Contacts of the helix formed by residues 119 - 132 (chain A) in PDB entry 1ORN
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 GLY 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A MET* 3.9 9.9 - - - -
118A VAL* 1.3 75.6 - - - +
120A ARG* 1.3 65.7 + - - -
122A THR 3.4 0.3 + - - -
123A ALA* 3.0 22.9 + - - +
20C T 2.9 38.0 + - - -
21C C 4.4 3.6 - - - -
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Residues in contact with ARG 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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109A ARG* 3.7 32.5 - - - +
113A MET* 3.8 29.8 - - + +
119A GLY* 1.3 71.9 - - - +
121A LYS* 1.3 64.0 + - - +
123A ALA* 3.9 0.7 - - - +
124A ASN* 2.9 30.4 + - - +
159A LEU* 3.8 33.1 - - - +
162A GLU* 2.8 42.6 + - - +
163A LYS* 5.6 0.2 - - - +
166A MET* 4.1 13.5 - - - +
20C T 3.8 3.4 + - - +
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Residues in contact with LYS 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 6.2 0.4 - - - +
37A VAL* 4.1 17.6 + - - +
40A SER* 3.9 2.2 + - - -
41A ALA* 5.7 0.2 - - - +
119A GLY 3.3 0.6 - - - -
120A ARG* 1.3 78.2 - - - +
122A THR* 1.3 69.0 + - - +
124A ASN* 3.3 0.8 + - - +
125A VAL* 3.1 40.1 + - - +
137A ALA* 3.7 16.7 - - + +
138A VAL 3.8 30.5 - - - +
139A ASP* 4.1 6.1 - - - -
178A HIS* 6.4 0.4 - - - -
18C PED 1.5 77.5 - - + +
19C G 3.9 19.1 - - - +
20C T 3.5 16.0 + - - +
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Residues in contact with THR 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 4.5 7.6 - - + -
37A VAL* 3.6 34.7 + - + +
38A VAL* 4.1 23.8 - - + +
41A ALA* 5.6 2.3 - - - +
117A GLY 4.3 2.1 + - - -
118A VAL* 3.7 23.3 - - + -
119A GLY 4.0 1.1 - - - -
121A LYS* 1.3 78.1 + - - +
123A ALA* 1.3 65.0 + - - +
125A VAL* 3.3 3.3 + - - +
126A VAL* 3.1 23.0 + - - +
19C G 3.8 4.5 + - - -
20C T 2.7 27.9 + - - -
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Residues in contact with ALA 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ARG* 3.5 39.7 - - + +
112A LEU* 3.9 16.6 - - + -
113A MET* 3.7 6.7 - - + -
118A VAL* 3.7 6.3 - - + +
119A GLY 3.0 17.4 + - - +
120A ARG 3.9 0.7 - - - +
122A THR* 1.3 78.0 - - - +
124A ASN* 1.3 61.9 + - - +
126A VAL* 3.3 2.6 + - - +
127A VAL* 3.0 28.6 + - - +
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Residues in contact with ASN 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ARG* 2.9 32.6 + - - +
120A ARG* 2.9 24.4 + - - +
121A LYS* 3.7 4.5 - - - +
123A ALA* 1.3 74.1 - - - +
125A VAL* 1.3 64.8 + - - +
127A VAL* 3.4 6.2 - - - +
128A SER* 3.1 27.4 + - - -
135A ALA* 3.8 17.8 - - + +
136A ILE 3.1 15.0 + - - +
137A ALA* 3.8 16.2 - - + +
162A GLU* 3.1 32.1 + - - -
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Residues in contact with VAL 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A CYS* 5.0 7.4 - - - -
25A LEU* 5.6 0.7 - - + -
33A LEU* 4.8 3.4 - - + -
37A VAL* 3.7 28.7 - - + -
121A LYS* 3.1 31.5 + - - +
122A THR 3.3 6.7 + - - +
124A ASN* 1.3 76.1 - - - +
126A VAL* 1.3 59.6 + - - +
128A SER* 4.6 2.5 - - - -
129A VAL* 2.8 46.8 + - + +
137A ALA* 3.5 18.8 - - + -
178A HIS* 4.5 11.7 - - + +
179A HIS* 6.1 0.4 - - - +
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Residues in contact with VAL 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PRO 5.0 4.3 - - - +
33A LEU* 4.0 9.9 - - + -
34A LEU* 3.9 35.9 - - + +
37A VAL* 4.5 13.5 - - + -
105A VAL* 4.3 13.0 - - + -
112A LEU* 3.9 20.0 - - + -
122A THR* 3.1 17.3 + - + +
123A ALA* 3.7 4.7 - - - +
124A ASN 3.3 0.2 - - - -
125A VAL* 1.3 77.5 - - - +
127A VAL* 1.3 58.8 + - - +
130A ALA* 2.9 40.5 + - + +
131A PHE* 4.0 15.4 - - + -
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Residues in contact with VAL 127 (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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107A ARG 3.6 18.4 - - - +
109A ARG* 3.8 22.0 - - + +
112A LEU* 3.5 21.1 - - + -
123A ALA 3.0 16.0 + - - +
124A ASN* 3.4 16.8 - - - +
126A VAL* 1.3 74.2 - - - +
128A SER* 1.3 60.7 + - - +
131A PHE* 3.2 15.6 + - + +
132A GLY 3.2 9.5 + - - -
133A VAL* 2.9 41.3 + - + -
135A ALA* 4.0 14.4 - - + -
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Residues in contact with SER 128 (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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124A ASN 3.1 20.1 + - - -
125A VAL* 3.7 4.3 - - - -
127A VAL* 1.3 76.9 - - - +
129A VAL* 1.3 67.2 + - - +
132A GLY* 3.1 23.7 + - - -
133A VAL 3.1 16.2 - - - -
135A ALA* 4.2 9.9 + - - -
175A SER* 2.7 33.2 + - - -
178A HIS* 5.6 4.6 - - - -
179A HIS* 4.9 3.1 - - - -
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Residues in contact with VAL 129 (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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23A CYS* 4.2 16.2 - - + -
27A HIS* 4.1 22.1 + - + +
33A LEU* 3.8 16.6 - - + -
125A VAL* 2.8 32.8 + - + +
128A SER* 1.3 78.2 - - - +
130A ALA* 1.3 61.4 + - - +
132A GLY* 4.4 1.4 + - - -
178A HIS* 6.1 0.7 - - + -
179A HIS* 3.9 30.7 - - + +
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Residues in contact with ALA 130 (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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27A HIS* 5.8 2.7 - - + +
30A PRO* 4.1 25.7 - - + +
33A LEU* 3.7 15.9 - - + -
126A VAL* 2.9 25.3 + - + +
129A VAL* 1.3 77.3 - - - +
131A PHE* 1.3 76.4 + - + +
132A GLY 3.6 0.4 - - - -
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Residues in contact with PHE 131 (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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30A PRO* 3.9 35.2 - - + -
105A VAL* 3.9 20.6 - - + -
106A PRO 3.6 19.1 - - - -
107A ARG* 3.5 62.6 - - + +
126A VAL* 4.0 7.2 - - + -
127A VAL* 3.2 25.3 + - + +
130A ALA* 1.3 86.3 - - + +
132A GLY* 1.3 64.6 + - - +
133A VAL* 3.1 15.5 + - + +
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Residues in contact with GLY 132 (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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128A SER 3.1 18.1 + - - -
129A VAL 4.4 1.4 + - - -
130A ALA 3.6 2.0 - - - -
131A PHE* 1.3 75.7 - - - +
133A VAL* 1.3 62.2 + - - +
134A PRO* 3.5 7.8 - - - +
175A SER* 5.3 2.2 + - - -
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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