Contacts of the strand formed by residues 173 - 181 (chain D) in PDB entry 1EGE
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 ALA 173 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130D MET 3.6 7.9 - - - -
131D CYS* 3.6 1.6 - - - -
132D ALA* 3.5 24.7 - - + +
169D ASN 2.8 12.0 + - - +
170D GLY 4.3 0.4 + - - -
171D GLY 3.6 1.3 - - - -
172D LYS* 1.3 81.8 - - - +
174D ASN* 1.3 61.8 + - - +
175D TRP 3.6 3.1 - - - +
176D TYR* 3.4 31.9 + - + -
201D ALA* 3.7 13.6 - - - +
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Residues in contact with ASN 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D ARG* 5.1 6.2 - - - +
124D MET* 5.0 0.6 - - - +
129D LEU* 3.2 43.3 - - + +
130D MET 2.7 18.9 + - - +
172D LYS 3.9 0.4 + - - -
173D ALA* 1.3 72.9 + - - +
175D TRP* 1.3 74.5 + - + +
200D GLU* 3.9 3.5 - - - +
201D ALA* 3.0 27.4 + - - +
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Residues in contact with TRP 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D GLY 3.5 11.7 - - - -
105D GLN* 3.4 32.3 - - + -
108D ILE* 3.1 31.4 - - + -
120D TYR* 3.4 41.0 + + + -
121D LEU* 4.7 7.4 - - + -
123D ARG* 5.8 2.9 - - + -
124D MET* 3.6 17.4 - - + -
130D MET 4.0 0.4 + - - -
131D CYS* 3.3 27.4 - - + -
132D ALA 3.2 19.9 + - - -
173D ALA* 3.6 2.3 - - - +
174D ASN* 1.3 90.7 - - + +
176D TYR* 1.3 68.6 + - - +
177D PHE 4.5 5.2 - - - -
198D ILE* 3.1 28.0 - - + -
199D VAL 3.5 11.4 - - - +
200D GLU* 4.0 8.5 - - + -
201D ALA 4.1 1.3 - - - +
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Residues in contact with TYR 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D ALA* 3.3 24.9 - - + +
134D CYS* 3.7 15.5 - - + -
170D GLY* 2.8 35.0 + - - -
171D GLY* 4.7 1.9 - - - -
173D ALA* 3.4 23.6 + - + -
175D TRP* 1.3 78.3 - - - +
177D PHE* 1.3 68.9 + - - +
178D LEU* 5.3 0.2 - - + -
198D ILE* 3.7 3.1 - - - +
199D VAL* 2.8 52.5 + - + +
200D GLU 4.8 0.2 - - - -
201D ALA* 3.8 28.4 - - + +
206D ILE* 4.6 6.3 - - + +
208D ILE* 4.2 12.8 - - - +
225D ILE* 3.8 11.1 - - + +
227D PHE* 4.2 24.9 - + + -
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Residues in contact with PHE 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D GLY 3.7 19.7 - - - +
107D PRO* 3.6 27.1 - - + -
108D ILE* 5.2 3.8 - - + -
132D ALA 2.9 10.7 + - - +
133D TYR* 3.4 37.7 - + + -
134D CYS* 3.0 28.9 + - - +
135D VAL* 4.3 9.0 - - + -
175D TRP* 4.3 4.5 - - + -
176D TYR* 1.3 74.2 - - - +
178D LEU* 1.3 66.4 + - - +
179D LEU* 4.2 21.3 - - + -
196D GLY* 4.4 13.0 - - - -
197D PHE 4.3 1.8 - - - -
198D ILE* 4.8 2.9 - - - +
238D LEU* 4.3 26.5 - - + -
244D GLY 4.9 0.2 - - - -
247D VAL* 4.4 13.5 - - + -
248D ALA* 4.2 12.8 - - + -
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Residues in contact with LEU 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D CYS* 3.7 5.2 - - + +
149D THR* 4.8 4.5 - - + -
160D ILE* 3.9 38.1 - - + -
164D LYS* 3.6 22.7 - - - -
177D PHE* 1.3 80.1 - - - +
179D LEU* 1.3 89.3 + - - +
195D THR 3.9 0.2 - - - +
196D GLY* 3.0 5.1 - - - -
197D PHE* 2.8 49.0 + - + +
199D VAL* 3.6 23.6 - - + -
227D PHE* 4.4 26.0 - - + -
230D VAL* 6.2 1.1 - - + -
232D VAL* 5.2 0.2 - - + -
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Residues in contact with LEU 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D CYS 3.6 5.0 + - - +
135D VAL* 4.1 30.0 - - + +
144D VAL* 5.3 6.7 - - + -
147D ILE* 4.2 14.1 - - + -
149D THR* 4.4 0.5 - - - +
164D LYS* 3.4 11.2 + - - -
177D PHE* 4.2 15.7 - - + -
178D LEU* 1.3 94.0 - - - +
180D ALA* 1.3 77.5 + - - +
194D PHE* 3.4 34.3 - - + -
195D THR 3.8 3.4 - - - +
196D GLY* 4.4 1.1 - - - -
244D GLY* 3.6 37.7 - - - +
245D PHE* 4.7 2.7 - - - +
248D ALA* 4.3 9.4 - - + -
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Residues in contact with ALA 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D ILE* 4.8 2.9 - - - -
149D THR* 3.4 19.7 - - + +
151D ALA* 3.7 26.0 - - + +
160D ILE* 4.1 13.9 - - + -
179D LEU* 1.3 80.3 - - - +
181D ARG* 1.3 60.4 + - - +
194D PHE* 3.2 15.4 - - - +
195D THR 2.9 31.6 + - - +
197D PHE* 4.2 1.1 - - + -
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Residues in contact with ARG 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D ALA 5.4 5.0 + - - -
147D ILE 4.1 18.4 - - - +
148D LYS* 5.4 1.6 - - - +
149D THR 2.8 14.7 + - - +
150D LYS* 3.1 16.7 - - + +
151D ALA 2.8 22.7 + - - -
180D ALA* 1.3 71.7 - - - +
182D SER* 1.3 60.1 + - - +
183D ASP 3.1 28.0 + - - +
184D PRO* 3.5 6.3 + - - +
185D ASP 3.1 23.6 + - - -
186D PRO* 2.8 39.6 + - - +
188D ALA 4.5 3.4 + - - -
193D ALA* 3.4 22.4 - - + +
194D PHE* 3.9 21.5 - - + -
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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