Contacts of the strand formed by residues 170 - 177 (chain A) in PDB entry 1Q99
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 SER 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A GLY* 3.5 10.9 + - - +
167A GLY 2.9 28.6 + - - +
169A PHE* 1.3 88.1 - - - +
171A THR* 1.3 63.3 + - - +
172A VAL* 4.4 1.6 - - - +
187A LYS* 3.9 13.3 - - - +
188A ILE 3.2 25.4 - - - -
189A VAL* 3.9 6.3 - - - -
244A MET* 6.2 0.2 - - - -
901A ANP 3.3 25.0 + - - -
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Residues in contact with THR 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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143A GLY* 3.4 24.6 - - - -
144A TYR 4.6 1.5 + - - +
145A HIS 4.4 11.8 + - - +
163A LYS* 4.0 7.2 - - - -
165A GLY 3.9 3.6 - - - -
166A TRP* 3.6 37.0 - - + +
170A SER* 1.3 72.9 - - - +
172A VAL* 1.3 62.6 + - - +
173A TRP* 3.9 17.5 + - - -
186A MET 3.5 1.2 - - - +
187A LYS* 3.5 0.5 - - - -
188A ILE* 2.7 45.4 + - - +
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Residues in contact with VAL 172 (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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163A LYS* 3.6 4.7 - - - +
164A LEU* 2.7 40.1 + - + -
165A GLY 2.8 16.6 + - - +
170A SER* 4.4 3.8 - - - +
171A THR* 1.3 75.6 - - - +
173A TRP* 1.3 61.3 + - - +
185A ALA* 4.3 6.1 - - + -
186A MET 3.3 11.9 - - - +
187A LYS* 3.4 33.0 - - + -
901A ANP 3.1 58.6 - - + +
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Residues in contact with TRP 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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145A HIS 5.3 0.6 + - - -
147A ALA* 3.5 45.3 - - + +
148A PHE* 4.0 4.3 - - - -
149A LYS* 4.1 14.4 - - + -
160A LEU* 3.7 42.2 - - + -
162A ARG* 3.4 27.6 - - - -
163A LYS* 3.8 39.4 - - + +
164A LEU* 3.9 4.9 - - - -
171A THR* 3.9 19.0 + - - -
172A VAL* 1.3 80.6 - - - +
174A LEU* 1.3 63.0 + - - +
185A ALA* 3.4 4.2 - - - -
186A MET* 2.8 36.3 + - + +
188A ILE* 3.6 19.1 - - + -
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Residues in contact with LEU 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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160A LEU* 3.9 1.7 - - - -
161A VAL* 2.8 39.4 + - + -
162A ARG* 2.7 51.4 + - + +
164A LEU* 3.6 18.8 - - + +
173A TRP* 1.3 74.2 - - - +
175A ALA* 1.3 60.9 + - - +
183A HIS* 3.9 26.7 - - + -
184A VAL 3.5 6.1 - - - +
248A VAL* 3.5 36.6 - - + -
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Residues in contact with ALA 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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158A TYR* 4.4 1.3 - - + -
159A ILE 3.2 21.5 - - - +
160A LEU* 4.1 3.1 - - + -
161A VAL* 4.1 5.8 - - - -
173A TRP 3.7 0.2 + - - -
174A LEU* 1.3 75.0 - - - +
176A LYS* 1.3 60.7 + - - +
177A ASP 4.0 0.2 - - - -
183A HIS* 3.3 7.2 - - - +
184A VAL* 2.9 34.8 + - + -
186A MET* 3.8 38.8 - - + -
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Residues in contact with LYS 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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157A ARG 3.3 1.7 - - - +
158A TYR* 3.3 2.3 - - - -
159A ILE* 2.9 33.3 + - + +
161A VAL* 4.1 6.2 - - + +
175A ALA* 1.3 73.6 - - - +
177A ASP* 1.3 60.8 + - - +
178A MET* 3.2 46.4 + - + +
181A ASN* 2.9 33.9 + - - +
182A THR 3.6 8.7 - - - +
183A HIS* 4.4 27.6 - - + +
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Residues in contact with ASP 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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157A ARG* 3.1 21.9 + - - -
158A TYR* 3.2 26.8 + - + -
175A ALA 3.9 2.0 + - - -
176A LYS* 1.3 67.7 - - - +
178A MET* 1.3 54.9 + - - +
179A VAL 2.9 6.4 + - - -
180A ASN* 2.7 41.9 + - - -
181A ASN* 2.6 37.4 + - - -
182A THR* 2.7 27.6 + - - +
184A VAL* 4.2 11.0 - - + +
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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