Contacts of the helix formed by residues 117 - 122 (chain B) 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 TRP 117 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B TYR* 3.7 29.2 - + + -
115B ASP* 3.0 17.4 + - - +
116B PRO* 1.3 76.4 - - - +
118B HIS* 1.3 61.7 + - - +
119B ILE 3.1 0.2 - - - -
120B LEU* 2.9 46.8 + - + -
121B GLN* 3.2 33.6 + - + +
152B ILE* 3.8 27.1 - - + -
153B SER 4.1 4.0 - - - -
154B ARG* 3.4 69.0 - - + +
159B ASP* 3.8 16.6 + - + -
161B GLN* 3.5 25.1 + - + -
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Residues in contact with HIS 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLY 5.7 1.6 - - - -
66A GLU* 2.9 18.4 + - - -
70A ALA* 4.5 0.2 - - - +
72A GLU* 4.1 8.1 - - + +
73A THR* 2.7 46.8 + - - -
76A ASN* 5.4 1.1 - - - +
110B TYR* 2.6 31.7 + + + -
114B ILE* 3.7 17.0 - - + -
115B ASP* 2.9 17.6 + - - +
117B TRP* 1.3 77.5 - - - +
119B ILE* 1.3 54.5 + - - +
121B GLN* 3.1 17.0 + - - +
122B THR* 2.7 56.4 + - + +
126B GLU* 4.0 9.4 - - + -
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Residues in contact with ILE 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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103B PHE* 4.1 9.9 - - + -
106B ALA* 4.0 23.3 - - + -
107B ALA* 4.0 15.5 - - - +
110B TYR* 3.4 38.1 - - + -
116B PRO* 3.0 19.2 + - + +
118B HIS* 1.3 77.6 + - - +
120B LEU* 1.3 62.0 + - + +
122B THR* 3.5 4.7 + - - -
123B GLY* 3.0 8.1 + - - -
124B GLY* 2.9 28.2 + - - +
127B ILE* 4.0 8.7 - - + -
163B PHE* 3.5 41.8 - - + +
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Residues in contact with LEU 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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103B PHE* 3.7 32.1 - - + -
117B TRP* 2.9 56.2 + - + +
119B ILE* 1.3 79.8 - - + +
121B GLN* 1.3 62.0 + - - +
122B THR 3.3 0.4 + - - -
123B GLY 3.8 4.9 + - - -
152B ILE* 4.0 10.8 - - + -
161B GLN* 3.3 44.1 + - + +
162B ALA 3.8 17.1 - - - +
163B PHE* 3.6 25.4 - - + -
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Residues in contact with GLN 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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72A GLU* 3.5 37.9 + - + +
155A LYS* 3.7 24.6 - - - +
156A THR* 3.8 24.2 + - + +
117B TRP* 3.2 31.0 + - + +
118B HIS* 3.1 27.7 + - - +
120B LEU* 1.3 77.2 - - - +
122B THR* 1.3 59.8 + - + +
123B GLY 3.6 0.2 - - - -
154B ARG* 5.1 3.6 + - - -
161B GLN* 4.3 8.6 + - - +
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Residues in contact with THR 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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66A GLU* 3.9 8.1 - - - +
70A ALA* 4.7 1.3 - - + -
72A GLU* 5.3 1.1 - - + -
155A LYS* 4.1 25.1 - - + +
110B TYR* 4.2 2.1 + - - -
118B HIS* 2.7 55.8 + - + +
119B ILE* 3.6 5.5 + - - -
121B GLN* 1.3 82.6 - - + +
123B GLY* 1.3 62.7 + - - +
124B GLY* 3.2 4.7 + - - -
125B LYS* 3.5 19.2 + - - +
126B GLU* 4.5 9.5 - - - +
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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