Contacts of the strand formed by residues 153 - 160 (chain G) 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 ILE 153 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E VAL* 6.3 0.4 - - + -
151E LEU* 4.1 20.6 - - + -
152E GLY* 3.2 25.7 + - - +
129G GLY* 4.4 4.5 - - - -
130G TRP 3.3 18.8 - - - +
131G ASP* 3.4 25.8 - - + +
138G LEU* 5.0 0.2 - - + -
140G PHE* 3.6 32.8 - - + -
149G PHE* 5.5 0.4 - - + -
150G PRO* 3.8 40.3 + - + +
151G LEU 3.3 3.3 - - - +
152G GLY* 1.3 78.0 - - - +
154G VAL* 1.3 71.1 + - - +
155G PRO* 3.4 1.0 - - + +
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Residues in contact with VAL 154 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152E GLY* 5.0 1.6 - - - -
129G GLY* 3.0 4.6 - - - -
130G TRP* 2.6 59.7 + - + +
132G THR* 4.1 12.3 - - + -
152G GLY 4.4 3.4 - - - +
153G ILE* 1.3 73.8 - - - +
155G PRO* 1.3 77.3 - - + +
156G LEU* 3.6 5.0 + - + +
193G ARG* 5.3 2.0 - - + +
197G ALA* 4.2 25.6 - - + +
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Residues in contact with PRO 155 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151E LEU* 4.2 33.4 - - + +
152E GLY* 4.0 12.3 - - - +
74G VAL* 5.4 1.3 - - + -
78G ILE* 3.7 28.0 - - + +
127G ALA* 6.1 0.4 - - + -
128G LEU 3.9 5.8 - - - +
129G GLY* 4.3 0.9 - - - -
153G ILE* 3.4 10.9 - - + +
154G VAL* 1.3 95.6 - - + +
156G LEU* 1.3 65.9 + - - +
158G LEU* 4.6 8.7 - - + -
193G ARG* 4.0 14.9 + - - +
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Residues in contact with LEU 156 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78G ILE* 4.6 2.4 - - - +
82G ASN* 3.4 10.8 + - - -
95G LEU* 5.5 0.9 - - + -
128G LEU* 2.9 31.3 + - + +
129G GLY 4.3 4.5 - - - -
130G TRP* 4.3 2.7 - - + -
137G LEU* 3.6 31.6 - - + -
154G VAL* 3.9 14.1 - - + +
155G PRO* 1.3 82.4 - - - +
157G LEU* 1.3 59.8 + - - +
190G VAL* 4.1 15.4 - - + +
193G ARG* 3.3 55.5 - - + +
194G TYR* 3.8 19.7 - - + +
197G ALA* 4.2 10.3 - - + -
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Residues in contact with LEU 157 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82G ASN* 3.3 26.7 - - + +
109G PHE* 4.4 10.8 - - + -
113G PHE* 4.2 17.5 - - + -
127G ALA* 3.2 1.0 - - - -
128G LEU* 2.8 40.8 + - + -
155G PRO 4.0 0.2 - - - -
156G LEU* 1.3 79.5 - - - +
158G LEU* 1.3 68.9 + - - +
181G PHE* 3.9 23.1 - - + -
182G TRP* 4.4 13.2 - - + -
185G VAL* 4.1 9.6 - - + -
187G TRP* 4.2 27.4 - - + -
190G VAL* 4.0 19.5 - - + -
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Residues in contact with LEU 158 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151E LEU* 4.2 13.0 - - + -
75G ASN* 3.9 42.2 - - + +
78G ILE* 4.3 21.3 - - + -
79G TRP* 3.5 18.4 - - + -
82G ASN* 2.9 12.4 + - - +
113G PHE* 4.5 2.7 - - - -
125G TRP* 3.6 24.5 - - + -
126G ALA 3.3 4.0 - - - +
127G ALA* 3.0 33.0 - - + -
128G LEU 4.5 0.7 - - - +
155G PRO* 4.6 8.7 - - + -
157G LEU* 1.3 84.7 - - - +
159G LEU* 1.3 63.4 + - - +
160G ASP 4.1 0.2 - - - -
181G PHE* 3.8 10.2 - - - -
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Residues in contact with LEU 159 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79G TRP* 3.8 3.1 - - + -
113G PHE* 3.8 26.0 - - + -
114G HIS* 6.1 1.3 - - - -
117G ALA* 4.1 16.4 - - + -
125G TRP* 3.3 3.7 - - - -
126G ALA* 2.9 29.0 + - + +
158G LEU* 1.3 75.5 - - - +
160G ASP* 1.3 68.0 + - - +
161G MET* 3.3 12.1 + - - +
177G PHE* 3.5 36.3 - - + -
178G ALA* 4.2 19.1 - - + +
181G PHE* 3.7 39.0 - - + -
182G TRP* 5.7 1.1 - - - +
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Residues in contact with ASP 160 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G HIS* 2.9 14.9 + - - -
76G HIS* 3.6 1.4 + - - -
79G TRP* 3.6 16.4 - - + -
125G TRP* 3.3 32.3 - - + -
159G LEU* 1.3 71.0 - - - +
161G MET* 1.3 57.9 + - - +
162G TRP* 2.8 40.9 + - - +
164G HIS* 3.4 0.3 + - - -
165G ALA* 3.5 16.6 - - + +
177G PHE* 3.4 23.9 - - - -
999G FE 2.0 30.2 - - - -
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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