.2 - - - -
95D GLY* 1.3 75.9 - - - +
97D VAL* 1.3 58.9 + - - +
99D ASP* 4.6 0.4 - - - -
100D GLY 3.0 22.7 + - - -
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Residues in contact with VAL 97 (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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35D THR* 3.7 27.8 - - - +
36D TYR* 3.7 5.2 - - - +
37D GLY* 3.5 33.4 - - - +
65D ILE* 4.0 16.0 - - + +
91D ALA* 4.0 5.6 - - + -
92D VAL 3.8 18.2 - - - +
93D GLY* 4.2 9.9 - - - +
94D GLY 3.1 15.0 + - - +
96D SER* 1.3 76.6 - - - +
98D LEU* 1.3 60.1 + - - +
100D GLY* 3.5 0.7 + - - -
101D THR* 2.7 34.0 + - - +
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Residues in contact with LEU 98 (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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91D ALA* 3.8 24.5 - - + +
93D GLY 3.8 17.9 - - - +
94D GLY 3.0 21.4 + - - +
95D GLY* 3.9 2.2 - - - +
97D VAL* 1.3 75.2 - - - +
99D ASP* 1.3 58.9 + - - +
101D THR* 3.3 3.8 + - - -
102D LYS* 2.9 32.6 + - - +
133D MET* 3.9 7.3 - - + +
135D CYS* 3.7 25.4 - - + -
136D VAL 4.8 0.9 - - - +
137D LEU* 4.0 15.9 - - + -
144D SER* 3.7 16.6 - - - +
145D GLU* 3.4 37.9 - - - +
170D PRO* 5.6 0.4 - - + -
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Residues in contact with ASP 99 (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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69D PRO* 4.3 2.2 - - + -
95D GLY 2.8 26.0 + - - +
96D SER* 4.0 2.7 - - - +
98D LEU* 1.3 68.8 - - - +
100D GLY* 1.3 65.4 + - - +
102D LYS* 3.2 5.0 + - - +
103D PHE 3.1 17.8 + - - -
142D THR* 5.6 4.2 - - - +
144D SER* 2.6 32.4 + - - -
149D GLY 3.6 6.4 - - - +
150D ALA* 3.6 22.0 - - + +
151D VAL* 3.1 35.5 + - - +
152D ILE* 3.4 10.1 - - - +
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Residues in contact with GLY 100 (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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65D ILE* 4.7 1.6 - - - -
69D PRO* 4.1 3.9 - - - +
74D LEU* 3.6 35.1 - - - +
96D SER 3.0 18.3 + - - -
97D VAL 3.9 0.9 - - - -
99D ASP* 1.3 76.9 - - - +
101D THR* 1.3 56.4 + - - +
103D PHE* 3.4 4.2 + - - +
104D ILE* 3.0 31.3 + - - +
152D ILE* 4.1 0.4 - - - -
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Residues in contact with THR 101 (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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35D THR* 2.6 36.0 + - + +
65D ILE* 4.5 0.5 - - - +
89D LEU* 3.7 32.5 - - + +
91D ALA* 3.5 10.2 - - + +
97D VAL 2.7 20.7 + - - -
98D LEU 3.5 5.4 - - - -
99D ASP 3.2 0.2 - - - -
100D GLY* 1.3 75.4 - - - +
102D LYS* 1.3 59.1 + - - +
104D ILE* 3.7 7.6 - - - +
105D ALA* 2.9 28.4 + - - +
133D MET* 4.0 15.0 - - + -
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Residues in contact with LYS 102 (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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98D LEU* 2.9 18.6 + - - +
99D ASP* 3.2 8.5 + - - +
101D THR* 1.3 75.9 - - - +
103D PHE* 1.3 62.9 + - - +
105D ALA* 3.4 2.2 + - - +
106D ALA* 3.3 17.3 + - - +
133D MET* 3.6 13.0 - - - -
144D SER* 2.8 32.7 + - - +
147D ASN* 2.7 34.3 + - - -
149D GLY 2.8 29.9 + - - +
150D ALA* 4.0 10.8 - - + -
163D PHE* 3.9 2.2 - - + -
168D VAL* 3.3 50.9 - - + +
170D PRO* 4.0 7.6 - - - -
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Residues in contact with PHE 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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71D TYR* 3.9 25.4 - + - -
74D LEU* 3.8 27.4 - - + -
75D MET* 4.1 14.4 - - - -
78D VAL* 4.6 1.3 - - + -
99D ASP 3.1 5.9 + - - -
100D GLY 3.6 7.0 - - - +
101D THR 3.2 0.2 - - - -
102D LYS* 1.3 74.4 - - - +
104D ILE* 1.3 62.5 + - + +
106D ALA* 3.3 0.9 + - - +
107D ALA* 2.8 52.1 + - + +
116D PRO* 3.4 28.5 - - + -
119D ILE* 4.2 9.4 - - + -
120D LEU* 3.6 26.9 - - + -
152D ILE* 3.7 27.4 - - + -
163D PHE* 3.8 14.2 - + + -
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Residues in contact with ILE 104 (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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33D LEU* 5.3 0.4 - - + -
35D THR* 4.5 9.6 - - + -
65D ILE* 4.4 9.6 - - + -
74D LEU* 3.8 34.8 - - + +
77D ALA* 3.5 23.8 - - + +
78D VAL* 4.0 17.4 - - + +
81D VAL* 3.9 27.4 - - + -
89D LEU* 4.2 12.1 - - + +
100D GLY 3.0 24.1 + - - +
101D THR* 3.3 11.6 + - - +
103D PHE* 1.3 75.9 - - - +
105D ALA* 1.3 63.5 + - - +
108D ALA* 3.1 24.3 + - - +
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Residues in contact with ALA 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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89D LEU* 3.7 15.0 - - + +
101D THR 2.9 17.3 + - - +
102D LYS* 3.5 10.1 - - - +
103D PHE 3.2 0.2 - - - -
104D ILE* 1.3 79.1 - - - +
106D ALA* 1.3 59.3 + - - +
108D ALA 4.1 2.4 + - - -
109D ASN 4.1 5.0 + - - -
130D ALA* 3.3 11.2 - - + -
131D ILE* 3.0 49.5 + - - +
133D MET* 4.9 6.3 - - - -
168D VAL* 4.6 3.6 - - + -
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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
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102D LYS 3.3 12.1 + - - +
103D PHE 4.0 1.3 - - - +
105D ALA* 1.3 78.3 - - - +
107D ALA* 1.3 64.9 + - - +
108D ALA 3.2 1.8 - - - -
109D ASN* 3.2 6.6 + - - +
110D TYR* 3.2 22.9 + - - +
119D ILE* 3.9 9.4 - - + -
127D ILE* 3.7 35.4 - - + -
129D SER 4.1 4.7 - - - +
130D ALA* 3.8 7.2 - - - +
163D PHE* 4.6 2.9 - - + -
168D VAL* 4.0 10.1 - - + -
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Residues in contact with ALA 107 (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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78D VAL* 3.8 14.2 - - + +
82D ARG* 2.9 22.5 + - - -
103D PHE* 2.8 39.4 + - + +
106D ALA* 1.3 73.7 - - - +
108D ALA* 1.3 59.5 + - - +
110D TYR* 3.2 13.4 + - - +
116D PRO* 3.5 25.3 - - + +
119D ILE* 3.8 8.7 - - + +
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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
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78D VAL* 4.0 8.4 - - + +
81D VAL* 3.6 31.9 - - + -
82D ARG* 3.2 30.9 + - + +
104D ILE* 3.1 19.9 + - + +
105D ALA 4.2 0.9 - - - +
107D ALA* 1.3 78.8 - - - +
109D ASN* 1.3 61.3 + - - +
110D TYR 4.3 0.9 - - - +
131D ILE* 3.6 12.6 - - + -
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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