Contacts of the helix formed by residues 117 - 127 (chain B) in PDB entry 1ORZ
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 LEU 117 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A ARG* 5.2 6.3 - - - +
64B ARG* 2.9 34.1 - - - +
104B LEU* 5.7 2.2 - - + -
107B MET* 3.7 29.4 - - + -
115B PRO* 2.8 38.1 - - + +
116B ASP* 1.3 70.6 + - - +
118B THR* 1.3 53.8 + - - +
119B ASN* 3.2 3.8 - - - +
120B PHE* 2.6 37.0 + - + +
121B TYR* 2.9 39.1 + - + +
161B LEU 5.8 1.3 - - - +
162B CYS 5.1 3.6 - - - +
163B ALA* 4.7 10.1 - - + -
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Residues in contact with THR 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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108B PHE* 6.4 1.8 - - + -
116B ASP* 2.9 32.5 + - - +
117B LEU* 1.3 76.0 - - - +
119B ASN* 1.3 82.6 + - + +
120B PHE 3.1 0.3 + - - -
121B TYR* 3.2 11.5 + - - +
122B GLN* 3.1 43.6 + - - +
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Residues in contact with ASN 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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107B MET* 4.0 20.9 - - - +
108B PHE* 5.1 6.2 - - + +
116B ASP 3.0 24.5 + - - -
117B LEU 3.9 1.0 - - - -
118B THR* 1.3 84.9 - - + +
120B PHE* 1.3 73.5 + - - +
122B GLN* 3.5 11.1 + - - +
123B GLN* 3.3 28.6 + - - +
172B TYR* 2.6 33.5 + - - +
176B GLN* 3.8 20.9 - - - +
177B GLU* 4.2 11.4 - - - +
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Residues in contact with PHE 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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107B MET* 4.2 10.3 - - + -
117B LEU* 2.6 22.8 + - + +
119B ASN* 1.3 81.1 + - - +
121B TYR* 1.3 82.8 + + - -
122B GLN 3.3 0.2 + - - -
123B GLN* 3.3 14.2 + - + +
124B TYR* 3.3 15.6 + + + +
161B LEU* 3.7 41.7 - - + -
163B ALA* 3.8 28.7 - - + -
166B SER* 4.2 19.5 - - - -
172B TYR* 3.8 4.7 - + - -
183B ALA* 3.3 35.7 - - + -
184B VAL* 5.1 2.5 - - + -
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Residues in contact with TYR 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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57A PHE* 3.5 58.8 - + + +
60A ARG* 3.7 20.4 + - - -
168A TYR* 5.1 3.8 - + - +
180A ILE* 5.0 5.7 - - + +
64B ARG* 5.0 2.0 + - - -
117B LEU* 2.9 49.2 + - + +
118B THR* 3.2 9.9 + - - +
120B PHE* 1.3 95.6 - + - +
122B GLN* 1.3 60.8 + - + +
124B TYR* 2.8 31.5 + + + +
125B LYS* 2.9 12.1 + - + +
161B LEU* 4.6 14.4 + - + -
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Residues in contact with GLN 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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118B THR* 3.1 36.0 + - - +
119B ASN* 3.7 4.7 - - - +
120B PHE 3.2 0.2 - - - -
121B TYR* 1.3 76.6 - - + +
123B GLN* 1.3 66.2 + - - +
125B LYS* 2.7 51.4 + - - +
126B SER* 3.1 12.8 + - - +
177B GLU* 3.2 29.8 - - - +
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Residues in contact with GLN 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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119B ASN 3.3 18.8 - - - +
120B PHE* 3.3 6.7 + - + +
121B TYR 3.3 0.4 - - - -
122B GLN* 1.3 79.1 - - - +
124B TYR* 1.3 62.5 + - - +
126B SER* 3.1 22.9 + - - -
127B ILE* 3.6 0.7 + - - +
172B TYR* 3.9 7.9 - - + +
176B GLN 2.9 26.4 + - - +
177B GLU* 3.0 39.4 + - - +
179B TYR 4.0 2.8 + - - -
180B LEU* 3.3 46.2 - - - +
184B VAL* 3.0 17.9 - - + +
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Residues in contact with TYR 124 (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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165A HIS* 5.2 8.0 + - - +
168A TYR* 4.9 22.0 - + - -
169A GLY* 5.7 2.4 - - - -
172A LEU* 5.1 6.1 - - + -
120B PHE* 3.3 13.7 + + + +
121B TYR* 2.8 24.9 - + + +
123B GLN* 1.3 79.9 - - - +
125B LYS* 1.3 57.3 + - + +
127B ILE* 2.7 27.7 - - - +
129B PRO* 2.9 46.9 + - + +
161B LEU* 3.9 32.9 - - + +
183B ALA 5.2 0.4 - - - -
184B VAL* 3.5 13.9 - - + +
187B GLN* 2.9 53.1 + - + -
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Residues in contact with LYS 125 (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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172A LEU* 4.3 24.5 - - + -
121B TYR* 2.9 7.8 + - - +
122B GLN* 2.7 61.4 - - - +
124B TYR* 1.3 76.3 - - - +
126B SER* 1.3 66.1 + - - +
128B GLN* 2.8 23.2 + - - +
129B PRO* 3.5 9.8 - - + +
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Residues in contact with SER 126 (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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122B GLN 3.1 13.8 + - - -
123B GLN* 3.1 16.5 + - - -
125B LYS* 1.3 77.9 - - - +
127B ILE* 1.3 61.1 + - - +
128B GLN* 3.2 14.5 + - - +
180B LEU* 4.2 15.9 - - - +
206B MET* 4.8 8.3 - - - +
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Residues in contact with ILE 127 (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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123B GLN 3.6 0.4 + - - +
124B TYR* 2.7 25.5 + - - +
126B SER* 1.3 73.8 - - - +
128B GLN* 1.3 73.3 + - - +
129B PRO* 3.1 29.8 - - + -
180B LEU* 3.3 27.8 - - + -
184B VAL* 2.9 42.8 - - + +
187B GLN* 4.1 14.4 - - + -
188B ALA* 4.1 17.9 - - + +
191B TRP* 4.4 5.2 - - + -
203B ARG* 3.7 14.6 + - - +
206B MET* 5.9 1.2 - - - +
207B LEU* 5.3 4.3 - - + -
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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
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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