Contacts of the strand formed by residues 172 - 178 (chain E) in PDB entry 1GEC
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 172 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148E ILE* 4.2 19.1 + - + +
150E GLU* 2.6 44.2 + - - +
168E LYS* 3.1 5.6 - - - -
169E SER 3.0 31.0 + - - +
170E GLY 3.2 9.9 - - - +
171E GLY* 1.3 81.1 - - - +
173E GLY* 1.3 66.3 + - - +
174E TYR* 4.0 3.1 + - - -
194E ARG* 4.7 5.2 - - + -
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Residues in contact with GLY 173 (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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148E ILE* 4.4 0.2 - - - +
167E GLY 3.3 9.9 - - - -
168E LYS* 3.5 15.7 - - - +
171E GLY 4.2 1.0 + - - -
172E LYS* 1.3 79.4 - - - +
174E TYR* 1.3 61.7 + - - +
194E ARG* 3.8 5.9 - - - +
195E ARG* 3.2 35.2 + - - -
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Residues in contact with TYR 174 (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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4E SER* 5.1 2.8 + - - -
5E VAL 5.6 0.6 + - - -
148E ILE* 3.6 28.3 - - + -
166E TYR* 3.1 35.7 + - - +
167E GLY* 2.9 44.3 + - - +
168E LYS 3.7 5.0 + - - -
169E SER* 3.9 17.9 - - - -
172E LYS 4.2 2.2 - - - -
173E GLY* 1.3 73.8 - - - +
175E ILE* 1.3 71.2 + - - +
176E LEU* 4.2 13.0 - - + +
192E ARG* 3.7 40.8 - - + -
193E ILE 3.2 17.7 - - - +
195E ARG* 3.9 5.8 + - - +
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Residues in contact with ILE 175 (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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121E LEU* 4.6 14.4 - - + -
122E LEU* 3.6 31.2 - - + -
125E ILE* 4.3 6.5 - - + -
163E ALA* 3.9 18.6 - - + -
165E GLY 3.6 5.8 - - - +
166E TYR* 4.0 4.5 - - + -
174E TYR* 1.3 83.6 - - - +
176E LEU* 1.3 63.5 + - - +
177E ILE* 3.6 29.2 + - + +
191E ILE 3.4 1.6 - - - +
192E ARG* 3.4 3.1 - - - -
193E ILE* 3.0 33.9 + - + +
195E ARG* 3.9 20.0 - - + -
206E VAL* 4.9 15.0 - - + -
207E TYR* 5.0 2.2 - - + -
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Residues in contact with LEU 176 (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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5E VAL 4.8 1.1 - - - +
6E ASP* 3.7 22.9 - - + +
8E ARG* 3.5 32.3 - - - +
163E ALA* 3.4 3.5 - - - -
164E VAL* 2.7 47.4 + - + -
165E GLY* 2.7 27.5 + - - +
174E TYR* 3.9 16.4 - - + +
175E ILE* 1.3 69.9 - - - +
177E ILE* 1.3 58.5 + - - +
187E GLU* 5.3 1.6 - - - +
190E TYR* 4.1 21.5 - - + -
191E ILE 3.8 3.1 - - - +
192E ARG* 4.0 20.4 - - + -
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Residues in contact with ILE 177 (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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132E VAL* 4.8 2.7 - - + -
134E VAL* 4.5 0.4 - - + -
141E PHE* 6.4 0.2 - - + -
161E VAL* 3.3 44.0 - - + -
162E THR 3.3 2.5 - - - +
163E ALA* 3.8 13.0 - - - +
175E ILE* 3.8 20.4 - - + -
176E LEU* 1.3 79.5 - - - +
178E LYS* 1.3 65.8 + - - +
179E ASN* 3.7 1.2 + - - +
190E TYR* 3.2 12.3 - - - -
191E ILE* 2.8 51.8 + - + +
193E ILE* 4.1 21.8 - - + -
206E VAL* 4.1 21.3 - - + -
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Residues in contact with LYS 178 (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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13E VAL* 3.8 10.6 - - + +
14E THR* 2.9 41.3 + - - +
15E PRO 3.4 15.8 + - - -
16E VAL* 3.9 14.4 - - + +
17E LYS* 4.5 5.8 - - - +
32E ALA* 4.5 24.2 - - + +
35E GLU* 4.7 0.4 + - - -
161E VAL* 3.7 3.6 - - - +
162E THR* 2.7 38.9 + - - +
164E VAL* 4.1 9.1 - - + +
176E LEU 4.3 0.2 + - - -
177E ILE* 1.3 72.7 - - - +
179E ASN* 1.3 67.4 + - - +
190E TYR* 3.3 32.9 - - + +
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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