Contacts of the strand formed by residues 216 - 221 (chain B) in PDB entry 5H1C
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 TYR 216 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155B GLY* 3.7 2.1 - - - -
156B LYS* 2.0 77.4 - - + +
157B ALA* 3.0 11.0 - - - -
158B MET* 2.0 52.3 - - + -
188B ASN* 5.2 3.3 - - + -
189B VAL 5.3 0.9 + - - -
190B ALA* 3.6 20.5 + - + +
210B MET* 4.6 29.6 - - + +
211B MET* 4.2 12.5 - - + +
214B SER* 2.9 16.8 + - - -
215B ARG* 1.3 78.5 - - - +
217B ALA* 1.3 52.6 + - - +
218B LEU 4.7 0.4 - - - +
261B VAL* 2.3 34.0 - - + +
86C PHE* 6.3 0.7 - + - -
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Residues in contact with ALA 217 (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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102B ILE* 4.8 1.6 - - + -
144B CYS* 3.6 26.0 - - + +
153B GLY* 4.8 8.5 - - - -
155B GLY* 2.9 31.5 - - - +
156B LYS 2.7 9.3 + - - -
157B ALA* 5.3 0.2 - - + -
216B TYR* 1.3 70.7 - - - +
218B LEU* 1.3 50.5 - - - +
261B VAL* 1.5 59.7 - - - +
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Residues in contact with LEU 218 (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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102B ILE* 5.6 0.4 - - + -
117B ILE* 5.9 0.2 - - + -
140B LEU* 4.0 19.3 - - + +
141B ALA* 4.9 1.1 - - - -
144B CYS* 3.7 29.6 - - - -
156B LYS 4.0 2.4 + - - -
157B ALA* 3.8 6.4 - - + +
158B MET* 3.2 29.9 + - - +
216B TYR* 5.7 0.2 - - - -
217B ALA* 1.3 78.3 - - - +
219B LEU* 1.3 73.9 + - - +
220B ILE* 3.5 28.8 - - + +
261B VAL* 2.1 9.0 - - - +
262B ALA* 3.0 45.3 - - + +
264B VAL* 3.3 17.0 - - + -
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Residues in contact with LEU 219 (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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158B MET* 3.6 37.5 - - + +
160B ILE* 4.1 23.8 - - + -
204B LEU* 5.2 2.9 - - + -
207B ALA* 4.8 8.3 - - + -
211B MET* 5.8 4.5 - - + -
218B LEU* 1.3 77.4 - - - +
220B ILE* 1.3 62.4 + - - +
221B VAL* 5.4 3.6 - - + -
252B LEU* 4.7 12.8 - - + -
255B LEU* 3.5 35.9 - - + -
261B VAL* 3.7 3.6 - - + +
262B ALA 2.7 16.8 + - - +
263B VAL* 4.8 12.1 - - + -
264B VAL 3.1 22.8 + - - -
86C PHE* 6.1 0.4 - - + -
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Residues in contact with ILE 220 (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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137B CYS* 3.3 57.0 - - + +
140B LEU* 4.8 0.7 - - + -
141B ALA* 3.9 16.2 - - + +
157B ALA* 5.9 2.2 - - + -
158B MET 3.3 9.2 + - - +
159B TYR* 3.8 24.9 - - + -
160B ILE* 3.0 27.6 + - - +
218B LEU* 3.5 29.6 - - + +
219B LEU* 1.3 77.6 - - - +
221B VAL* 1.3 76.2 + - - +
222B ASP 4.4 0.2 - - - +
264B VAL* 4.0 12.1 - - + -
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Residues in contact with VAL 221 (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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160B ILE* 3.7 31.4 - - + +
162B THR* 4.8 6.1 - - + -
200B GLN* 5.2 1.8 - - - +
204B LEU* 6.3 0.2 - - + -
219B LEU* 5.4 4.7 - - + -
220B ILE* 1.3 84.7 - - - +
222B ASP* 1.3 57.1 + - - +
223B SER 3.9 3.1 - - - +
224B ALA* 3.4 38.1 - - + +
248B PHE* 5.0 13.7 - - + -
252B LEU* 5.6 10.5 - - + -
263B VAL* 6.0 2.5 - - + -
264B VAL 2.9 18.1 + - - +
265B ILE* 3.6 2.4 - - + -
266B THR* 2.8 30.8 + - - -
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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