Contacts of the helix formed by residues 109 - 123 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A TYR* 3.5 39.8 - - - +
69A GLU* 4.6 1.2 + - - -
74A HIS* 4.1 15.9 + - + -
85A TYR* 3.0 11.3 + - - -
107A HIS 4.3 0.2 - - - -
108A ILE* 1.3 72.1 - - - +
110A ASP* 1.3 59.5 + - - +
111A GLU* 3.3 15.2 + - - +
112A ILE* 3.0 32.8 + - - +
113A LYS 3.0 22.9 + - - -
7001A GOL 3.6 23.8 - - - +
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Residues in contact with ASP 110 (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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84A ARG* 2.8 41.5 + - - -
85A TYR* 2.7 29.5 + - - -
109A ASN* 1.3 74.3 - - - +
111A GLU* 1.3 59.0 + - + +
113A LYS* 3.5 7.9 + - - +
114A CYS* 3.0 31.1 + - - +
7001A GOL 3.1 16.9 + - - +
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Residues in contact with GLU 111 (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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62A LEU* 3.6 19.8 - - + +
66A TYR* 2.7 36.2 + - + -
109A ASN* 3.3 16.3 + - - +
110A ASP* 1.3 77.8 - - + +
112A ILE* 1.3 57.4 + - - +
114A CYS* 3.8 5.4 - - - +
115A ALA* 3.1 27.9 + - - +
118A ARG* 4.8 1.9 + - - -
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Residues in contact with ILE 112 (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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59A LEU* 4.6 1.1 - - + -
62A LEU* 4.1 20.4 - - + +
66A TYR* 4.0 22.4 - - + -
74A HIS* 5.9 0.9 - - - +
107A HIS 3.7 13.0 - - - +
108A ILE* 3.9 12.6 - - + -
109A ASN* 3.0 35.6 + - - +
111A GLU* 1.3 74.4 - - - +
113A LYS* 1.3 59.3 + - - +
115A ALA* 3.2 2.3 + - - +
116A LEU* 2.9 37.2 + - + +
379A TRP* 3.6 55.4 - - + -
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Residues in contact with LYS 113 (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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84A ARG* 3.3 20.4 + - - +
85A TYR* 3.9 23.5 - - + +
103A TYR* 2.9 31.8 + - + +
108A ILE* 3.7 13.4 - - + +
109A ASN 3.0 16.6 + - - +
110A ASP* 3.7 8.7 + - - +
112A ILE* 1.3 75.1 - - - +
114A CYS* 1.3 63.1 + - - +
116A LEU* 3.3 8.6 + - + +
117A LEU* 3.1 37.1 + - + +
366A GLU* 4.5 23.0 + - - +
367A GLN* 5.7 1.4 + - - -
372A LEU* 4.7 9.0 - - + -
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Residues in contact with CYS 114 (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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110A ASP 3.0 19.5 + - - +
111A GLU* 3.8 6.5 - - - +
113A LYS* 1.3 76.9 - - - +
115A ALA* 1.3 56.3 + - - +
117A LEU* 3.3 12.3 + - - +
118A ARG* 3.0 54.3 + - - +
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Residues in contact with ALA 115 (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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55A SER* 4.4 4.3 - - - +
58A GLN* 4.7 1.1 - - + -
59A LEU* 3.7 17.7 - - + +
62A LEU* 3.5 22.0 - - + -
111A GLU 3.1 19.2 + - - +
112A ILE 3.2 3.8 + - - +
114A CYS* 1.3 74.0 - - - +
116A LEU* 1.3 59.8 + - - +
118A ARG* 3.4 29.4 + - - +
119A LEU* 3.1 25.1 + - - +
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Residues in contact with LEU 116 (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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59A LEU* 3.9 24.9 - - + -
108A ILE* 4.3 14.6 - - + -
112A ILE* 2.9 34.7 + - + +
113A LYS* 3.6 9.0 - - - +
115A ALA* 1.3 75.0 - - - +
117A LEU* 1.3 62.4 + - - +
119A LEU* 3.2 16.5 + - + +
120A ALA 3.2 9.2 + - - -
375A LEU* 3.4 60.8 - - + +
376A VAL* 4.8 1.1 - - + +
378A VAL* 4.9 6.3 - - + -
379A TRP* 4.1 21.1 - - + +
383A PHE* 5.6 0.2 - - + -
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Residues in contact with LEU 117 (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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113A LYS* 3.1 34.4 + - + +
114A CYS* 3.3 11.2 + - - +
116A LEU* 1.3 77.4 - - + +
118A ARG* 1.3 61.9 + - - +
120A ALA* 3.3 5.9 + - + +
121A GLU* 3.2 26.8 + - - +
365A PRO* 3.7 38.9 - - + +
366A GLU* 4.1 26.2 - - + +
371A LEU* 4.1 4.9 - - + -
372A LEU* 4.5 7.4 - - + -
375A LEU* 3.9 19.5 - - + -
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Residues in contact with ARG 118 (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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54A ALA 5.7 0.2 - - - -
55A SER* 4.1 15.7 - - - +
58A GLN* 3.2 37.6 - - - +
62A LEU* 5.9 0.2 - - - +
111A GLU 4.8 1.6 + - - -
114A CYS* 3.0 37.8 + - - +
115A ALA* 3.6 32.8 - - - +
116A LEU 3.3 0.2 - - - -
117A LEU* 1.3 75.0 - - + +
119A LEU* 1.3 59.7 + - - +
121A GLU* 3.3 15.5 + - - +
122A GLU* 2.9 30.7 + - - +
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Residues in contact with LEU 119 (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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50A LEU* 4.2 5.6 - - + -
53A CYS* 4.9 2.0 - - + -
55A SER* 3.5 24.4 - - - +
56A TRP* 3.8 38.6 - - + +
59A LEU* 3.8 20.0 - - + -
115A ALA 3.1 13.2 + - - +
116A LEU* 3.2 9.6 + - + +
118A ARG* 1.3 75.6 - - - +
120A ALA* 1.3 57.9 + - - +
122A GLU* 3.3 1.0 + - - +
123A ARG* 3.0 46.0 + - + +
375A LEU* 4.6 10.8 - - + -
378A VAL* 4.3 10.1 - - + -
556A ILE* 4.0 17.9 - - + -
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Residues in contact with ALA 120 (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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116A LEU 3.2 8.7 + - - +
117A LEU* 3.4 13.0 - - - +
118A ARG 3.3 0.2 - - - -
119A LEU* 1.3 80.9 - - - +
121A GLU* 1.3 59.3 + - + +
123A ARG* 5.0 0.2 - - - -
124A GLY 3.4 3.1 + - - -
125A ILE* 3.1 43.0 + - + +
126A ARG 4.9 0.3 + - - -
365A PRO* 6.4 0.4 - - + -
371A LEU* 4.0 30.5 - - + -
375A LEU* 4.4 9.8 - - + +
556A ILE* 5.4 2.0 - - - -
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Residues in contact with GLU 121 (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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117A LEU* 3.2 15.7 + - - +
118A ARG* 3.6 17.6 - - - +
119A LEU 3.3 0.2 - - - -
120A ALA* 1.3 78.3 - - + +
122A GLU* 1.3 61.2 + - - +
124A GLY* 3.2 14.3 + - - -
126A ARG* 4.8 21.6 + - - +
127A GLN* 5.0 3.8 + - - +
365A PRO* 5.3 12.0 - - + +
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Residues in contact with GLU 122 (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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53A CYS* 3.3 22.5 - - - +
54A ALA* 3.1 26.0 + - - +
55A SER* 2.7 42.5 + - - +
118A ARG* 2.9 15.2 + - - +
119A LEU 3.8 3.8 - - - +
121A GLU* 1.3 77.6 - - - +
123A ARG* 1.3 59.7 + - + +
124A GLY 3.2 1.1 + - - -
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Residues in contact with ARG 123 (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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47A ASP* 5.1 1.0 + - - -
49A THR* 3.3 42.0 + - - -
50A LEU* 3.9 13.5 - - + +
53A CYS* 3.8 19.9 - - - -
119A LEU* 3.0 36.8 + - + +
120A ALA 4.3 2.2 - - - +
122A GLU* 1.3 77.4 - - - +
124A GLY* 1.3 61.7 + - - +
125A ILE* 3.5 16.1 - - + +
128A PHE* 5.6 1.4 - - - +
419A ARG* 5.8 0.2 - - - +
555A ALA* 3.8 8.6 + - - +
556A ILE* 2.9 36.9 + - + +
557A TRP 3.9 2.8 + - - -
558A GLY* 3.6 23.8 - - - +
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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