Contacts of the helix formed by residues 119 - 134 (chain A) in PDB entry 4OWW
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 MET 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A TYR* 3.8 22.7 - - + +
111A LEU* 4.0 26.2 - - + -
112A ALA* 3.6 35.0 - - + -
115A SER* 2.9 29.6 + - - +
117A ASP* 3.2 1.8 - - - -
118A GLY* 1.3 79.6 - - - +
120A ASN* 1.3 63.1 + - - +
121A ILE* 3.3 3.6 - - - -
122A VAL* 3.0 14.9 + - + +
123A LEU* 3.0 32.7 + - + +
152A LEU* 3.8 18.8 - - - -
155A SER* 5.5 1.8 - - - -
157A VAL* 4.4 12.8 - - + -
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Residues in contact with ASN 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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117A ASP* 3.2 27.3 + - + +
118A GLY 3.1 4.2 - - - +
119A MET* 1.3 76.1 - - - +
121A ILE* 1.3 58.6 + - - +
123A LEU* 3.4 7.9 + - - +
124A ASN* 3.1 49.7 + - - +
158A LEU* 5.3 17.6 + - - +
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Residues in contact with ILE 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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86A HIS* 4.8 7.0 - - + +
87A GLU* 4.2 30.1 - - + +
90A CYS* 3.4 34.8 - - + -
91A LEU* 3.5 25.2 - - + +
117A ASP* 3.1 24.6 + - - +
120A ASN* 1.3 78.1 - - - +
122A VAL* 1.3 69.0 + - + +
124A ASN* 3.8 10.8 - - - +
125A LYS* 3.2 22.5 + - - +
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Residues in contact with VAL 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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90A CYS* 4.0 10.5 - - + +
91A LEU* 4.9 2.0 - - + -
94A PHE* 3.8 29.8 - - + -
111A LEU* 3.9 38.6 - - + -
119A MET* 3.0 19.4 + - + +
121A ILE* 1.3 92.0 - - + +
123A LEU* 1.3 63.6 + - + +
125A LYS* 3.3 7.0 + - - +
126A ILE* 2.9 36.5 + - + +
148A LEU* 4.8 3.8 - - + -
152A LEU* 5.5 2.0 - - + -
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Residues in contact with LEU 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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119A MET* 3.0 23.9 + - + +
120A ASN* 3.4 6.9 + - - +
121A ILE 3.4 0.2 - - - -
122A VAL* 1.3 76.7 - - + +
124A ASN* 1.3 66.5 + - - +
126A ILE* 3.3 7.1 + - + +
127A ASN* 3.0 30.6 + - - +
152A LEU* 3.9 27.1 - - + -
157A VAL* 3.9 20.6 - - + -
158A LEU 3.4 25.8 - - - +
159A GLY* 3.5 24.5 - - - +
160A ALA* 3.7 6.5 - - + +
163A VAL* 3.7 16.3 - - + +
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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
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120A ASN* 3.1 39.9 + - - +
121A ILE* 3.8 12.6 - - - +
122A VAL 3.3 0.2 - - - -
123A LEU* 1.3 76.9 - - - +
125A LYS* 1.3 59.2 + - - +
127A ASN* 3.3 11.2 + - - +
128A GLN* 2.9 27.3 + - - +
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Residues in contact with LYS 125 (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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48A LEU* 4.3 12.8 - - + +
51A ARG* 3.5 23.2 - - - +
52A LEU* 3.9 27.1 - - + -
87A GLU* 5.4 0.2 + - - -
91A LEU* 4.0 17.3 - - + +
94A PHE* 4.0 23.1 - - + -
121A ILE 3.2 14.2 + - - +
122A VAL 3.7 4.3 - - - +
123A LEU 3.3 0.2 - - - -
124A ASN* 1.3 76.9 - - - +
126A ILE* 1.3 60.7 + - - +
128A GLN* 3.2 31.4 + - - +
129A ILE* 2.9 35.5 + - + +
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Residues in contact with ILE 126 (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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94A PHE* 3.6 22.2 - - + -
122A VAL* 2.9 24.5 + - + +
123A LEU* 3.5 13.7 - - + +
124A ASN 3.3 0.2 - - - -
125A LYS* 1.3 76.5 - - - +
127A ASN* 1.3 57.6 + - - +
129A ILE* 3.3 5.3 + - - +
130A LEU* 2.9 40.0 + - + +
145A LEU* 4.1 16.8 - - + +
148A LEU* 3.8 17.7 - - + -
149A VAL* 4.8 2.2 - - + -
152A LEU* 3.6 31.0 - - + -
163A VAL* 3.6 26.0 - - + -
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Residues in contact with ASN 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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123A LEU* 3.0 21.2 + - - +
124A ASN* 3.6 12.1 + - - +
126A ILE* 1.3 75.7 - - - +
128A GLN* 1.3 58.0 + - - +
130A LEU* 3.4 1.0 + - - +
131A MET* 2.9 39.2 + - + +
159A GLY 5.5 0.6 + - - -
162A GLY* 4.9 2.2 - - - -
163A VAL* 3.5 27.8 - - - +
166A THR* 2.9 34.6 + - + +
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Residues in contact with GLN 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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48A LEU* 3.3 29.5 - - + +
124A ASN 2.9 16.1 + - - +
125A LYS* 3.2 29.0 + - - +
126A ILE 3.2 0.2 - - - -
127A ASN* 1.3 77.0 - - - +
129A ILE* 1.3 58.3 + - - +
131A MET* 3.3 3.9 + - - +
132A GLU* 2.8 63.8 + - + +
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Residues in contact with ILE 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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36A LEU* 5.1 4.9 - - + -
48A LEU* 4.1 22.0 - - + -
52A LEU* 4.1 13.7 - - + -
94A PHE* 3.7 36.3 - - + -
98A LEU* 4.1 10.8 - - + -
125A LYS* 2.9 16.4 + - + +
126A ILE* 3.3 4.7 + - - +
128A GLN* 1.3 75.8 - - - +
130A LEU* 1.3 59.3 + - - +
133A LYS* 2.8 38.5 + - + -
134A TYR 3.2 8.0 + - - -
137A LEU* 4.0 33.4 - - + -
145A LEU* 4.4 9.9 - - + -
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Residues in contact with LEU 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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126A ILE* 2.9 34.5 + - + +
129A ILE* 1.3 77.4 - - + +
131A MET* 1.3 61.3 + - - +
132A GLU 3.5 0.2 + - - -
134A TYR* 3.5 26.0 + - + +
145A LEU* 3.6 26.5 - - + -
163A VAL* 4.0 4.7 - - + +
166A THR* 3.6 21.1 - - + -
167A PHE* 3.6 57.0 - - + +
170A GLN* 3.1 29.4 - - + +
307A PRO* 4.4 0.2 - - - +
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Residues in contact with MET 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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127A ASN* 2.9 23.1 + - + +
128A GLN* 4.0 3.8 - - - +
130A LEU* 1.3 77.4 - - - +
132A GLU* 1.3 65.5 + - + +
166A THR* 3.6 24.2 - - + -
169A LYS* 3.9 29.8 - - - -
170A GLN* 3.9 11.4 - - - -
307A PRO* 3.3 36.0 - - + +
310A GLU* 5.6 0.2 - - - +
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Residues in contact with GLU 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 GLN* 2.8 50.2 + - + +
131A MET* 1.3 87.8 - - + +
133A LYS* 1.3 84.3 + - + +
134A TYR 3.8 1.3 - - - -
136A LYS* 5.3 2.9 - - - -
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Residues in contact with LYS 133 (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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37A LEU* 4.0 20.4 - - + -
46A ASP* 2.5 44.0 + - - +
48A LEU* 4.1 26.3 - - + +
128A GLN 4.6 0.2 - - - +
129A ILE* 2.8 34.0 + - + +
132A GLU* 1.3 102.3 + - + +
134A TYR* 1.3 63.2 + - - +
135A LEU 3.3 2.7 - - - -
136A LYS* 2.9 27.0 + - - +
137A LEU* 3.0 11.7 + - - +
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Residues in contact with TYR 134 (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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129A ILE 3.2 5.2 + - - +
130A LEU* 3.5 38.2 + - + +
132A GLU 3.8 1.2 - - - -
133A LYS* 1.3 75.5 - - - +
135A LEU* 1.3 69.7 + - + +
137A LEU* 3.1 26.4 + - + +
142A ARG* 2.9 68.1 + - + +
167A PHE* 4.2 17.9 - + - -
170A GLN* 3.9 25.6 - - + +
179A LYS 5.1 1.2 + - - -
182A TRP* 4.0 4.9 - - - -
183A LEU* 3.4 39.6 - - + +
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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