Contacts of the strand formed by residues 172 - 177 (chain B) in PDB entry 5NC5
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 VAL 172 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B ILE* 3.3 24.2 - - + +
167B SER* 4.0 14.1 - - - +
169B THR* 3.3 29.6 + - + +
171B GLY* 1.3 75.8 - - - +
173B GLY* 1.3 60.0 + - - +
174B ASP 4.1 2.5 - - - +
175B VAL* 3.8 25.6 - - + -
291B ILE* 3.9 19.1 - - + -
292B LYS 3.7 4.0 - - - -
294B ALA* 4.1 1.9 - - - +
302B THR* 3.9 14.8 - - + -
306B ILE* 4.2 9.4 - - + -
70C ASN* 5.6 0.2 - - - +
71C GLY* 4.2 8.8 + - - -
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Residues in contact with GLY 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B GLY 3.5 3.0 + - - -
172B VAL* 1.3 73.8 - - - +
174B ASP* 1.3 64.3 + - - +
292B LYS* 3.0 10.6 + - - -
293B LEU 4.4 1.6 - - - -
294B ALA* 3.6 20.8 - - - +
70C ASN* 3.5 8.6 + - - -
71C GLY* 3.5 25.8 - - - +
110C LYS* 3.8 7.8 + - - -
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Residues in contact with ASP 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B VAL* 3.6 1.4 - - - +
173B GLY* 1.3 81.7 - - - +
175B VAL* 1.3 78.9 + - - +
176B GLN* 4.0 21.3 + - - +
290B GLY 3.7 0.8 - - - +
291B ILE* 3.5 2.6 - - - +
292B LYS* 3.1 52.8 + - + +
70C ASN* 3.7 11.2 + - - +
110C LYS* 4.3 10.7 + - - -
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Residues in contact with VAL 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B LYS* 3.4 32.7 + - + +
166B ILE* 4.3 7.0 - - + -
167B SER* 3.6 30.3 - - - +
172B VAL* 3.8 18.4 - - + -
174B ASP* 1.3 88.1 + - - +
176B GLN* 1.3 64.2 + - - +
289B LEU* 3.7 39.3 - - + -
290B GLY 3.4 4.9 - - - +
291B ILE* 4.4 5.8 - - + -
70C ASN* 4.1 3.9 + - - +
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Residues in contact with GLN 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B GLU* 4.8 10.5 + - - -
136B PHE* 4.3 20.9 - - + -
163B LYS* 4.3 1.3 - - - +
174B ASP* 4.0 14.8 + - - +
175B VAL* 1.3 77.3 - - - +
177B LEU* 1.3 66.8 + - - +
178B PHE* 3.7 14.9 + - + -
289B LEU* 3.3 4.7 - - - -
290B GLY 2.7 39.1 + - - +
292B LYS* 5.2 7.7 + - - -
1120B PUY 5.0 2.4 - - - -
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Residues in contact with LEU 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B SER* 4.1 6.3 - - - +
158B VAL* 3.6 20.9 - - + -
159B ALA* 3.6 27.4 - - + -
163B LYS* 3.8 25.1 - - + +
176B GLN* 1.3 75.6 - - - +
178B PHE* 1.4 59.2 + - - +
179B GLY* 3.2 27.6 + - - +
180B SER* 3.8 15.7 - - - +
181B GLN 4.3 1.1 - - - +
287B SER* 3.4 25.4 - - - +
288B GLY 3.5 10.1 - - - +
289B LEU* 4.5 2.0 - - + -
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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