Contacts of the helix formed by residues 97 - 114 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C ASP* 4.6 1.4 + - - -
96C GLY* 1.3 71.8 - - - -
98C GLY* 1.3 61.1 + - - -
99C SER 3.2 3.6 - - - -
100C PRO* 2.9 22.0 - - - +
101C HIS* 2.8 19.6 - - - -
137C ASN* 4.4 0.4 - - - -
138C THR* 3.4 1.4 + - - -
139C THR* 3.8 14.8 - - - -
1385C NAD 3.2 28.6 + - - -
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Residues in contact with GLY 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C GLY* 1.3 71.0 - - - -
99C SER* 1.3 62.9 + - - +
101C HIS* 3.2 9.4 + - - +
102C ASP* 3.0 25.8 + - - +
139C THR* 4.4 0.2 + - - -
142C THR* 3.5 19.2 + - - -
144C SER* 3.7 6.5 + - - -
1385C NAD 3.0 34.2 + - - -
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Residues in contact with SER 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ASP* 5.0 1.6 - - - -
68C VAL* 3.1 10.4 - - - +
69C MET 2.7 28.2 + - - -
70C PRO* 4.3 2.7 - - - -
71C ASN 4.1 4.0 - - - -
72C PRO* 3.3 17.8 - - - +
98C GLY* 1.3 76.9 - - - +
100C PRO* 1.3 72.7 - - - +
102C ASP 3.2 0.2 + - - -
103C CYS* 3.0 21.1 + - - +
1385C NAD 3.2 33.9 + - - -
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Residues in contact with PRO 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C VAL* 3.8 21.7 - - - +
38C SER* 4.0 11.7 - - - -
39C ASP* 3.9 11.7 - - - +
68C VAL* 3.7 17.0 - - + -
94C SER* 3.8 2.5 - - - -
95C LEU 3.8 14.6 - - - +
96C GLY* 3.9 1.8 - - - -
97C GLY 2.9 38.4 - - - +
99C SER* 1.3 89.5 - - - +
101C HIS* 1.3 52.0 + - - +
103C CYS* 3.6 3.6 - - + +
104C ALA* 2.7 36.2 + - - +
1385C NAD 3.7 3.4 - - - +
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Residues in contact with HIS 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C SER* 2.5 36.7 + - - +
96C GLY 3.2 19.5 + - - -
97C GLY 2.8 22.2 - - - -
98C GLY* 3.2 10.3 + - - +
99C SER 3.1 0.6 - - - -
100C PRO* 1.3 77.3 - - - +
102C ASP* 1.3 57.9 + - - +
104C ALA* 3.1 3.6 + - - +
105C LYS* 2.8 35.2 + - - +
133C LEU* 5.3 0.2 - - - +
135C SER* 3.8 9.7 + - - +
136C ILE 3.0 33.7 - - - -
137C ASN* 3.2 19.1 + - - +
142C THR* 4.7 0.2 - - - -
144C SER* 3.8 17.9 - - - +
145C GLU* 4.0 18.8 - - + +
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Residues in contact with ASP 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C PRO* 3.9 4.5 - - + -
98C GLY 3.0 12.5 + - - +
99C SER 3.8 3.4 - - - +
101C HIS* 1.3 75.8 - - - +
103C CYS* 1.3 63.2 + - - +
105C LYS* 3.3 6.9 + - - -
106C ALA* 3.1 19.6 + - - +
144C SER* 2.8 22.1 + - - -
149C PHE 3.4 17.5 - - - +
150C CYS* 3.3 10.8 - - - -
151C ILE* 3.4 48.4 + - - +
152C ILE* 3.8 2.4 - - - +
1385C NAD 3.5 21.7 + - - -
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Residues in contact with CYS 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C VAL* 4.3 1.3 - - + -
65C TYR* 4.3 1.1 - - - -
68C VAL* 3.9 26.9 - - + -
72C PRO* 4.0 14.5 - - + +
76C ALA* 4.0 29.2 - - - -
77C VAL* 4.1 7.0 - - - -
99C SER 3.0 16.1 + - - +
100C PRO 3.6 3.8 - - - +
102C ASP* 1.3 75.9 - - - +
104C ALA* 1.3 63.8 + - - +
106C ALA* 3.2 4.7 + - - +
107C ILE* 3.0 44.6 + - - +
152C ILE* 4.4 5.4 - - - -
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Residues in contact with ALA 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C VAL* 4.1 11.1 - - + +
92C VAL* 3.8 22.1 - - + +
94C SER* 3.5 20.6 - - - -
100C PRO 2.7 22.6 + - - +
101C HIS 3.4 4.3 - - - +
103C CYS* 1.3 74.6 - - - +
105C LYS* 1.3 56.9 + - - +
107C ILE* 3.4 7.0 + - - +
108C ALA* 2.8 32.8 + - - +
133C LEU* 3.9 7.0 - - + -
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Residues in contact with LYS 105 (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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101C HIS* 2.8 21.1 + - - +
102C ASP* 3.5 15.9 - - - +
103C CYS 3.2 0.2 - - - -
104C ALA* 1.3 72.4 - - - +
106C ALA* 1.3 57.4 + - - +
108C ALA* 3.3 2.8 + - - +
109C LEU* 2.9 31.3 + - - +
130C ALA* 5.1 0.7 - - - +
133C LEU* 3.8 16.8 - - + -
135C SER* 5.6 0.4 - - - +
144C SER* 2.7 33.2 + - - -
147C THR* 2.8 38.8 + - - -
149C PHE 2.9 22.1 + - - +
150C CYS* 4.0 7.2 - - - -
168C VAL* 3.5 35.9 - - + +
170C PRO* 4.1 9.6 - - - -
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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
----------------------------------------------------------
77C VAL* 3.7 26.2 - - + -
102C ASP 3.1 9.7 + - - +
103C CYS 3.5 7.9 - - - +
105C LYS* 1.3 79.1 - - - +
107C ILE* 1.3 63.9 + - - +
109C LEU* 3.1 5.2 + - - +
110C VAL* 2.9 32.1 + - + +
117C VAL* 4.6 9.0 - - + -
150C CYS* 3.7 15.8 - - - -
152C ILE* 4.0 6.5 - - + -
163C ILE* 5.5 2.0 - - + -
168C VAL* 5.8 0.4 - - - -
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Residues in contact with ILE 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C LEU* 4.0 10.1 - - + -
37C VAL* 4.1 20.0 - - + -
65C TYR* 4.8 0.2 - - + -
77C VAL* 3.6 23.3 - - + +
80C GLY* 3.6 25.4 - - - -
81C LEU* 3.4 20.6 - - + +
84C LEU* 3.6 25.6 - - + -
92C VAL* 4.8 2.5 - - + -
103C CYS* 3.0 38.7 + - - +
104C ALA* 3.7 4.3 - - - +
106C ALA* 1.3 73.5 - - - +
108C ALA* 1.3 58.5 + - - +
111C ALA* 2.9 31.2 + - - +
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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
----------------------------------------------------------
92C VAL* 4.2 17.0 - - + +
104C ALA 2.8 22.4 + - - +
105C LYS* 3.6 5.2 - - - +
106C ALA 3.2 0.2 - - - -
107C ILE* 1.3 72.9 - - - +
109C LEU* 1.3 60.6 + - - +
111C ALA* 3.4 13.8 - - - +
112C THR 4.0 0.5 + - - -
130C ALA* 3.2 7.1 - - + +
131C LEU* 2.9 46.0 + - - +
133C LEU* 4.4 12.3 - - + -
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Residues in contact with LEU 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 LYS 2.9 17.7 + - - +
106C ALA* 3.6 5.8 - - - +
108C ALA* 1.3 74.1 - - - +
110C VAL* 1.3 63.9 + - + +
111C ALA 3.1 2.1 + - - -
112C THR* 3.3 2.4 + - - -
113C ASN* 2.9 59.4 + - - +
120C TYR* 3.7 41.5 - - + -
126C SER* 3.6 19.7 - - - +
128C LYS 4.3 0.2 - - - +
130C ALA* 3.5 17.5 - - + -
163C ILE* 5.9 2.0 - - + -
165C ASP* 5.4 0.4 - - + +
167C HIS* 4.1 11.4 - - + -
168C VAL* 4.2 19.5 - - + -
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Residues in contact with VAL 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C VAL* 5.0 1.8 - - + -
81C LEU* 3.7 29.2 - - + -
106C ALA* 2.9 22.7 + - - +
107C ILE 4.2 0.9 - - - +
109C LEU* 1.3 78.6 - - + +
111C ALA* 1.3 59.3 + - - +
112C THR 3.1 0.2 - - - -
114C GLY* 2.7 47.3 + - - +
115C GLY 3.6 13.2 - - - +
116C GLU* 5.2 0.4 - - - -
117C VAL* 4.3 27.4 - - + +
120C TYR* 4.3 17.3 - - + -
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Residues in contact with ALA 111 (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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81C LEU* 4.2 8.0 - - + +
84C LEU* 4.2 23.3 - - + +
107C ILE 2.9 20.7 + - - +
108C ALA* 3.4 13.7 - - - +
109C LEU 3.1 0.2 - - - -
110C VAL* 1.3 78.6 - - - +
112C THR* 1.3 59.8 + - - +
131C LEU* 4.2 13.7 - - + -
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Residues in contact with THR 112 (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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109C LEU 3.3 8.1 + - - -
111C ALA* 1.3 80.7 - - - +
113C ASN* 1.3 68.7 + - - +
114C GLY 3.5 1.6 - - - -
128C LYS* 4.2 14.1 + - - +
129C PRO 2.9 23.8 + - - +
130C ALA* 3.4 5.2 - - - -
131C LEU* 3.6 39.5 - - + +
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Residues in contact with ASN 113 (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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109C LEU* 2.9 51.0 + - - +
112C THR* 1.3 81.7 + - - +
114C GLY* 1.3 64.9 + - - +
115C GLY* 3.6 0.9 + - - -
120C TYR* 2.9 30.4 + - + +
126C SER* 3.6 8.4 - - - -
127C LYS* 3.6 4.6 + - - +
128C LYS* 2.9 46.2 + - - +
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Residues in contact with GLY 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C VAL* 2.7 36.5 + - - +
111C ALA 4.6 0.2 - - - -
112C THR 3.5 1.8 - - - -
113C ASN* 1.3 73.8 - - - +
115C GLY* 1.3 68.9 + - - +
120C TYR* 2.9 17.3 + - - -
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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
------------------------------------------------------------
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