Contacts of the helix formed by residues 94 - 108 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A GLY* 1.3 75.2 - - - -
95A GLY* 1.3 64.9 + - - -
96A SER 3.2 3.6 - - - -
97A VAL* 3.1 7.5 + - - +
98A LEU* 3.0 24.2 + - - +
137A LEU* 4.4 3.4 - - - -
138A THR* 3.6 3.2 + - - -
139A LEU* 3.9 18.6 - - - -
1388A NZQ 3.3 22.2 + - - -
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Residues in contact with GLY 95 (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 GLY* 1.3 72.1 - - - -
96A SER* 1.3 55.1 + - - +
98A LEU* 4.4 7.6 - - - -
99A ASP* 2.8 36.6 + - - +
137A LEU* 4.6 3.8 - - - +
139A LEU 4.6 0.2 + - - -
142A THR* 3.8 20.4 + - - -
144A SER* 4.6 1.8 - - - -
1388A NZQ 2.8 30.6 + - - -
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Residues in contact with SER 96 (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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65A ILE* 3.4 12.3 - - - +
66A GLU 3.4 23.3 - - - -
67A PRO* 3.8 1.1 - - - -
68A ASN 3.0 17.7 + - - -
69A PRO* 3.4 14.8 - - - +
95A GLY* 1.3 73.6 - - - +
97A VAL* 1.3 61.1 + - - +
100A GLY 2.9 22.9 + - - -
1388A NZQ 2.6 43.4 + - - -
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Residues in contact with VAL 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A THR* 3.7 32.8 - - - +
36A TYR* 3.7 5.4 - - - +
37A GLY* 3.5 34.3 - - - +
65A ILE* 3.8 16.2 - - + +
91A ALA* 4.0 2.2 - - + -
92A VAL 3.8 17.9 - - - +
93A GLY* 4.1 13.2 - - - +
94A GLY 3.1 10.8 + - - +
96A SER* 1.3 76.4 - - - +
98A LEU* 1.3 60.7 + - + +
100A GLY* 3.9 0.5 - - - -
101A THR* 2.7 33.8 + - - +
1388A NZQ 4.3 1.8 + - - +
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Residues in contact with LEU 98 (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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91A ALA* 3.9 24.9 - - + +
93A GLY 3.7 17.3 - - - +
94A GLY 3.0 21.2 + - - +
95A GLY* 3.9 2.9 - - - +
97A VAL* 1.3 77.4 - - - +
99A ASP* 1.3 56.7 + - - +
101A THR* 3.2 3.8 + - - -
102A LYS* 2.9 32.9 + - - +
133A MET* 3.8 6.3 - - + +
135A CYS* 3.7 26.7 - - + -
136A VAL 4.7 0.9 - - - +
137A LEU* 4.0 15.0 - - + -
144A SER* 3.6 16.6 - - - +
145A GLU* 3.4 38.1 - - - +
170A PRO* 5.6 0.9 - - + -
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Residues in contact with ASP 99 (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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69A PRO* 4.3 2.7 - - + -
95A GLY 2.8 23.4 + - - +
96A SER* 4.0 2.5 - - - +
98A LEU* 1.3 68.7 - - - +
100A GLY* 1.3 66.6 + - - +
102A LYS* 3.2 5.9 + - - +
103A PHE 3.0 18.0 + - - -
144A SER* 2.7 28.9 + - - -
149A GLY 3.7 2.1 - - - +
150A ALA* 3.5 18.4 - - + +
151A VAL* 3.0 28.0 + - - +
152A ILE* 3.5 9.7 - - - +
1388A NZQ 2.9 38.1 + - - -
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Residues in contact with GLY 100 (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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65A ILE* 4.5 1.8 - - - -
69A PRO* 4.0 5.3 - - - +
74A LEU* 3.5 35.8 - - - +
96A SER 2.9 18.6 + - - -
97A VAL 3.9 1.3 - - - -
99A ASP* 1.3 74.7 - - - +
101A THR* 1.3 56.1 + - - +
103A PHE* 3.3 3.3 + - - +
104A ILE* 3.0 31.4 + - - +
152A ILE* 4.1 0.9 - - - -
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Residues in contact with THR 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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35A THR* 2.6 32.9 + - + +
65A ILE* 4.2 1.4 - - - +
89A LEU* 3.7 34.7 - - + +
91A ALA* 3.5 9.9 - - + +
97A VAL 2.7 20.4 + - - -
98A LEU 3.5 5.2 - - - -
100A GLY* 1.3 74.6 - - - +
102A LYS* 1.3 59.5 + - - +
104A ILE* 3.3 7.9 + - - +
105A ALA* 2.9 28.4 + - - +
133A MET* 3.8 15.3 - - + -
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Residues in contact with LYS 102 (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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98A LEU* 2.9 18.9 + - - +
99A ASP* 3.5 6.7 - - - +
101A THR* 1.3 75.6 - - - +
103A PHE* 1.3 63.4 + - - +
105A ALA* 3.3 2.0 + - - +
106A ALA* 3.2 18.4 + - - +
133A MET* 3.5 12.1 - - - -
144A SER* 2.8 40.7 + - - +
147A ASN* 2.8 23.4 + - - -
149A GLY 2.8 30.2 + - - +
150A ALA* 4.0 10.5 - - + -
163A PHE* 4.0 2.2 - - + -
168A VAL* 3.4 53.7 - - + +
170A PRO* 4.0 7.6 - - - -
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Residues in contact with PHE 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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71A TYR* 4.0 20.4 - + - -
74A LEU* 3.8 30.7 - - + -
75A MET* 4.3 12.8 - - - -
78A VAL* 4.5 1.8 - - + -
99A ASP 3.0 5.7 + - - -
100A GLY 3.5 7.4 - - - +
102A LYS* 1.3 74.3 - - - +
104A ILE* 1.3 63.7 + - - +
106A ALA* 3.3 1.4 + - - +
107A ALA* 2.8 42.9 + - + +
116A PRO* 3.4 38.8 - - + -
117A TRP 4.7 0.2 - - - -
119A ILE* 4.0 10.5 - - + -
120A LEU* 3.5 28.3 - - + -
152A ILE* 3.7 25.8 - - + -
163A PHE* 3.9 13.6 - + + -
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Residues in contact with ILE 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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35A THR* 4.4 10.3 - - + -
65A ILE* 4.4 9.6 - - + -
74A LEU* 3.7 28.9 - - + +
77A ALA* 3.4 34.5 - - + +
78A VAL* 4.2 11.1 - - + +
81A VAL* 3.8 30.1 - - + -
89A LEU* 4.1 12.6 - - + -
100A GLY 3.0 22.5 + - - +
101A THR* 3.3 11.0 + - - +
103A PHE* 1.3 75.1 - - - +
105A ALA* 1.3 64.5 + - - +
107A ALA* 3.9 0.2 - - - +
108A ALA* 3.0 25.3 + - - +
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Residues in contact with ALA 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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89A LEU* 3.6 15.9 - - + -
101A THR 2.9 17.9 + - - +
102A LYS* 3.5 9.6 - - - +
104A ILE* 1.3 78.2 - - - +
106A ALA* 1.3 59.7 + - - +
108A ALA* 3.9 4.0 + - - +
109A ASN 4.1 2.6 + - - -
130A ALA* 3.4 8.9 - - + -
131A ILE* 3.1 52.4 + - - +
133A MET* 4.9 5.2 - - - -
168A VAL* 4.6 3.4 - - + -
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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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102A LYS 3.2 13.1 + - - +
103A PHE 4.0 2.2 - - - +
105A ALA* 1.3 75.1 - - - +
107A ALA* 1.3 66.3 + - - +
108A ALA 3.2 2.4 + - - -
109A ASN* 3.3 5.2 + - - +
110A TYR* 3.2 23.7 + - - +
119A ILE* 4.0 9.2 - - + -
127A ILE* 3.8 35.8 - - + +
129A SER 4.2 4.3 - - - +
130A ALA* 4.0 6.7 - - - -
163A PHE* 4.7 2.7 - - + -
168A VAL* 4.0 9.6 - - + -
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Residues in contact with ALA 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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78A VAL* 3.7 26.7 - - + -
82A ARG* 2.8 23.9 + - - -
103A PHE* 2.8 30.1 + - + +
104A ILE 3.9 0.2 - - - +
106A ALA* 1.3 73.7 - - - +
108A ALA* 1.3 58.9 + - - +
110A TYR* 3.3 11.5 + - - +
116A PRO* 3.7 21.5 - - + +
119A ILE* 3.9 9.3 - - + +
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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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78A VAL* 4.4 6.2 - - + +
81A VAL* 3.6 31.2 - - + -
82A ARG* 3.6 29.3 + - + +
104A ILE 3.0 17.6 + - - +
105A ALA 4.1 1.1 - - - +
106A ALA 3.2 0.4 - - - -
107A ALA* 1.3 77.2 - - - +
109A ASN* 1.3 63.1 + - - +
110A TYR 3.8 1.2 + - - +
131A ILE* 3.6 14.8 - - + -
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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