Contacts of the strand formed by residues 118 - 127 (chain A) in PDB entry 1I04
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 PHE 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A GLU* 3.6 32.5 - - - -
37A TRP* 3.8 3.0 - - - -
112A LYS* 3.6 35.2 - - + -
113A THR* 2.7 28.4 + - - -
114A ASP* 2.7 57.3 + - - +
115A TYR 3.9 1.0 + - - -
117A ASN* 1.3 75.8 - - - +
119A LEU* 1.3 58.0 + - - +
120A MET* 4.1 22.0 - - + -
137A LEU* 4.4 0.9 - - + -
138A TYR 3.2 7.6 - - - +
144A LEU* 3.9 20.6 - - + -
148A ILE* 4.0 24.9 - - + -
151A ARG* 3.9 12.3 - - - -
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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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33A ILE* 3.9 33.7 - - + -
37A TRP* 3.7 28.7 - - + -
60A LEU* 5.9 0.7 - - + -
63A ILE* 4.6 9.4 - - + -
110A ILE* 3.8 27.6 - - + -
112A LYS 3.6 2.5 - - - -
113A THR* 3.7 8.7 - - - +
118A PHE* 1.3 77.2 - - - +
120A MET* 1.3 74.8 + - - +
121A ALA* 4.1 8.5 - - + +
136A GLY 3.6 0.7 - - - +
137A LEU* 3.5 2.9 - - - +
138A TYR* 2.8 51.9 + - + +
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Residues in contact with MET 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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110A ILE* 3.4 13.3 - - - +
111A PRO* 3.1 26.4 - - + +
112A LYS* 2.7 29.3 + - - +
118A PHE* 4.1 15.9 - - + -
119A LEU* 1.3 78.3 - - - +
121A ALA* 1.3 60.8 + - - +
135A MET* 4.7 2.0 - - + -
136A GLY 3.2 6.7 - - - +
137A LEU* 3.7 17.5 - - + -
148A ILE* 3.9 11.2 - - + +
151A ARG* 4.1 16.6 - - + +
152A PHE* 3.6 43.5 - - + +
155A LEU* 4.0 22.2 - - - -
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Residues in contact with ALA 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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108A PHE* 4.9 13.0 - - + -
109A THR 3.5 10.5 - - - +
110A ILE* 4.9 2.2 - - + -
111A PRO* 4.1 1.1 - - - -
119A LEU* 4.1 8.9 - - + +
120A MET* 1.3 73.7 - - - +
122A HIS* 1.3 61.1 + - - +
123A LEU* 6.1 0.9 - - + -
134A LEU* 4.0 3.5 - - + +
135A MET* 3.3 8.9 - - - +
136A GLY 2.8 32.1 + - - +
138A TYR* 4.0 22.7 - - + +
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Residues in contact with HIS 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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108A PHE* 3.1 3.7 - - - -
109A THR* 3.0 45.3 + - - +
111A PRO* 3.8 11.4 - - + +
121A ALA* 1.3 74.3 - - - +
123A LEU* 1.3 64.5 + - - +
124A ILE* 3.8 30.1 - - + +
133A GLN* 2.7 33.2 + - + +
134A LEU 3.5 7.2 - - - -
135A MET* 3.5 27.6 - - + -
159A HIS* 3.4 25.6 + + + -
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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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56A PHE* 4.4 16.4 - - + -
100A VAL* 5.5 2.0 - - + -
106A ASN* 3.8 30.7 - - + +
107A THR 3.4 9.4 - - - +
108A PHE* 3.7 18.6 - - + -
121A ALA* 4.1 1.7 - - + -
122A HIS* 1.3 74.7 + - - +
124A ILE* 1.3 81.6 + - - +
125A ASN* 3.6 9.4 - - + +
132A PHE* 4.6 2.0 - - + -
133A GLN* 3.4 5.2 - - - +
134A LEU* 2.7 63.3 + - + +
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Residues in contact with ILE 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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97A GLU* 5.6 2.9 - - - +
105A PHE 3.6 1.7 - - - +
106A ASN* 3.4 3.3 - - - -
107A THR* 2.9 47.6 + - - +
122A HIS* 3.8 25.8 - - + +
123A LEU* 1.3 79.9 - - - +
125A ASN* 1.3 63.7 + - - +
126A GLU* 4.8 11.2 - - + +
131A THR* 3.8 24.9 - - + -
132A PHE 3.7 3.8 - - - +
133A GLN* 4.7 8.3 - - + +
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Residues in contact with ASN 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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49A LYS* 5.5 1.0 + - - -
56A PHE* 3.4 8.7 - - - -
102A TYR 3.6 1.2 + - - -
103A ASP 2.9 27.1 + - - +
104A GLY* 3.9 3.6 - - - -
105A PHE 3.5 2.7 - - - -
106A ASN* 2.8 27.6 + - - +
123A LEU* 3.6 2.6 - - + +
124A ILE* 1.3 73.5 - - - +
126A GLU* 1.3 73.9 + - - +
127A LYS* 3.7 7.4 + - - +
130A GLU 4.9 0.7 - - - +
131A THR* 3.3 9.5 - - - +
132A PHE* 3.0 67.4 + - + -
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Residues in contact with GLU 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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104A GLY* 3.4 1.0 - - - -
105A PHE* 2.7 68.2 + - + +
107A THR* 5.4 2.6 - - - +
124A ILE* 4.8 9.4 - - + +
125A ASN* 1.3 81.8 + - - +
127A LYS* 1.3 60.7 + - - +
128A ASP 3.8 3.9 + - - +
130A GLU 3.8 4.7 - - - +
131A THR* 3.7 18.8 - - + +
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Residues in contact with LYS 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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49A LYS* 4.8 13.2 - - - +
55A ASN* 5.0 2.0 - - - +
103A ASP* 2.7 41.0 + - - +
104A GLY* 4.4 6.1 - - - -
125A ASN* 3.7 11.1 + - - +
126A GLU* 1.3 72.8 - - - +
128A ASP* 1.3 74.0 + - + +
129A GLY 3.6 0.7 - - - -
130A GLU* 3.3 17.8 + - + +
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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