Contacts of the helix formed by residues 113 - 125 (chain Q) in PDB entry 1OCR
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 GLU 113 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111Q PHE 3.7 1.2 + - - -
112Q GLU* 1.3 71.9 - - - +
114Q GLU* 1.3 63.8 + - - +
116Q VAL* 3.5 11.1 + - - +
117Q ALA* 3.0 24.7 + - - +
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Residues in contact with GLU 114 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130O PRO* 5.7 3.1 - - - +
112Q GLU* 3.1 8.9 + - + +
113Q GLU* 1.3 76.6 - - - +
115Q TRP* 1.3 66.8 + - - +
117Q ALA* 2.9 16.8 + - - +
118Q LYS* 3.0 38.5 + - + +
51X LYS* 3.1 32.0 + - - +
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Residues in contact with TRP 115 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128O LEU* 3.3 31.6 - - + -
129O LYS 3.4 19.5 - - - -
130O PRO* 3.5 22.7 - - + -
131O GLY 3.7 10.0 - - - +
132O GLU 3.3 17.1 + - - -
109Q HIS* 3.2 36.8 - + - +
110Q THR* 3.5 39.6 - - + +
112Q GLU* 3.1 17.0 + - + +
114Q GLU* 1.3 80.3 - - - +
116Q VAL* 1.3 52.7 + - - +
118Q LYS* 3.1 9.0 + - - +
119Q GLN* 2.7 63.3 + - + +
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Residues in contact with VAL 116 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110Q THR 3.7 12.6 - - - +
111Q PHE* 3.4 20.4 - - + +
112Q GLU 3.1 14.9 + - - +
113Q GLU* 3.6 13.2 - - - +
115Q TRP* 1.3 74.5 - - - +
117Q ALA* 1.3 57.3 + - - +
119Q GLN* 3.8 14.9 - - - +
120Q THR* 2.4 41.0 + - - +
41X ASN* 5.2 10.3 - - - +
44X PRO* 5.8 1.6 - - + -
47X ARG* 4.3 12.8 - - - +
48X VAL* 3.9 25.4 - - + -
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Residues in contact with ALA 117 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113Q GLU 3.0 14.5 + - - +
114Q GLU* 2.9 13.3 + - - +
116Q VAL* 1.3 78.6 - - - +
118Q LYS* 1.3 61.8 + - - +
120Q THR* 3.5 4.3 + - - -
121Q LYS 3.2 13.2 + - - -
48X VAL* 3.8 15.0 - - + -
49X THR 3.8 11.2 - - - +
50X PRO* 3.6 0.9 - - - +
51X LYS* 3.1 38.1 + - + -
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Residues in contact with LYS 118 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130O PRO* 3.7 27.4 - - + -
131O GLY* 4.0 8.3 - - - +
114Q GLU* 3.0 43.9 + - + +
115Q TRP* 3.6 7.0 - - - +
117Q ALA* 1.3 73.4 - - - +
119Q GLN* 1.3 56.5 + - - +
121Q LYS* 2.9 5.4 + - - +
122Q ARG* 2.8 33.8 + - - +
51X LYS* 3.1 36.0 - - + +
52X GLU 2.7 25.9 + - - +
53X TRP* 3.8 19.0 - - + +
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Residues in contact with GLN 119 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445N ASP* 4.4 18.8 + - - +
131O GLY* 3.6 18.5 - - - +
132O GLU 3.6 3.6 - - - +
133O LEU* 3.4 36.0 - - + +
134O ARG 4.7 0.5 + - - -
110Q THR* 4.6 4.3 + - - -
115Q TRP* 2.7 45.0 + - + +
116Q VAL* 3.8 15.5 + - - +
118Q LYS* 1.3 74.3 - - - +
120Q THR* 1.3 55.1 + - - +
122Q ARG* 3.2 2.6 + - - +
123Q MET* 2.8 44.1 + - - +
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Residues in contact with THR 120 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116Q VAL* 2.4 29.0 + - - +
117Q ALA 3.6 6.3 - - - -
118Q LYS 3.2 0.2 - - - -
119Q GLN* 1.3 74.0 + - - +
121Q LYS* 1.3 61.1 + - - +
123Q MET* 3.6 11.2 - - - +
124Q LEU* 2.9 29.7 + - + +
134Q PHE* 4.2 10.8 - - + -
145Q TRP* 3.9 27.8 - - + -
44X PRO* 3.8 21.0 - - + +
48X VAL* 4.0 9.4 - - + +
50X PRO* 4.0 14.1 - - + -
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Residues in contact with LYS 121 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117Q ALA 3.2 4.7 + - - +
118Q LYS 2.9 10.0 + - - +
120Q THR* 1.3 78.0 - - - +
122Q ARG* 1.3 53.8 + - - +
124Q LEU* 2.9 8.0 + - + -
125Q ASP* 2.7 65.6 + - - +
138Q TRP* 6.1 2.2 - - - -
143Q ASN* 5.2 10.1 + - - -
50X PRO* 3.8 22.9 - - + +
51X LYS 3.2 30.3 - - - +
52X GLU* 4.1 24.0 + - - +
53X TRP* 3.9 7.6 - - + -
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Residues in contact with ARG 122 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131O GLY 3.0 35.3 + - - +
132O GLU* 3.2 16.7 + - - +
133O LEU* 3.8 7.7 - - - +
137O GLU* 2.6 36.7 + - - -
141O ARG* 3.5 20.6 - - - +
191O LEU* 3.9 8.1 - - - +
193O TYR* 3.2 15.4 + - - -
118Q LYS 2.8 12.1 + - - +
119Q GLN 3.5 4.0 - - - +
121Q LYS* 1.3 76.7 - - - +
123Q MET* 1.3 62.7 + - + +
125Q ASP* 2.9 4.7 + - - +
126Q MET* 2.9 35.8 + - - +
68V ILE* 4.9 6.9 - - + +
53X TRP* 3.6 50.7 - - + +
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Residues in contact with MET 123 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1O MET* 3.9 31.6 - - + -
3O TYR* 4.5 9.0 - - + -
4O PRO* 5.0 4.7 - - + -
131O GLY 5.9 0.2 - - - +
133O LEU* 4.7 5.6 - - + -
119Q GLN* 2.8 42.9 + - + +
120Q THR* 3.6 10.8 - - - +
122Q ARG* 1.3 79.0 - - + +
124Q LEU* 1.3 63.5 + - - +
125Q ASP 3.1 0.9 + - - -
126Q MET* 3.1 10.7 + - - +
127Q LYS 3.1 16.3 + - - -
128Q VAL* 3.1 32.9 + - + -
134Q PHE* 3.7 35.9 - - + -
135Q SER* 4.7 0.2 - - - -
44X PRO* 6.0 0.9 - - - -
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Residues in contact with LEU 124 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120Q THR* 2.9 24.3 + - + +
121Q LYS* 3.5 7.0 - - + +
123Q MET* 1.3 75.1 - - - +
125Q ASP* 1.3 64.6 + - - +
127Q LYS* 3.3 3.3 + - - +
134Q PHE* 4.1 15.0 - - + -
135Q SER* 3.9 19.3 - - - +
138Q TRP* 3.4 51.1 - - + +
140Q TYR* 2.4 40.8 + - + +
145Q TRP* 4.1 5.6 - - + -
50X PRO* 3.4 34.8 - - + -
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Residues in contact with ASP 125 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121Q LYS* 2.7 45.0 + - - +
122Q ARG* 3.2 10.8 - - - +
124Q LEU* 1.3 72.3 - - - +
126Q MET* 1.3 57.0 + - - +
127Q LYS* 3.0 19.4 + - - +
140Q TYR* 5.4 2.4 - - - -
62V GLU 5.6 0.3 - - - -
63V MET* 3.7 15.9 - - - +
66V ALA* 3.8 23.3 - - + +
68V ILE* 3.9 17.3 - - + +
52X GLU* 5.1 1.6 - - - +
53X TRP* 2.8 27.4 + - - -
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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