Contacts of the strand formed by residues 295 - 300 (chain B) 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 295 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A SER* 5.0 5.2 - - - +
252B ILE* 4.9 6.1 - - + -
253B ALA* 3.9 35.4 - - + +
255B TYR* 3.0 31.7 - - + -
288B ALA* 5.0 6.0 - - + +
289B ALA 4.5 0.2 - - - -
290B SER* 3.3 27.8 - - - +
292B GLY* 5.8 3.6 - - - +
294B ASN* 1.3 87.3 + - - +
296B SER* 1.3 62.7 + - - +
297B VAL* 3.1 7.4 + - + +
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Residues in contact with SER 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A PRO* 4.4 7.4 - - - -
101A ASP* 5.3 3.6 - - - -
102A ARG* 5.5 3.8 - - - -
104A VAL* 3.5 29.1 - - - +
255B TYR* 3.4 20.3 + - - -
289B ALA* 2.5 63.4 + - - +
291B ASP* 3.5 6.9 + - - -
294B ASN* 3.7 3.7 - - - +
295B LEU* 1.3 71.9 - - - +
297B VAL* 1.3 55.9 + - - +
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Residues in contact with VAL 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A PRO* 4.4 1.2 - - - +
101A ASP* 2.9 29.0 + - - +
252B ILE* 3.8 24.0 - - + -
255B TYR* 3.9 5.1 - - + -
256B TYR* 3.4 30.5 + - + +
266B ILE* 3.7 21.1 - - + -
286B ILE* 3.6 30.3 - - + -
287B LEU 3.9 1.8 - - - +
288B ALA* 4.0 13.2 - - + +
289B ALA* 4.9 0.2 - - - -
295B LEU* 3.8 10.3 - - + +
296B SER* 1.3 74.9 - - - +
298B ILE* 1.3 65.4 + - - +
299B VAL* 5.3 1.3 - - + -
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Residues in contact with ILE 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 6.0 0.2 - - + -
67A VAL* 4.3 12.6 - - + -
87A LEU* 5.2 2.0 - - + -
98A ILE* 3.5 45.3 - - + -
99A VAL 5.0 3.4 - - - +
100A PRO* 5.1 2.9 - - + -
110A LEU* 4.7 9.0 - - + -
266B ILE* 3.5 22.9 - - - +
267B VAL* 3.9 23.7 + - + -
287B LEU* 3.4 35.1 + - + +
289B ALA* 3.8 22.9 - - + +
297B VAL* 1.3 76.2 - - - +
299B VAL* 1.3 72.9 + - - +
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Residues in contact with VAL 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A VAL 2.9 23.6 + - - +
101A ASP* 3.4 29.6 + - - +
256B TYR* 5.4 0.2 - - - +
264B LYS* 3.6 29.6 - - + +
265B LYS* 2.9 25.4 - - + +
266B ILE* 4.0 2.7 - - + -
297B VAL* 3.6 3.4 + - + +
298B ILE* 1.3 83.0 - - - +
300B PRO* 1.3 83.1 - - + +
301B ASP* 3.7 1.6 + - - +
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Residues in contact with PRO 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ALA* 5.2 5.6 - - + -
91A ASP* 5.8 2.7 - - - +
96A SER* 4.2 22.9 - - - +
97A VAL 4.4 8.3 - - - +
98A ILE* 5.6 2.9 - - + -
219B VAL* 4.5 14.1 - - + -
265B LYS* 3.1 43.2 - - + +
266B ILE* 4.7 1.8 - - - +
267B VAL* 4.9 7.8 - - + -
298B ILE* 4.8 1.3 - - - +
299B VAL* 1.3 98.0 - - + +
301B ASP* 1.3 66.1 + - - +
302B ARG 4.4 8.2 - - - +
304B VAL* 6.3 0.2 - - + -
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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