Contacts of the strand formed by residues 136 - 143 (chain E) in PDB entry 1GN2
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 LYS 136 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130E TRP* 3.5 10.0 - - - -
131E ASP* 2.7 36.9 + - - +
134E GLY* 3.2 18.8 - - - +
135E ASN* 1.3 75.2 - - - +
137E LEU* 1.3 67.5 + - - +
138E LEU* 3.8 18.0 + - + +
2G ALA 2.9 38.5 + - - +
3G GLU* 4.1 6.3 - - - +
4G TYR* 3.9 37.7 - - + +
41G ASN* 4.7 1.0 + - - -
44G VAL* 4.4 19.3 - - + +
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Residues in contact with LEU 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E LEU* 5.0 4.9 - - + -
98E ALA* 4.7 8.1 - - + -
99E ILE* 3.9 37.5 - - + +
102E ALA* 4.0 23.2 - - + +
103E PHE* 3.9 17.5 - - + -
128E LEU* 4.1 18.2 - - + -
129E GLY 3.5 8.3 - - - +
130E TRP* 3.7 20.7 - - + -
136E LYS* 1.3 73.4 - - - +
138E LEU* 1.3 69.5 + - - +
156E LEU* 3.6 29.4 - - + -
194E TYR* 4.3 9.6 - - + -
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Residues in contact with LEU 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E PHE* 4.2 6.0 - - + -
127E ALA 3.8 0.2 - - - +
128E LEU* 3.5 3.1 - - - +
129E GLY* 2.7 38.9 + - - +
131E ASP* 3.8 20.2 - - + -
136E LYS* 4.2 14.1 - - + +
137E LEU* 1.3 83.2 - - - +
139E ILE* 1.3 64.4 + - - +
140E PHE* 4.0 21.5 - - + -
4G TYR* 3.8 7.0 - - - +
44G VAL* 4.7 13.0 - - + -
47G LEU* 6.1 1.8 - - + -
66G LEU* 4.5 22.7 - - + -
70G LEU* 3.6 30.7 - - + -
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Residues in contact with ILE 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E PHE* 3.5 33.4 - - + -
109E PHE* 3.8 26.0 - - + +
112E GLN* 3.5 29.7 + - + +
113E PHE* 3.9 23.6 - - + +
116E ALA* 4.1 15.9 - - + -
127E ALA 3.3 9.4 - - - +
128E LEU* 4.3 7.0 - - + -
138E LEU* 1.3 77.4 - - - +
140E PHE* 1.3 65.1 + - - +
63G GLU* 2.6 35.5 - - - +
66G LEU* 3.7 11.7 - - - +
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Residues in contact with PHE 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E ALA* 4.8 0.4 - - - +
126E ALA* 3.8 3.6 - - - -
127E ALA* 2.8 40.1 + - + +
129E GLY* 4.6 5.2 - - - -
138E LEU* 4.0 34.3 - - + -
139E ILE* 1.3 84.0 - - - +
141E GLN* 1.3 63.2 + - - +
142E VAL* 3.8 7.6 + - + -
148E ASN 4.3 12.3 - - - +
149E PHE* 4.1 18.6 - - + -
150E PRO* 3.5 23.8 - - + -
153E ILE* 3.6 44.6 - - + -
63G GLU* 3.6 4.3 - - - -
66G LEU* 4.1 22.2 - - + -
67G ALA* 4.4 9.6 - - + -
70G LEU* 4.4 1.8 - - + -
151G LEU* 5.7 2.0 - - + -
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Residues in contact with GLN 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E ALA* 3.0 29.7 + - + +
119E THR* 2.7 41.0 + - - -
120E VAL* 3.7 15.7 - - + +
125E TRP 3.7 2.9 - - - +
126E ALA* 5.0 0.7 - - - +
140E PHE* 1.3 73.3 - - - +
142E VAL* 1.3 62.8 + - - +
143E TYR* 3.5 23.9 + - + -
148E ASN* 3.0 31.3 + - - +
59G ILE* 5.1 0.4 - - - +
60G LEU* 3.7 30.0 - - - +
63G GLU* 4.0 23.6 + - + +
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Residues in contact with VAL 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E ASN* 5.1 1.1 - - - +
120E VAL* 4.5 2.3 - - - +
124E GLY* 3.0 5.2 - - - -
125E TRP* 3.0 49.1 + - + +
127E ALA* 4.4 21.1 - - + -
140E PHE* 4.7 5.8 - - + +
141E GLN* 1.3 72.7 - - - +
143E TYR* 1.3 75.3 + - - +
144E ASP 4.2 2.7 - - - +
145E HIS* 3.8 25.1 - - - +
147E THR 3.3 11.2 - - - +
148E ASN* 4.4 0.7 - - - -
149E PHE* 3.6 24.9 - - + -
151G LEU* 4.8 7.6 - - + -
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Residues in contact with TYR 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E VAL* 4.5 13.0 - - + -
121E GLN 5.6 1.8 - - - -
123E CYS 3.8 5.2 - - - +
141E GLN* 3.5 34.9 + - + -
142E VAL* 1.3 77.0 - - - +
144E ASP* 1.3 76.7 + - - +
145E HIS 2.9 4.7 + - - -
147E THR* 2.8 47.4 + - + -
148E ASN* 3.4 26.7 + - + -
64F LYS* 4.7 16.7 + - - -
60G LEU* 4.5 14.0 - - + +
64G LYS* 3.7 28.1 - - + +
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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