Contacts of the strand formed by residues 169 - 173 (chain A) in PDB entry 2EYZ
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 169 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ARG* 3.1 17.7 - - - -
104A TYR* 5.3 0.4 - - - -
114A LEU* 5.0 9.0 - - + -
115A ILE 4.1 7.3 + - - -
116A GLU* 2.8 48.8 - - + +
117A PRO* 4.6 0.2 - - + -
150A ASP* 5.7 0.2 - - + -
151A LEU 5.9 0.2 - - - -
153A PHE* 4.6 7.4 - + - -
165A PRO* 3.2 19.2 - - - +
166A GLU* 3.0 42.0 + - - +
167A GLU 3.7 0.8 - - - -
168A GLN* 1.3 117.0 + - + +
170A TRP* 1.3 66.4 + - - +
181A MET* 4.0 13.5 - - + -
182A ILE* 3.0 13.9 - - - +
183A PRO* 3.1 50.0 - - + -
184A VAL* 3.7 1.2 - - - +
185A PRO* 5.8 0.9 - - + +
186A TYR* 5.6 4.3 - + - -
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Residues in contact with TRP 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A GLU* 6.0 1.8 - - - -
137A VAL* 5.1 9.6 - - + -
161A ILE* 3.6 30.5 - - + -
163A ASP 3.7 5.4 - - - +
164A LYS* 3.1 49.6 - - + -
165A PRO* 3.8 0.7 - - - -
166A GLU 4.3 1.1 - - - -
169A TRP* 1.3 84.1 - - - +
171A ASN* 1.3 59.5 + - - +
181A MET* 3.0 4.1 - - - -
182A ILE* 2.6 47.2 + - + +
183A PRO 6.0 0.4 - - - -
184A VAL* 2.8 25.8 - - + +
187A VAL* 6.0 4.5 - - + -
189A LYS* 4.6 14.8 - - + -
191A ARG* 6.2 0.4 - - - -
223A GLN* 3.9 12.3 - - + -
224A PRO* 3.1 24.7 - - + +
226A VAL* 3.3 35.0 - - + -
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Residues in contact with ASN 171 (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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128A ILE* 5.4 13.9 - - - +
149A GLU* 4.9 6.8 + - - +
161A ILE* 3.4 5.2 - - - -
162A ARG* 2.7 38.4 + - + -
163A ASP* 2.7 32.1 + - + +
165A PRO* 3.3 28.4 - - - +
170A TRP* 1.3 70.0 - - - +
172A ALA* 1.3 59.1 + - - +
180A GLY* 2.7 28.3 - - - +
181A MET* 3.3 10.0 - - - +
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Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LEU* 4.0 7.6 - - - +
159A LEU* 3.5 26.4 - - + +
160A ARG 3.0 23.3 - - - +
161A ILE* 4.3 1.6 - - + +
162A ARG* 4.8 2.2 - - - +
170A TRP 3.7 1.8 + - - -
171A ASN* 1.3 73.9 - - - +
173A GLU* 1.3 60.5 + - - +
179A ARG* 4.7 4.0 - - - -
180A GLY 2.7 32.2 + - - +
181A MET* 4.4 0.4 - - - +
182A ILE* 3.9 19.7 - - + -
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Residues in contact with GLU 173 (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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158A ILE 4.2 1.2 - - - +
159A LEU* 3.0 27.4 - - - +
160A ARG* 3.5 11.2 + - + +
172A ALA* 1.3 74.9 - - - +
174A ASP* 1.3 73.3 + - - +
177A GLY* 3.4 24.1 - - - +
178A LYS 3.1 20.9 - - - +
179A ARG* 2.6 55.7 + - - +
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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