Contacts of the strand formed by residues 263 - 268 (chain B) in PDB entry 4HYY
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 ALA 263 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B PHE* 4.5 0.4 - - + -
101B ILE* 4.0 14.4 - - + -
116B ILE* 3.7 22.2 - - + +
117B GLU 3.6 15.5 - - - +
118B SER* 3.6 16.8 - - - +
218B LYS 2.8 15.6 + - - +
219B LEU* 3.3 5.6 - - + +
220B LEU 2.9 23.0 + - - -
262B VAL* 1.3 76.2 - - - +
264B VAL* 1.3 60.0 + - - +
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Residues in contact with VAL 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ILE* 4.9 1.6 - - - -
120B ALA 3.1 7.9 + - - +
121B ILE* 3.3 18.6 - - + -
122B THR* 2.8 33.9 + - - +
220B LEU* 3.2 23.8 - - + +
222B ILE* 4.9 1.8 - - + -
253B LEU* 4.1 19.3 - - + +
256B ILE* 5.4 0.2 - - + -
257B SER* 3.6 28.9 - - - +
262B VAL* 4.0 12.8 - - + -
263B ALA* 1.3 76.7 - - - +
265B PHE* 1.3 56.1 + - - +
266B VAL* 3.9 21.3 - - + -
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Residues in contact with PHE 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ILE* 4.1 25.1 - - + -
122B THR* 3.4 17.0 - - + -
124B ALA* 3.7 28.5 - - + -
132B LYS 4.5 1.1 - - - -
135B LEU* 3.5 31.9 - - + -
136B SER* 3.8 27.6 - - - -
139B LEU* 3.8 22.0 - - + -
219B LEU* 4.3 12.8 - - + -
220B LEU 3.0 6.2 + - - +
221B ILE* 3.3 16.8 - - + +
222B ILE 3.0 22.9 + - - -
263B ALA 4.2 0.4 - - - -
264B VAL* 1.3 71.8 - - - +
266B VAL* 1.3 65.8 + - - +
267B THR* 4.0 14.1 - - + -
301B ILE* 5.4 1.6 - - + -
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Residues in contact with VAL 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B ILE* 4.3 9.2 - - + -
122B THR 3.0 8.3 + - - +
123B GLU* 3.4 24.6 - - + -
124B ALA* 2.9 27.4 + - - +
222B ILE* 3.3 27.1 - - + +
225B ILE* 3.9 34.1 - - + -
250B LEU* 6.3 0.2 - - + -
253B LEU* 4.4 3.1 - - + -
264B VAL* 3.9 20.0 - - + -
265B PHE* 1.3 83.6 - - - +
267B THR* 1.3 64.8 + - - +
293B LEU* 5.2 3.1 - - + -
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Residues in contact with THR 267 (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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124B ALA* 3.3 8.3 - - + +
132B LYS* 3.7 31.6 - - + +
136B SER* 3.8 17.7 - - - +
221B ILE* 6.0 0.2 - - + -
222B ILE 3.2 4.4 + - - +
223B ASP* 2.6 33.5 + - + +
224B SER* 2.8 16.0 - - - -
225B ILE* 2.8 33.1 + - - +
265B PHE* 4.0 10.5 - - + -
266B VAL* 1.3 78.4 - - - +
268B ASN* 1.3 61.4 + - - +
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Residues in contact with ASN 268 (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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123B GLU* 3.0 30.4 - - - +
124B ALA 3.2 4.0 + - - -
125B PHE* 3.2 25.1 - - + +
126B GLY 4.0 0.2 + - - -
132B LYS* 3.6 11.2 - - - +
225B ILE* 3.7 19.9 - - + +
226B MET* 3.9 5.3 - - - +
267B THR* 1.3 79.1 - - - +
269B GLN* 1.3 76.0 + - - +
287B PRO* 4.1 2.3 - - - +
288B ILE* 3.0 54.8 + - - +
293B LEU* 3.5 2.6 - - - +
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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