Contacts of the strand formed by residues 95 - 100 (chain A) in PDB entry 1PYB
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 LEU 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A ILE* 4.1 17.3 - - + +
53A ALA* 4.0 30.1 - - + +
55A TYR* 3.0 31.9 - - + -
56A TYR* 3.0 11.1 - - - -
88A ALA* 5.3 9.4 - - + -
89A ALA 3.8 2.0 - - - -
90A SER* 4.1 26.7 - - - +
93A GLU 3.8 8.9 + - - +
94A ASN* 1.3 71.3 - - - +
96A SER* 1.3 61.5 + - - +
97A VAL* 4.6 1.2 - - - +
311B SER* 4.4 8.5 - - - +
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Residues in contact with SER 96 (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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55A TYR* 4.6 3.8 - - - -
56A TYR* 3.8 9.6 - - - -
88A ALA* 3.7 3.5 - - - +
89A ALA* 2.7 65.7 + - - +
91A ASP* 2.8 15.6 + - - -
94A ASN 3.4 1.6 + - - -
95A LEU* 1.3 75.0 - - - +
97A VAL* 1.3 62.7 + - - +
300B PRO* 4.2 20.9 - - - +
301B ASP 5.1 1.6 - - - -
302B ARG* 4.7 11.0 - - - -
304B VAL* 5.1 2.5 - - - -
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Residues in contact with VAL 97 (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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52A ILE* 3.9 20.2 - - + -
56A TYR* 3.3 40.9 + - + +
61A LEU* 5.0 2.5 - - + -
64A LYS* 4.0 9.9 - - + -
66A ILE* 3.6 41.5 - - + -
86A ILE* 5.2 3.8 - - + -
87A LEU 4.7 2.9 - - - +
88A ALA* 5.0 5.4 - - + +
89A ALA* 5.5 0.4 - - - -
95A LEU 4.6 0.9 - - - +
96A SER* 1.3 75.3 - - - +
98A ILE* 1.3 64.1 + - - +
99A VAL* 3.3 8.4 + - + -
300B PRO* 4.4 3.2 - - - +
301B ASP* 3.0 28.7 + - - +
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Residues in contact with ILE 98 (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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66A ILE* 3.4 22.6 - - + +
67A VAL* 3.5 27.5 + - + +
87A LEU* 3.3 46.1 + - + +
89A ALA* 4.5 14.4 - - + +
97A VAL* 1.3 73.2 - - - +
99A VAL* 1.3 66.7 + - - +
217B LEU* 6.3 0.2 - - + -
267B VAL* 4.6 9.6 - - + -
287B LEU* 5.6 3.1 - - + -
298B ILE* 3.5 37.5 - - + -
299B VAL 5.4 0.9 - - - -
300B PRO* 5.6 3.1 - - + -
310B LEU* 4.2 17.9 - - + -
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Residues in contact with VAL 99 (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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64A LYS* 3.6 28.9 - - + +
65A LYS* 3.2 27.8 - - + +
97A VAL* 3.3 9.2 + - + -
98A ILE* 1.3 83.6 - - - +
100A PRO* 1.3 80.2 - - + +
298B ILE* 5.0 1.1 - - - +
299B VAL 2.9 28.2 + - - +
301B ASP* 3.1 33.5 + - - +
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Residues in contact with PRO 100 (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 VAL* 5.0 5.8 - - + -
65A LYS* 3.3 25.6 - - + +
67A VAL* 5.0 12.5 - - + -
98A ILE 4.6 1.1 - - - +
99A VAL* 1.3 99.4 - - + +
101A ASP* 1.3 65.3 + - - +
102A ARG 3.5 6.4 + - - +
104A VAL* 3.5 37.5 - - + -
289B ALA* 4.5 11.4 - - + -
296B SER* 4.4 9.9 - - - -
297B VAL 4.4 7.9 - - - +
298B ILE* 5.1 3.1 - - - -
301B ASP* 5.3 0.9 - - - +
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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