Contacts of the strand formed by residues 159 - 169 (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 HIS 159 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19E GLN* 3.2 28.3 - - - -
25E CYS* 3.3 23.3 - - + -
133E VAL* 3.1 8.0 - - - +
134E VAL* 2.8 41.7 + - + +
136E SER* 3.3 22.6 + - - +
141E PHE* 4.6 2.2 - + - -
158E ASP* 1.3 82.5 + - - +
160E ALA* 1.3 59.8 + - - +
161E VAL* 3.3 24.0 - - + +
179E ASN* 2.8 24.9 + - - -
180E SER* 4.4 0.9 - - - -
181E TRP* 3.5 24.1 - + - -
3I VAL* 3.9 4.7 - - - +
4I GLY 4.5 1.0 + - - -
5I 0HQ 3.9 3.2 - - + +
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Residues in contact with ALA 160 (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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25E CYS* 3.4 33.6 - - - +
26E TRP* 3.9 7.0 - - - -
29E SER* 3.1 22.2 + - - +
68E GLN* 4.6 9.6 - - + -
131E SER* 4.5 5.6 - - - +
132E VAL 3.2 8.5 - - - +
133E VAL* 4.4 1.3 - - + +
159E HIS* 1.3 74.7 - - - +
161E VAL* 1.3 66.0 + - - +
180E SER* 4.7 3.5 + - - -
3I VAL* 3.8 20.5 - - + +
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Residues in contact with VAL 161 (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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29E SER* 3.6 4.8 - - - -
131E SER* 3.5 5.0 - - - -
132E VAL* 2.7 39.1 + - + +
134E VAL* 3.9 21.5 - - + -
141E PHE* 5.3 2.5 - - + -
159E HIS* 3.3 37.0 - - + +
160E ALA* 1.3 73.9 - - - +
162E THR* 1.3 63.8 + - - +
177E ILE* 3.3 38.1 - - + -
178E LYS 3.7 3.6 - - - +
179E ASN* 3.5 19.1 - - - +
180E SER 5.2 0.4 - - - +
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Residues in contact with THR 162 (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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29E SER* 3.3 19.2 + - - -
32E ALA* 3.3 30.8 - - + +
33E THR* 3.7 17.5 - - + -
129E PRO* 4.1 11.0 - - + -
130E VAL 3.3 13.0 - - - +
161E VAL* 1.3 73.6 - - - +
163E ALA* 1.3 61.2 + - - +
164E VAL* 3.2 20.8 + - + +
177E ILE* 3.3 2.9 - - - -
178E LYS* 2.7 45.7 + - - +
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Residues in contact with ALA 163 (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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125E ILE* 3.8 32.4 - - + +
129E PRO* 3.7 4.2 - - - +
130E VAL* 2.8 32.7 + - + +
132E VAL* 3.9 20.7 - - + +
161E VAL 4.2 1.0 - - - -
162E THR* 1.3 68.0 - - - +
164E VAL* 1.3 60.5 + - - +
165E GLY 3.6 1.3 - - - -
175E ILE* 3.9 12.3 - - + -
176E LEU 3.4 7.4 - - - -
177E ILE* 3.8 6.4 - - + +
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Residues in contact with VAL 164 (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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6E ASP* 3.8 0.9 - - - -
7E TRP* 2.9 40.5 + - + -
8E ARG* 4.4 8.5 - - + -
13E VAL* 4.0 25.6 - - + -
125E ILE* 4.3 0.7 - - - -
129E PRO* 4.6 5.6 - - + -
162E THR* 3.5 28.5 - - + +
163E ALA* 1.3 73.5 - - - +
165E GLY* 1.3 53.6 + - - -
176E LEU* 2.7 39.7 + - + +
178E LYS* 4.1 11.0 - - + -
190E TYR* 3.9 20.0 - - + -
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Residues in contact with GLY 165 (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* 3.0 27.6 - - - -
6E ASP* 4.3 0.7 - - - -
125E ILE* 3.8 5.5 - - - +
163E ALA 3.6 1.2 - - - -
164E VAL* 1.3 80.2 - - - +
166E TYR* 1.3 59.8 + - - +
175E ILE* 3.6 5.7 - - - +
176E LEU* 2.7 36.7 + - - +
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Residues in contact with TYR 166 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1E LEU 3.5 10.0 + - - -
2E PRO* 2.8 46.7 + - - +
3E GLU 4.2 2.0 - - - -
4E SER* 3.6 12.4 + - - -
5E VAL* 3.0 60.7 + - + +
122E LEU* 3.7 40.6 - - + -
125E ILE* 3.9 13.9 - - + -
126E ALA* 4.1 2.6 - - - +
165E GLY* 1.3 73.3 - - - +
167E GLY* 1.3 62.2 + - - +
168E LYS* 4.1 4.9 - - - -
174E TYR* 3.1 32.5 + - - +
175E ILE* 4.0 11.9 - - + -
176E LEU* 4.3 0.6 - - - +
195E ARG* 4.1 13.2 - - - +
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Residues in contact with GLY 167 (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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3E GLU 3.8 15.5 - - - -
4E SER* 4.3 5.6 - - - -
166E TYR* 1.3 80.6 - - - +
168E LYS* 1.3 70.9 + - - +
174E TYR* 2.9 43.2 + - - -
195E ARG* 3.2 1.4 + - - -
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Residues in contact with LYS 168 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2E PRO 5.2 0.2 + - - -
3E GLU* 3.4 32.3 + - - +
4E SER* 5.5 0.2 - - - -
122E LEU* 6.1 0.2 - - - +
166E TYR* 4.1 8.9 - - - -
167E GLY* 1.3 87.2 + - - +
169E SER* 1.3 62.5 + - - +
170E GLY 4.3 0.2 - - - -
171E GLY 4.9 7.9 - - - +
172E LYS 3.1 17.0 - - - +
173E GLY* 3.5 7.9 - - - +
174E TYR* 3.7 4.1 + - - -
195E ARG* 2.8 32.0 - - - +
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Residues in contact with SER 169 (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* 4.0 10.9 - - - +
168E LYS* 1.3 75.4 - - - +
170E GLY* 1.3 64.9 - - - +
172E LYS* 3.0 17.8 + - - +
174E TYR* 3.9 18.6 - - - -
192E ARG* 3.7 17.7 + - - -
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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