Contacts of the strand formed by residues 252 - 256 (chain B) in PDB entry 1SID
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 252 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161B GLN* 2.8 15.7 + - - +
163B HIS* 4.5 6.6 + - - -
244B THR* 6.5 1.6 - - + -
250B PRO* 3.3 15.9 - - + +
251B PRO* 1.3 78.5 - - - +
253B LEU* 1.3 70.7 + - - +
254B GLN* 5.5 5.2 - - - +
286B MET* 4.3 1.0 - - - +
242C ASN* 4.6 2.9 - - - +
243C TYR* 3.0 17.3 - - - +
244C THR* 3.4 26.7 - - + -
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Residues in contact with LEU 253 (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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129B VAL* 3.7 44.9 - - + +
132B SER* 3.8 28.3 - - - +
163B HIS* 4.1 12.1 - - + +
252B VAL* 1.3 77.8 - - - +
254B GLN* 1.3 85.2 + - + +
255B PHE 4.1 0.4 - - - -
286B MET* 3.3 41.7 - - + -
302B LEU* 4.6 1.1 - - + -
242C ASN* 3.2 12.8 - - - +
243C TYR* 2.8 33.6 + - + +
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Residues in contact with GLN 254 (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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128B GLU* 3.8 12.3 - - - +
252B VAL* 5.5 3.8 - - - +
253B LEU* 1.3 96.5 + - + +
255B PHE* 1.3 64.5 + - - +
256B THR* 2.9 12.3 + - + +
241C GLY 3.5 11.1 - - - +
242C ASN* 3.6 13.2 + - - +
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Residues in contact with PHE 255 (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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128B GLU* 3.3 13.7 - - - -
129B VAL 3.5 7.6 - - - -
130B VAL* 3.3 25.8 - - + -
131B GLY 3.5 5.8 - - - -
132B SER* 3.1 45.8 - - - -
133B GLY 4.0 1.6 - - - -
253B LEU 4.1 1.4 + - - -
254B GLN* 1.3 73.1 - - - +
256B THR* 1.3 64.1 + - - +
162C TYR* 3.3 35.4 - + - -
164C VAL* 4.1 12.1 - - + -
228C HIS* 3.7 12.8 - - + -
229C PRO* 4.4 12.3 - - + -
239C TYR* 3.7 8.5 - - + -
240C PHE* 3.2 2.8 - - - -
241C GLY* 2.7 49.0 + - - +
242C ASN* 4.9 2.7 - - - -
243C TYR 5.5 0.2 - - - -
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Residues in contact with THR 256 (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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126B LYS* 5.7 2.3 - - - +
127B THR 4.6 5.0 - - - +
128B GLU* 3.1 23.3 - - - +
254B GLN* 2.9 11.9 + - + +
255B PHE* 1.3 75.3 + - - +
257B ASN* 1.3 55.0 + - - +
258B THR* 2.6 32.0 + - - +
259B LEU* 4.0 19.6 + - + +
239C TYR* 2.5 30.3 + - - -
240C PHE* 3.5 8.6 - - + -
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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