Contacts of the strand formed by residues 173 - 178 (chain A) in PDB entry 1NZL
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 THR 173 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A LEU* 3.5 4.5 - - + +
169A ASN* 3.4 21.6 - - - +
170A PRO* 2.7 38.6 + - - +
172A GLY* 1.3 77.7 - - - +
174A PHE* 1.3 62.6 + - - +
190A VAL* 3.3 2.3 - - - -
191A SER* 2.8 37.6 + - - -
245A ASN* 3.1 26.7 + - - +
247A CYS* 3.4 26.7 - - + -
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Residues in contact with PHE 174 (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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150A TRP* 3.7 26.0 - + + -
164A LEU* 3.9 2.2 - - - -
172A GLY 3.8 3.8 - - - -
173A THR* 1.3 77.0 - - - +
175A LEU* 1.3 66.7 + - - +
176A VAL* 4.6 0.9 - - + -
188A LEU* 3.5 20.0 - - + -
189A SER 3.2 15.0 - - - +
190A VAL* 4.2 1.6 - - + -
229A VAL* 3.5 37.9 - - + -
233A SER* 6.0 0.9 - - - -
243A LEU* 3.7 41.5 - - + -
244A THR 5.1 0.2 - - - -
245A ASN 2.8 35.9 + - - -
246A VAL* 3.7 15.6 - - + +
247A CYS* 2.8 30.6 + - - +
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Residues in contact with LEU 175 (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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150A TRP 3.4 7.9 - - - -
152A PHE* 3.8 41.3 - - + -
155A ILE* 4.6 4.7 - - + -
160A SER* 3.8 31.9 - - - +
163A LEU* 4.5 1.6 - - + -
164A LEU* 4.0 22.7 - - + -
174A PHE* 1.3 78.9 - - - +
176A VAL* 1.3 67.5 + - - +
177A ARG* 4.0 20.9 - - + -
188A LEU* 3.7 4.9 - - - +
189A SER* 3.1 32.3 + - - -
247A CYS* 3.9 15.0 - - + -
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Residues in contact with VAL 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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150A TRP* 2.7 37.3 + - + +
151A TYR* 3.6 16.7 - - + -
152A PHE* 2.8 27.9 + - - +
174A PHE* 4.6 2.5 - - + -
175A LEU* 1.3 79.5 - - - +
177A ARG* 1.3 70.5 + - - +
186A TYR* 4.2 7.2 - - + -
187A CYS 3.3 8.7 - - - +
188A LEU* 4.0 18.2 - - + -
206A ILE* 4.1 19.7 - - + -
225A LEU* 4.3 10.1 - - + -
229A VAL* 4.1 11.2 - - + -
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Residues in contact with ARG 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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151A TYR* 4.6 1.3 - - - -
153A GLY 3.4 16.4 - - - +
155A ILE* 3.5 34.9 + - + +
156A THR 4.2 0.4 - - - -
157A ARG* 3.7 26.5 - - - +
160A SER* 3.5 16.0 + - - -
175A LEU* 4.0 4.9 - - + -
176A VAL* 1.3 75.8 - - - +
178A GLU* 1.3 73.4 + - - +
180A GLU* 4.5 6.7 - - - +
186A TYR* 3.3 12.3 - - - +
187A CYS* 2.8 56.7 + - + +
189A SER* 3.1 13.5 + - - -
203A HIS* 3.0 34.6 + - - +
2000A CL 4.2 14.1 - - - +
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Residues in contact with GLU 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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151A TYR* 3.3 26.6 + - - +
153A GLY* 2.9 24.4 + - - +
154A LYS* 4.3 16.4 + - - +
155A ILE 4.5 5.4 - - - +
177A ARG* 1.3 87.4 + - - +
179A SER* 1.3 68.5 + - - +
180A GLU* 3.4 3.6 + - - +
185A ALA 3.9 5.8 - - - +
186A TYR* 4.4 6.9 - - + -
187A CYS 4.7 0.2 - - - -
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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