Contacts of the strand formed by residues 113 - 122 (chain A) in PDB entry 1N1M
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 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A ILE* 3.5 7.3 - - - +
108A SER* 3.1 27.6 + - - +
111A GLY 3.6 0.4 - - - -
112A GLN* 1.3 97.8 - - + +
114A ILE* 1.3 68.6 + - - +
134A ILE* 4.0 11.2 - - + -
135A TYR 3.4 3.1 - - - -
136A ASP* 3.4 43.1 - - + -
137A LEU* 4.7 0.4 - - - +
138A ASN* 4.7 4.5 - - - -
143A ILE* 4.2 2.2 - - + -
157A TRP* 3.5 20.6 - + + -
162A HIS* 3.5 39.9 - + + -
177A GLU* 5.0 3.4 - - - -
178A PRO* 3.4 38.4 - - + -
179A ASN* 5.9 1.3 - - - -
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Residues in contact with ILE 114 (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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76A ILE* 6.2 0.7 - - + -
89A PHE* 4.7 4.5 - - + -
90A LEU* 4.3 24.5 - - + -
95A PHE* 4.8 6.3 - - + -
105A TYR* 4.2 17.5 - - + -
106A SER 3.8 3.1 - - - +
107A ILE* 4.3 17.0 - - + +
113A PHE* 1.3 82.6 - - - +
115A LEU* 1.3 68.7 + - - +
116A LEU* 3.5 22.7 + - + +
133A ASP 3.5 0.2 - - - +
134A ILE* 3.4 4.4 - - - -
135A TYR* 3.0 45.4 + - + +
137A LEU* 4.0 32.8 - - + -
157A TRP* 4.5 2.0 - - - -
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Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ASP 3.5 1.9 - - - +
105A TYR* 3.4 7.3 - - - -
106A SER* 2.8 56.1 + - - +
114A ILE* 1.3 71.5 - - - +
116A LEU* 1.3 59.9 + - - +
117A GLU* 5.5 2.0 - - + +
132A TYR* 3.7 32.3 - - + -
133A ASP 3.6 9.0 - - - +
134A ILE* 3.9 9.4 - - + +
148A ILE* 3.8 28.0 - - + -
155A VAL* 3.3 33.4 - - + +
157A TRP* 4.0 18.2 - - + +
164A LEU* 5.2 1.8 - - + -
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Residues in contact with LEU 116 (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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95A PHE* 3.6 36.3 - - + -
98A PHE* 4.3 13.5 - - + -
102A ILE* 4.0 16.6 - - + -
104A ASP 3.8 0.7 - - - -
105A TYR* 3.4 35.7 - - + -
114A ILE* 3.6 21.1 - - + +
115A LEU* 1.3 73.8 - - - +
117A GLU* 1.3 60.8 + - - +
118A TYR* 3.9 3.7 - - + -
131A SER 3.7 0.5 - - - +
132A TYR* 3.2 11.0 - - - +
133A ASP* 2.7 42.2 + - + +
135A TYR* 4.7 1.6 - - + -
142A LEU* 4.1 16.8 - - + -
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Residues in contact with GLU 117 (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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102A ILE* 3.4 6.3 - - - +
103A ASN* 3.0 45.6 + - - +
104A ASP* 2.9 43.6 + - + +
115A LEU* 5.3 2.5 - - + +
116A LEU* 1.3 72.1 - - - +
118A TYR* 1.3 62.4 + - - +
120A TYR* 4.2 1.2 - - - -
128A TYR* 2.8 41.7 + - - -
130A ALA* 4.0 12.1 - - + -
131A SER 3.8 2.0 - - - -
132A TYR* 3.5 27.5 - - + -
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Residues in contact with TYR 118 (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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98A PHE* 3.9 13.0 - + + -
100A HIS* 3.4 44.1 + + + -
101A SER 3.3 22.7 - - - +
102A ILE* 4.5 2.0 - - + -
103A ASN* 4.0 3.8 - - - -
116A LEU* 3.9 8.7 - - + -
117A GLU* 1.3 74.4 - - - +
119A ASN* 1.3 97.3 + - - +
120A TYR* 3.2 2.5 - - - -
130A ALA* 3.4 2.5 - - - +
131A SER* 2.7 62.5 + - - +
132A TYR 3.9 5.5 + - - -
133A ASP* 2.9 37.3 + - - -
147A ARG* 5.8 1.6 - - - -
150A ASN* 4.3 5.6 + - - -
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Residues in contact with ASN 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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100A HIS* 4.6 11.8 + - - -
101A SER 4.6 2.4 + - - -
118A TYR* 1.3 105.0 - - - +
120A TYR* 1.3 59.5 + - - +
121A VAL* 3.2 18.8 + - + +
129A THR 3.5 0.7 - - - +
130A ALA* 3.5 10.8 - - - -
131A SER* 2.8 27.5 + - - +
150A ASN* 4.6 2.4 + - - +
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Residues in contact with TYR 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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103A ASN* 3.5 39.7 - - - +
117A GLU* 4.2 1.6 - - - -
118A TYR 3.2 0.6 - - - -
119A ASN* 1.3 73.0 - - - +
121A VAL* 1.3 61.1 + - - +
122A LYS* 3.5 35.6 + - + +
127A SER 5.1 0.3 + - - -
128A TYR* 3.3 52.4 - + + +
129A THR 3.9 2.9 - - - -
130A ALA* 4.3 3.6 - - + -
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Residues in contact with VAL 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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119A ASN* 3.8 10.3 - - + +
120A TYR* 1.3 74.8 - - - +
122A LYS* 1.3 71.1 + - - +
123A GLN* 4.8 0.5 - - - +
128A TYR* 3.6 1.5 - - - -
129A THR* 3.0 45.7 + - - +
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Residues in contact with LYS 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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120A TYR* 3.5 30.1 + - + +
121A VAL* 1.3 86.0 - - - +
123A GLN* 1.3 93.5 + - - +
124A TRP* 3.0 21.2 + - - +
125A ARG* 5.0 2.9 - - - +
127A SER 4.5 1.6 - - - +
128A TYR* 3.7 10.3 - - - -
709A ASP* 5.5 0.2 + - - -
739A ASP* 3.2 26.0 + - - +
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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