Contacts of the strand formed by residues 175 - 181 (chain A) 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 TRP 175 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A GLY 3.5 24.7 - - - -
105A GLN* 3.8 11.0 - - + -
108A ILE* 3.5 28.5 - - + -
120A TYR* 3.3 27.4 + + + +
121A LEU* 4.3 2.2 - - + -
123A ARG* 4.0 7.0 - - - -
124A MET* 3.2 29.7 - - + +
130A MET 4.2 0.6 + - - -
131A CYS* 3.2 55.4 - - + -
132A ALA 3.2 2.4 + - - -
173A ALA* 3.8 2.8 - - - +
174A ASN* 1.3 99.7 - - - +
176A TYR* 1.3 80.0 + - - +
177A PHE* 4.4 2.9 - - + -
198A ILE* 4.1 18.6 - - + -
199A VAL 3.2 12.1 - - - +
200A GLU* 4.1 8.7 - - + -
201A ALA 4.1 1.1 - - - +
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Residues in contact with TYR 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ALA* 3.3 14.6 - - + -
134A CYS* 3.3 30.7 - - - -
170A GLY* 3.6 16.3 - - - -
171A GLY* 3.3 22.3 + - - -
173A ALA* 3.5 23.2 + - + +
175A TRP* 1.3 82.7 - - - +
177A PHE* 1.3 61.8 + - - +
178A LEU* 5.4 0.4 - - + -
197A PHE 3.8 0.2 - - - +
198A ILE* 3.4 6.1 - - - -
199A VAL* 2.7 48.7 + - + +
200A GLU 4.9 0.2 - - - -
201A ALA* 3.5 29.6 - - + +
206A ILE* 4.8 5.2 - - + -
208A ILE* 3.4 17.3 - - + +
225A ILE* 3.6 21.4 - - + +
227A PHE* 4.6 10.1 - + + -
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Residues in contact with PHE 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A GLY 3.9 17.5 - - - +
107A PRO* 3.8 16.8 - - + -
108A ILE* 5.9 2.0 - - + -
132A ALA 2.8 14.0 + - - +
133A TYR* 3.4 33.2 - + - -
134A CYS* 2.9 30.7 + - - +
135A VAL* 4.1 9.6 - - + -
175A TRP* 4.3 3.1 - - + -
176A TYR* 1.3 74.2 - - - +
178A LEU* 1.3 77.7 + - - +
179A LEU* 4.3 7.2 - - + -
196A GLY* 4.2 5.8 - - - -
197A PHE 3.7 2.9 - - - -
198A ILE* 4.9 2.0 - - + +
238A LEU* 3.6 32.1 - - + -
247A VAL* 4.4 3.4 - - + -
248A ALA* 3.4 42.2 - - + -
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Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A CYS* 3.6 19.3 - - + -
149A THR* 4.7 1.8 - - + -
160A ILE* 4.0 26.0 - - + -
164A LYS* 3.7 17.9 - - - -
176A TYR* 5.2 0.9 - - + -
177A PHE* 1.3 81.4 - - - +
179A LEU* 1.3 64.4 + - - +
180A ALA* 4.4 6.1 - - + -
195A THR 3.9 1.2 - - - +
196A GLY* 2.9 27.2 - - - -
197A PHE* 3.0 38.3 + - + +
199A VAL* 4.1 14.6 - - + -
227A PHE* 3.6 36.3 - - + -
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Residues in contact with LEU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A CYS 3.2 13.7 + - - +
135A VAL* 3.9 10.8 - - + -
144A VAL* 3.8 27.6 - - + +
147A ILE* 3.0 18.8 - - + +
164A LYS* 2.9 28.8 + - - -
177A PHE* 4.3 3.1 - - + -
178A LEU* 1.3 74.4 - - - +
180A ALA* 1.3 60.7 - - - +
194A PHE* 3.8 21.1 - - + -
196A GLY* 4.3 6.3 - - - +
244A GLY* 3.7 33.0 - - - +
245A PHE* 4.1 6.3 - - - +
248A ALA* 3.8 28.5 - - + -
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Residues in contact with ALA 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A ILE* 4.4 1.6 - - - -
149A THR* 3.5 28.5 - - + +
150A LYS 4.6 0.2 - - - +
151A ALA* 3.7 22.4 - - + -
160A ILE* 4.9 0.4 - - + -
178A LEU* 4.0 11.9 + - + -
179A LEU* 1.3 75.0 - - - +
181A ARG* 1.3 62.2 + - - +
194A PHE* 3.1 8.6 - - - +
195A THR* 2.9 37.5 + - - +
197A PHE* 4.5 2.2 - - + -
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Residues in contact with ARG 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A ALA 5.4 3.2 + - - -
146A GLY* 5.7 3.8 - - - -
147A ILE 4.0 9.1 + - - +
148A LYS* 4.8 13.1 - - + +
149A THR 2.7 20.2 + - - +
150A LYS* 3.7 11.1 - - + +
151A ALA* 3.1 25.1 + - - +
180A ALA* 1.3 70.6 - - - +
182A SER* 1.3 61.2 + - - +
183A ASP 3.0 29.9 + - - +
184A PRO* 3.5 18.3 + - + +
185A ASP 4.0 7.9 + - - -
186A PRO* 4.3 16.4 + - - +
188A ALA 5.0 2.6 + - - -
193A ALA* 3.1 40.2 - - - +
194A PHE* 3.5 25.9 - - + -
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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