Contacts of the strand formed by residues 169 - 175 (chain A) in PDB entry 1PPD
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 ASN 169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A ILE* 3.5 23.4 - - - +
168A PRO* 1.3 86.0 - - + +
170A TYR* 1.3 76.7 + - - +
190A LYS* 3.3 29.6 - - - +
191A ARG* 3.1 27.8 + - - +
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Residues in contact with TYR 170 (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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4A TYR* 3.7 24.1 - + - -
5A VAL 5.6 0.4 + - - -
148A ILE* 4.2 13.7 - - + -
166A TYR* 3.3 12.5 + - - +
167A GLY* 2.9 53.0 + - - +
168A PRO* 4.4 3.8 - - + -
169A ASN* 1.3 97.6 - - - +
171A ILE* 1.3 69.0 + - - +
172A LEU* 4.4 10.8 - - + -
188A ARG* 3.7 50.9 - - + -
189A ILE 3.0 15.0 - - - +
191A ARG* 3.7 6.1 - - - +
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Residues in contact with ILE 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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118A GLN* 5.1 0.7 - - + -
121A LEU* 4.0 12.3 - - + -
122A LEU* 4.0 27.6 - - + -
125A ILE* 3.8 14.8 - - + -
163A ALA* 3.9 3.1 - - + -
165A GLY 3.7 10.1 - - - +
166A TYR* 4.2 1.6 - - + -
170A TYR* 1.3 79.3 - - - +
172A LEU* 1.3 62.8 - - - +
173A ILE* 3.7 27.6 + - + +
187A ILE 3.5 2.4 - - - +
188A ARG* 3.4 2.6 - - - -
189A ILE* 2.7 34.5 + - - +
191A ARG* 4.2 9.0 - - + -
202A LEU* 3.9 21.8 - - + -
203A TYR* 3.8 28.7 - - + +
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Residues in contact with LEU 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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5A VAL 4.9 1.1 - - - +
6A ASP* 3.7 22.2 - - + +
8A ARG* 3.7 28.3 - - - +
163A ALA* 3.4 4.7 - - - +
164A VAL* 2.8 48.9 + - + +
165A GLY* 2.8 25.1 + - - +
166A TYR 4.2 1.3 - - - +
170A TYR* 4.1 11.6 - - + -
171A ILE* 1.3 70.5 - - - +
173A ILE* 1.3 62.8 + - - +
183A GLU* 5.6 1.1 - - - +
186A TYR* 4.1 21.1 - - + -
187A ILE 3.6 3.8 - - - +
188A ARG* 3.9 23.6 - - + -
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Residues in contact with ILE 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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132A VAL* 3.6 20.4 - - + -
134A LEU* 5.1 1.3 - - + -
161A VAL* 3.4 32.5 - - + -
162A ALA 3.2 6.1 - - - +
163A ALA* 3.6 29.6 - - + -
171A ILE* 3.8 20.2 - - + +
172A LEU* 1.3 75.7 - - - +
174A LYS* 1.3 66.4 + - - +
175A ASN* 3.7 0.6 + - - +
186A TYR* 3.2 12.2 - - - -
187A ILE* 2.8 54.4 + - + +
189A ILE* 4.5 12.6 - - + -
202A LEU* 4.1 9.2 - - + -
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Residues in contact with LYS 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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13A VAL* 3.7 19.8 - - + +
14A THR* 2.8 41.4 + - - +
15A PRO 3.2 14.6 + - - -
16A VAL* 4.0 15.5 - - + +
17A LYS* 4.4 6.1 - - - +
32A VAL* 3.9 27.4 - - + +
35A GLU* 4.2 6.3 + - - -
161A VAL* 3.6 5.5 - - - +
162A ALA* 2.7 36.7 + - + +
164A VAL* 4.2 8.2 - - + +
172A LEU 4.4 0.4 + - - -
173A ILE* 1.3 71.5 - - - +
175A ASN* 1.3 69.2 + - - +
186A TYR* 3.5 24.2 - - + -
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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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16A VAL* 3.8 18.7 - - - +
17A LYS 4.2 1.6 + - - +
141A PHE* 4.2 4.7 - - - -
159A HIS* 2.8 27.4 + - - -
161A VAL* 3.3 11.1 - - + +
173A ILE* 3.7 5.2 + - + -
174A LYS* 1.3 84.2 - - - +
176A SER* 1.3 70.8 + - - +
177A TRP* 3.3 43.0 - - - +
181A TRP* 3.4 32.7 - - + -
185A GLY 3.1 18.6 + - - +
187A ILE* 5.1 0.4 - - + -
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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