Contacts of the helix formed by residues 109 - 123 (chain B) in PDB entry 2O2C
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 ASN 109 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B TYR* 3.3 43.6 - - - +
74B HIS* 4.0 19.6 + - + +
81B ARG* 4.5 0.2 - - - +
85B TYR* 3.0 10.9 + - - -
107B HIS 4.3 0.2 - - - -
108B ILE* 1.3 73.7 - - - +
110B ASP* 1.3 64.9 + - - +
111B GLU* 3.3 9.5 + - - +
112B ILE* 3.0 31.7 + - - +
113B LYS 3.0 18.0 + - - -
7002B GOL 3.8 16.8 - - - +
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Residues in contact with ASP 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ARG* 3.0 41.4 + - - -
85B TYR* 2.8 22.5 + - - -
109B ASN* 1.3 71.4 - - - +
111B GLU* 1.3 57.3 + - + +
113B LYS* 3.5 6.5 + - - +
114B CYS* 3.0 41.0 + - - -
7002B GOL 2.9 25.3 + - - +
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Residues in contact with GLU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B GLN* 4.9 4.0 + - - -
62B LEU* 3.7 26.5 - - + +
65B GLN* 5.3 0.9 + - - -
66B TYR* 2.7 32.9 + - + -
109B ASN* 3.2 11.6 + - - +
110B ASP* 1.3 78.1 - - + +
112B ILE* 1.3 57.6 + - - +
114B CYS* 3.5 5.9 + - - +
115B ALA* 3.1 28.1 + - - +
118B ARG* 5.7 0.3 + - - -
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Residues in contact with ILE 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B LEU* 4.5 1.1 - - + -
62B LEU* 3.9 28.5 - - + +
66B TYR* 4.0 21.3 - - + +
74B HIS* 6.0 0.4 - - - +
107B HIS 3.8 12.3 - - - +
108B ILE* 4.0 11.9 - - + -
109B ASN* 3.0 31.6 + - - +
111B GLU* 1.3 72.9 - - - +
113B LYS* 1.3 60.3 + - - +
115B ALA* 3.2 2.8 + - - +
116B LEU* 2.9 36.6 + - + +
379B TRP* 3.6 50.0 - - + -
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Residues in contact with LYS 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ARG* 3.1 23.6 + - - +
85B TYR* 3.8 28.8 - - + +
103B TYR* 2.9 32.5 + - + +
108B ILE* 3.7 12.5 - - + +
109B ASN 3.0 16.2 + - - +
110B ASP* 3.7 9.1 + - - +
112B ILE* 1.3 75.8 - - - +
114B CYS* 1.3 62.8 + - - +
116B LEU* 3.3 8.4 + - - +
117B LEU* 3.1 35.0 + - + +
366B GLU* 4.7 19.2 + - - +
367B GLN* 5.9 0.2 + - - -
372B LEU* 4.7 11.2 - - + -
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Residues in contact with CYS 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ASP* 3.0 30.6 + - - +
111B GLU* 3.8 5.6 - - - +
113B LYS* 1.3 78.1 - - - +
115B ALA* 1.3 56.5 + - - +
117B LEU* 3.4 14.0 + - - +
118B ARG* 3.0 45.3 + - - +
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Residues in contact with ALA 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B SER* 4.1 5.9 - - - +
58B GLN* 4.6 11.7 - - + -
59B LEU* 3.7 18.7 - - + +
62B LEU* 3.6 19.3 - - + -
111B GLU 3.1 18.0 + - - +
112B ILE 3.2 4.7 + - - +
114B CYS* 1.3 74.7 - - - +
116B LEU* 1.3 61.1 + - - +
118B ARG* 3.3 15.5 + - - +
119B LEU* 3.0 25.6 + - - +
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Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B LEU* 3.9 24.9 - - + -
108B ILE* 4.3 13.5 - - + -
112B ILE* 2.9 33.2 + - + +
113B LYS* 3.6 9.0 - - - +
115B ALA* 1.3 75.8 - - - +
117B LEU* 1.3 62.9 + - - +
119B LEU* 3.3 16.0 + - + +
120B ALA 3.3 8.8 + - - -
375B LEU* 3.5 60.1 - - + +
376B VAL* 4.7 1.3 - - + +
378B VAL* 4.7 8.3 - - + -
379B TRP* 4.1 21.1 - - + +
383B PHE* 5.6 0.2 - - + -
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Residues in contact with LEU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B LYS* 3.1 31.4 + - + +
114B CYS* 3.7 12.6 - - - +
116B LEU* 1.3 75.2 - - - +
118B ARG* 1.3 63.3 + - - +
120B ALA* 3.3 6.4 + - - +
121B GLU* 3.2 21.1 + - - +
365B PRO* 3.7 36.7 - - + +
366B GLU* 4.1 31.9 - - + +
371B LEU* 4.1 4.0 - - + -
372B LEU* 4.4 8.5 - - + -
375B LEU* 3.8 20.9 - - + -
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Residues in contact with ARG 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B SER* 4.1 15.5 - - - +
58B GLN* 5.9 4.0 - - - +
114B CYS* 3.0 38.9 + - - +
115B ALA* 3.6 13.2 - - - +
116B LEU 3.3 0.2 - - - -
117B LEU* 1.3 74.4 - - - +
119B LEU* 1.3 59.9 + - - +
121B GLU* 3.2 20.4 + - + +
122B GLU* 2.9 34.6 + - + +
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Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B LEU* 3.9 23.8 - - + -
53B CYS* 4.7 5.2 - - + -
55B SER* 3.3 22.4 + - - +
56B TRP* 3.9 27.1 - - + +
59B LEU* 3.8 21.5 - - + -
115B ALA 3.0 12.8 + - - +
116B LEU* 3.4 13.0 - - + +
117B LEU 3.3 0.2 - - - -
118B ARG* 1.3 77.6 - - - +
120B ALA* 1.3 55.5 - - - +
122B GLU* 3.3 1.4 + - - +
123B ARG* 2.9 38.6 + - + +
375B LEU* 5.1 0.7 - - + -
378B VAL* 4.3 11.4 - - + -
556B ILE* 4.1 21.3 - - + -
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Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B LEU 3.3 8.7 + - - +
117B LEU* 3.3 11.8 + - - +
118B ARG 3.3 0.2 - - - -
119B LEU* 1.3 80.3 - - - +
121B GLU* 1.3 59.4 + - - +
123B ARG* 4.9 0.7 - - - -
124B GLY 3.3 3.6 + - - -
125B ILE* 3.1 49.2 + - + +
126B ARG 4.8 0.3 + - - -
365B PRO* 6.4 0.4 - - + -
371B LEU* 4.0 24.7 - - + -
375B LEU* 4.4 9.9 - - + -
556B ILE* 5.2 2.2 - - + -
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Residues in contact with GLU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B LEU 3.2 11.9 + - - +
118B ARG* 3.2 25.5 + - + +
120B ALA* 1.3 76.6 - - - +
122B GLU* 1.3 60.5 + - - +
124B GLY* 3.2 13.5 + - - -
125B ILE 5.3 0.2 - - - +
127B GLN* 4.9 4.1 + - - +
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Residues in contact with GLU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B CYS* 3.5 21.4 - - - +
54B ALA* 3.0 28.4 + - - +
55B SER* 2.5 41.4 + - - +
118B ARG* 2.9 18.7 + - + +
119B LEU 3.3 4.9 + - - +
121B GLU* 1.3 77.8 - - - +
123B ARG* 1.3 61.0 + - - +
124B GLY 3.2 1.0 + - - -
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Residues in contact with ARG 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ASP* 4.8 1.6 + - - -
49B THR* 3.0 41.6 + - - -
50B LEU* 4.0 13.4 - - + +
53B CYS* 3.8 18.8 - - - -
119B LEU* 2.9 34.4 + - + +
120B ALA* 3.6 2.9 + - - +
122B GLU* 1.3 77.1 - - - +
124B GLY* 1.3 63.6 + - - +
125B ILE* 3.5 16.0 + - + +
128B PHE* 5.6 0.5 - - - +
555B ALA* 3.9 8.2 + - - +
556B ILE* 2.9 36.8 + - + +
557B TRP 3.7 3.8 + - - -
558B GLY* 3.4 25.1 - - - +
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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