Contacts of the strand formed by residues 156 - 161 (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 LYS 156 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145B GLN* 5.3 0.7 - - - +
154B GLU 4.1 1.6 + - - +
155B GLY* 1.3 69.1 - - - -
157B ALA* 1.3 53.4 + - - +
188B ASN* 3.3 41.2 - - - +
214B SER* 3.2 33.0 + - - +
215B ARG 3.6 4.3 + - - +
216B TYR* 2.0 71.7 - - + +
217B ALA 2.7 17.2 + - - -
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Residues in contact with ALA 157 (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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141B ALA* 3.9 29.8 - - + +
144B CYS* 5.0 4.3 - - + -
145B GLN* 5.3 2.8 - - + +
155B GLY 3.4 4.9 + - - +
156B LYS* 1.3 73.6 - - - +
158B MET* 1.3 58.0 + - - +
159B TYR* 5.5 0.9 - - + -
188B ASN* 4.3 1.0 - - - +
189B VAL* 2.9 24.0 + - + +
190B ALA 2.8 28.6 + - - -
216B TYR* 3.0 2.6 - - - -
218B LEU* 3.8 19.3 - - + +
220B ILE* 5.9 2.0 - - + -
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Residues in contact with MET 158 (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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157B ALA* 1.3 71.7 - - - +
159B TYR* 1.3 61.4 + - - +
160B ILE* 4.0 3.1 + - + -
190B ALA* 3.7 15.9 - - + +
207B ALA* 4.8 12.6 - - - +
210B MET* 5.1 1.3 - - + -
211B MET* 3.2 27.8 - - - +
216B TYR* 2.0 79.4 - - + +
218B LEU 3.2 11.3 + - - +
219B LEU* 3.6 31.0 - - + +
220B ILE* 3.3 22.5 + - - +
261B VAL* 5.9 0.9 - - + -
86C PHE* 5.1 13.2 - - + -
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Residues in contact with TYR 159 (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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134B THR* 4.9 2.6 - - - -
137B CYS* 4.2 18.5 - - + +
138B HIS* 4.3 10.0 + + - -
141B ALA* 5.0 7.4 - - + -
157B ALA* 4.2 1.3 - - + +
158B MET* 1.3 74.7 - - - +
160B ILE* 1.3 58.7 + - - +
161B ASP* 3.1 21.6 + - + -
165B THR* 4.8 1.7 + - - -
166B PHE* 3.2 52.9 + + + +
189B VAL* 4.8 13.0 - - + -
190B ALA 3.3 7.2 + - - -
191B TYR* 3.9 13.7 - + - -
192B ALA 3.1 22.3 + - - -
220B ILE* 3.8 40.8 - - + -
222B ASP* 4.3 21.1 + - + +
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Residues in contact with ILE 160 (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* 4.0 1.5 + - + -
159B TYR* 1.3 72.7 - - - +
161B ASP* 1.3 67.5 + - - +
162B THR* 3.8 10.5 + - + +
192B ALA* 3.6 13.9 - - + +
194B ALA* 4.6 0.7 - - + -
200B GLN* 5.4 6.3 - - + +
203B LEU* 4.2 37.9 - - + +
204B LEU* 4.6 19.1 - - + -
207B ALA* 5.4 0.7 - - + -
219B LEU* 4.1 24.5 - - + -
220B ILE 3.0 14.9 + - - +
221B VAL* 3.7 37.6 - - + +
222B ASP 4.0 2.3 + - - -
248B PHE* 6.4 0.7 - - + -
86C PHE* 4.9 9.0 - - + -
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Residues in contact with ASP 161 (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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159B TYR* 3.1 31.2 + - + -
160B ILE* 1.3 73.9 - - - +
162B THR* 1.3 79.3 + - - +
163B GLU* 2.6 14.2 + - - +
164B GLY* 3.0 13.4 + - - -
165B THR* 2.7 30.5 + - - -
166B PHE* 2.8 15.7 + - - +
191B TYR* 3.5 17.4 - - + +
192B ALA 3.0 10.3 + - - +
193B ARG* 3.7 2.7 - - - -
194B ALA* 3.2 23.2 + - - +
222B ASP* 4.4 8.0 - - - +
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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