Contacts of the strand formed by residues 172 - 179 (chain A) in PDB entry 1PR9
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 ILE 172 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ALA* 4.4 13.7 - - + +
122A LEU* 4.2 30.5 - - + -
123A ILE* 4.2 11.4 - - + -
127A VAL 4.7 1.3 - - - +
129A GLY 3.3 20.4 - - - +
130A ALA 4.4 0.2 - - - +
131A ILE* 4.0 24.0 - - + -
164A ALA 4.8 1.4 - - - +
167A LEU* 3.4 38.3 + - + +
168A GLY* 3.9 5.6 + - - -
170A HIS* 3.2 25.3 - - + +
171A LYS* 1.3 83.0 - - - +
173A ARG* 1.3 72.9 + - - +
174A VAL* 4.0 3.0 + - + +
231A THR* 4.5 2.3 + - - -
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Residues in contact with ARG 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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129A GLY 3.1 9.9 + - - +
130A ALA* 3.3 9.5 - - + +
131A ILE 2.8 31.0 + - - -
171A LYS 5.2 3.8 - - - +
172A ILE* 1.3 76.5 - - - +
174A VAL* 1.3 59.3 + - - +
175A ASN* 3.6 6.5 - - - +
222A LEU 3.3 18.5 + - - -
223A LEU 3.8 5.7 + - - -
224A SER 2.7 31.7 + - - -
225A ASP* 4.3 9.3 + - - +
227A SER* 2.9 30.5 + - - -
228A GLY* 3.4 29.6 - - - -
230A THR 3.2 21.9 + - - +
231A THR* 3.5 14.1 - - - +
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Residues in contact with VAL 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A ILE* 3.3 16.8 - - + +
133A ASN* 3.8 18.8 - - - +
160A THR* 3.6 15.3 - - + +
163A MET* 3.8 46.0 - - + -
164A ALA* 4.0 9.9 - - - +
167A LEU* 4.1 15.9 - - + -
172A ILE* 4.2 4.0 - - + +
173A ARG* 1.3 80.5 - - - +
175A ASN* 1.3 63.7 + - - +
231A THR* 3.2 6.5 + - - -
232A GLY* 2.7 30.8 + - - -
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Residues in contact with ASN 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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131A ILE 2.9 9.6 + - - +
132A VAL* 3.4 5.2 - - + +
133A ASN* 2.8 26.9 + - - +
160A THR* 3.7 5.7 - - - +
173A ARG* 3.6 14.8 - - - +
174A VAL* 1.3 81.1 - - - +
176A ALA* 1.3 61.1 + - - +
222A LEU* 3.9 33.5 + - + +
230A THR* 2.8 23.9 + - - +
231A THR* 3.2 7.6 + - - +
232A GLY 3.2 5.2 + - - -
233A SER* 3.0 39.6 + - - +
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Residues in contact with ALA 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 VAL* 4.9 0.4 - - - -
133A ASN* 3.1 11.9 - - + +
135A SER* 4.3 11.0 - - - -
156A LEU* 5.8 0.4 - - + -
157A ASP* 4.3 2.7 - - - +
160A THR* 4.0 16.8 - - + +
175A ASN* 1.3 74.8 - - - +
177A VAL* 1.3 62.4 + - - +
178A ASN* 3.7 11.0 - - - +
222A LEU* 4.0 4.5 - - - +
233A SER 2.8 14.7 + - - +
234A THR* 3.5 11.1 - - + -
235A LEU* 2.9 26.5 + - - +
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Residues in contact with VAL 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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132A VAL* 4.2 4.0 - - + +
133A ASN 3.0 10.2 + - - +
134A VAL* 3.9 26.5 - - + -
135A SER* 2.8 28.2 + - - -
176A ALA* 1.3 70.8 - - - +
178A ASN* 1.3 61.3 + - - +
179A PRO* 3.4 5.2 - - + +
215A VAL* 4.5 9.0 - - + -
218A ALA* 3.9 30.3 - - + -
219A ILE* 4.0 16.4 - - + +
222A LEU* 3.6 26.7 - - + -
235A LEU* 3.5 9.0 - - + +
237A VAL* 4.9 3.8 - - + -
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Residues in contact with ASN 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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135A SER* 3.5 4.3 + - - -
136A SER 3.1 16.3 + - - +
137A GLN 3.8 2.4 + - - -
139A SER* 3.0 26.9 + - - -
157A ASP* 3.4 16.0 + - - -
176A ALA* 3.7 3.8 - - - +
177A VAL* 1.3 79.1 - - - +
179A PRO* 1.3 66.4 - - - +
180A THR 3.8 0.3 + - - -
234A THR* 3.2 25.0 - - - +
235A LEU 2.9 12.9 + - - +
236A PRO* 3.7 2.5 - - + +
237A VAL* 3.0 19.6 + - - +
238A GLU* 3.9 6.8 - - - +
242A TRP* 3.5 27.4 - - + -
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Residues in contact with PRO 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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19A ILE* 4.7 3.1 - - + -
134A VAL* 4.6 6.5 - - + -
135A SER 3.5 15.9 - - - +
136A SER* 4.0 0.4 + - - -
137A GLN* 2.9 20.7 + - - +
177A VAL* 3.4 9.9 - - + +
178A ASN* 1.3 88.3 - - - +
180A THR* 1.3 71.3 + - - +
182A VAL* 4.2 5.2 - - + -
210A ALA* 5.1 0.2 - - + -
215A VAL* 4.0 39.9 - - + -
237A VAL* 3.4 14.6 - - + +
245A NAP 3.3 21.2 - - + -
247A 2HP 4.7 0.3 + - - -
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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