Contacts of the helix formed by residues 94 - 110 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C GLY* 1.3 75.6 - - - -
95C GLY* 1.3 65.9 + - - -
96C SER 3.2 2.7 - - - -
97C VAL* 3.2 8.1 + - - +
98C LEU* 3.1 23.0 + - - +
137C LEU* 4.4 9.6 - - - -
139C LEU* 3.7 36.9 - - - +
140C PRO 5.5 0.7 - - - -
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Residues in contact with GLY 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C GLY* 1.3 71.6 - - - -
96C SER* 1.3 56.4 + - - +
98C LEU* 3.5 9.1 + - - +
99C ASP* 2.9 37.9 + - - +
137C LEU* 5.1 1.2 - - - +
139C LEU* 5.0 2.6 - - - +
140C PRO 5.3 0.6 + - - -
142C THR* 3.6 34.0 + - - +
144C SER* 4.3 3.6 - - - -
145C GLU* 5.9 0.2 - - - -
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Residues in contact with SER 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ILE* 3.6 3.9 - - - +
66C GLU 3.4 15.0 - - - -
67C PRO* 2.4 36.6 + - - +
69C PRO* 3.1 17.9 - - - +
94C GLY 3.2 1.0 - - - -
95C GLY* 1.3 73.6 - - - +
97C VAL* 1.3 64.2 + - - +
99C ASP* 3.4 2.6 + - - -
100C GLY 3.0 23.4 + - - -
139C LEU* 6.1 1.3 - - - +
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Residues in contact with VAL 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C THR* 3.8 31.4 - - - +
36C TYR* 3.8 8.7 - - - +
37C GLY* 3.5 31.6 - - - +
65C ILE* 3.9 16.3 - - + +
91C ALA* 4.0 8.5 - - + -
92C VAL 4.0 6.3 - - - +
93C GLY* 4.3 11.9 - - - -
94C GLY 3.2 13.3 + - - +
96C SER* 1.3 75.3 - - - +
98C LEU* 1.3 58.0 + - - +
100C GLY 3.4 0.7 + - - -
101C THR* 2.7 37.7 + - - +
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Residues in contact with LEU 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C ALA* 4.1 7.6 - - + +
93C GLY 5.2 0.4 - - - +
94C GLY 3.1 13.2 + - - +
95C GLY* 3.6 6.3 - - - +
97C VAL* 1.3 77.3 - - - +
99C ASP* 1.3 56.7 - - - +
101C THR* 3.3 3.3 + - - -
102C LYS* 3.0 33.1 + - - +
133C MET* 3.6 26.7 - - + +
135C CYS* 3.8 24.0 - - + -
137C LEU* 3.6 31.6 - - + -
144C SER* 3.5 27.8 - - - +
145C GLU* 3.7 22.0 - - - +
170C PRO* 4.0 10.8 - - + -
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Residues in contact with ASP 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C PRO* 4.3 4.0 - - + +
95C GLY 2.9 17.7 + - - +
96C SER* 3.7 5.6 - - - +
98C LEU* 1.3 72.1 - - - +
100C GLY* 1.3 66.3 + - - +
102C LYS* 3.2 7.1 + - - +
103C PHE 3.1 16.6 + - - -
144C SER* 2.6 35.3 + - - -
149C GLY 3.6 6.8 - - - +
150C ALA* 3.5 22.1 - - + +
151C VAL* 3.1 33.9 + - - +
152C ILE* 3.6 9.5 - - - +
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Residues in contact with GLY 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C ILE* 4.3 1.8 - - - -
69C PRO* 4.0 7.5 - - - +
74C LEU* 3.6 33.7 - - - +
96C SER 3.0 15.9 + - - -
97C VAL 3.9 1.3 - - - -
99C ASP* 1.3 76.0 - - - +
101C THR* 1.3 58.1 + - - +
103C PHE* 3.2 5.7 + - - +
104C ILE* 3.0 30.3 + - - +
152C ILE* 4.0 0.4 - - - -
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Residues in contact with THR 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C THR* 2.7 35.0 + - + +
65C ILE* 4.1 1.2 - - - +
89C LEU* 3.7 31.4 - - + -
91C ALA* 3.6 7.2 - - + +
97C VAL 2.7 21.4 + - - -
98C LEU 3.5 4.5 - - - -
100C GLY* 1.3 75.4 - - - +
102C LYS* 1.3 60.1 + - - +
104C ILE* 3.2 8.3 + - - +
105C ALA* 2.8 28.4 + - - +
133C MET* 3.7 19.1 - - + -
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Residues in contact with LYS 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C LEU* 3.0 20.4 + - - +
99C ASP 3.2 6.3 + - - +
101C THR* 1.3 75.8 - - - +
103C PHE* 1.3 61.0 + - - +
105C ALA* 3.3 5.3 + - - +
106C ALA* 3.1 19.6 + - - +
133C MET* 3.6 13.4 - - - -
144C SER* 2.8 29.6 + - - +
147C ASN* 2.7 38.4 + - - -
149C GLY 2.8 33.7 + - - +
150C ALA* 4.1 3.6 - - + -
163C PHE* 3.9 7.9 - - + -
168C VAL* 3.5 43.8 - - + +
170C PRO* 4.2 7.6 - - - -
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Residues in contact with PHE 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C TYR* 3.8 25.1 - + + -
74C LEU* 3.7 32.1 - - + -
75C MET* 4.1 12.8 - - - -
78C VAL* 4.6 1.1 - - + -
99C ASP 3.1 5.7 + - - -
100C GLY 3.4 7.2 - - - +
102C LYS* 1.3 73.3 - - - +
104C ILE* 1.3 62.9 - - - +
106C ALA 3.3 0.9 + - - -
107C ALA* 2.8 44.7 + - + +
116C PRO* 3.6 29.8 - - + -
119C ILE* 4.1 12.8 - - + -
120C LEU* 3.6 31.4 - - + -
152C ILE* 3.7 22.2 - - + -
163C PHE* 3.7 16.5 - + + -
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Residues in contact with ILE 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LEU* 5.1 0.2 - - + -
35C THR* 4.3 10.3 - - + -
65C ILE* 4.3 10.8 - - + -
74C LEU* 3.8 29.2 - - + +
77C ALA* 3.4 31.6 - - + -
78C VAL* 4.0 13.6 - - + +
81C VAL* 3.9 28.9 - - + -
89C LEU* 4.1 12.3 - - + -
100C GLY 3.0 19.6 + - - +
101C THR* 3.2 14.8 + - - +
103C PHE* 1.3 76.4 - - - +
105C ALA* 1.3 63.2 + - - +
108C ALA* 3.0 25.5 + - - +
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Residues in contact with ALA 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C LEU* 3.5 16.1 - - + +
101C THR 2.8 16.8 + - - +
102C LYS* 3.4 9.6 - - - +
104C ILE* 1.3 77.5 - - - +
106C ALA* 1.3 60.9 + - - +
108C ALA* 3.9 6.1 + - - +
109C ASN 4.0 4.3 + - - -
130C ALA* 3.3 10.0 - - + -
131C ILE* 3.1 45.3 + - - +
133C MET* 4.7 7.4 - - - -
168C VAL* 4.5 3.8 - - + -
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Residues in contact with ALA 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C LYS 3.1 15.6 + - - +
103C PHE 4.0 2.5 - - - +
105C ALA* 1.3 74.6 - - - +
107C ALA* 1.3 65.2 + - - +
109C ASN* 3.2 6.1 + - - +
110C TYR* 3.2 22.2 + - - +
119C ILE* 4.0 7.2 - - + -
127C ILE* 3.6 37.6 - - + +
129C SER 4.2 3.9 - - - +
130C ALA* 3.9 7.6 - - - +
163C PHE* 4.4 3.6 - - + -
168C VAL* 4.0 9.9 - - + -
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Residues in contact with ALA 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C VAL* 3.6 23.3 - - + -
82C ARG* 3.1 20.6 + - - -
103C PHE* 2.8 31.8 + - + +
106C ALA* 1.3 73.7 - - - +
108C ALA* 1.3 62.9 + - - +
110C TYR* 3.2 11.4 + - - +
116C PRO* 3.9 23.9 - - + +
119C ILE* 3.8 10.0 - - + +
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Residues in contact with ALA 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C VAL* 4.0 13.0 - - + +
81C VAL* 3.6 17.5 - - + -
82C ARG* 3.4 24.1 + - + +
104C ILE 3.0 17.6 + - - +
105C ALA 4.1 1.3 - - - +
106C ALA 3.2 0.2 - - - -
107C ALA* 1.3 78.4 - - - +
109C ASN* 1.3 62.3 + - - +
110C TYR 4.2 1.0 - - - +
131C ILE* 3.4 30.1 - - + -
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Residues in contact with ASN 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C ALA 4.0 0.6 + - - +
106C ALA 3.2 4.4 + - - +
107C ALA 3.2 0.2 - - - -
108C ALA* 1.3 80.8 + - - +
110C TYR* 1.3 64.4 + - - +
111C PRO* 3.8 2.4 - - - +
129C SER* 3.0 40.7 + - - +
130C ALA* 3.6 21.0 - - - +
131C ILE* 3.7 20.9 + - - +
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Residues in contact with TYR 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C ARG* 3.2 13.0 + - - +
106C ALA 3.2 9.8 + - - +
107C ALA* 3.2 17.1 + - - +
108C ALA 4.2 1.2 - - - +
109C ASN* 1.3 79.9 - - - +
111C PRO* 1.3 80.6 - - + +
112C GLU* 3.2 3.1 + - - +
114C ILE* 3.9 30.1 - - + -
116C PRO* 4.6 9.6 - - + -
118C HIS* 2.7 39.8 + + + -
119C ILE* 3.5 35.6 + - + +
122C THR* 4.0 6.1 + - - -
124C GLY* 6.1 0.3 - - - -
126C GLU* 3.9 25.8 + - + +
127C ILE* 4.1 20.9 - - + -
128C LYS 5.8 0.7 - - - -
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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
------------------------------------------------------------
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