Contacts of the strand formed by residues 163 - 168 (chain A) in PDB entry 1PYD
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 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A VAL 3.3 4.2 + - - -
96A LEU* 3.8 4.7 - - + +
97A HIS* 3.0 30.4 + - - +
133A SER* 4.5 2.5 - - - -
134A GLU* 4.7 0.9 - - + -
135A THR* 3.1 31.0 - - + +
152A CYS* 3.4 34.1 - - + +
155A THR* 4.1 15.3 - - + -
156A THR* 3.2 39.7 - - - +
161A ARG 4.0 0.9 - - - +
162A PRO* 1.3 81.2 - - - +
164A TYR* 1.3 64.1 + - - +
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Residues in contact with TYR 164 (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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74A PHE* 5.9 0.2 - - - -
78A GLU* 2.5 36.8 + - - -
97A HIS* 3.5 13.9 - - - -
99A VAL* 3.5 23.3 - - + +
101A VAL* 4.9 2.4 - - - +
126A HIS* 3.7 40.6 + + - +
129A SER* 3.5 28.7 - - - -
133A SER* 4.3 7.7 - - - +
135A THR 3.3 3.6 + - - -
136A THR* 3.2 18.4 - - + -
137A ALA* 2.8 35.7 + - - +
138A MET* 3.8 21.9 - - + +
163A VAL* 1.3 79.7 - - - +
165A LEU* 1.3 55.6 - - - +
166A GLY* 3.9 10.5 - - - -
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Residues in contact with LEU 165 (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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10A LEU* 4.1 19.7 - - + -
96A LEU* 4.0 24.2 - - + -
97A HIS 3.0 9.8 + - - +
98A VAL* 3.2 19.0 - - + +
99A VAL 3.0 24.5 + - - -
137A ALA* 3.5 5.2 - - + -
139A ILE* 3.5 30.1 - - + -
149A ILE* 4.1 26.9 - - + +
152A CYS* 4.1 16.8 - - + -
164A TYR* 1.3 74.3 - - - +
166A GLY* 1.3 70.1 + - - +
167A LEU* 4.5 10.3 - - + -
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Residues in contact with GLY 166 (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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99A VAL 3.4 9.4 - - - -
101A VAL* 4.5 2.0 - - - -
137A ALA 2.9 12.2 + - - -
138A MET* 3.9 23.1 - - - -
139A ILE* 3.0 27.5 + - - +
164A TYR* 3.9 9.8 - - - -
165A LEU* 1.3 77.8 - - - +
167A LEU* 1.3 58.0 + - - -
168A PRO* 4.1 3.4 - - - -
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Residues in contact with LEU 167 (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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6A LEU* 4.2 26.0 - - + -
7A GLY* 5.8 1.6 - - - -
10A LEU* 4.6 8.3 - - + -
33A LEU* 3.9 22.0 - - + -
98A VAL* 3.8 26.9 - - + -
99A VAL 3.0 12.4 + - - +
100A GLY* 3.5 6.7 - - - -
101A VAL* 3.3 16.4 + - - +
139A ILE* 4.4 22.2 - - + -
149A ILE* 4.7 8.3 - - + -
165A LEU* 4.5 5.4 - - + +
166A GLY* 1.3 70.7 - - - -
168A PRO* 1.3 75.3 - - + +
169A ALA* 4.4 0.5 - - - -
171A LEU* 5.4 1.8 - - + -
172A VAL* 3.6 25.2 - - + +
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Residues in contact with PRO 168 (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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101A VAL* 3.4 20.0 - - + +
102A PRO 3.7 15.3 - - - +
104A ILE* 3.8 17.5 - - + +
138A MET* 4.7 5.4 - - + -
139A ILE 2.8 31.4 - - - +
140A THR* 5.6 0.7 - - + -
166A GLY 4.0 3.1 - - - +
167A LEU* 1.3 89.4 - - + +
169A ALA* 1.3 64.8 - - - +
170A ASN* 3.3 19.1 + - - +
171A LEU* 3.6 14.4 + - + +
172A VAL* 3.2 14.9 + - - +
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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