Contacts of the strand formed by residues 155 - 160 (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 LYS 155 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154B GLY* 1.3 73.0 - - - -
156B ILE* 1.3 64.5 + - - +
186B ASP 4.7 4.0 + - - -
187B ASN* 3.4 45.3 - - + +
189B LEU* 5.5 2.6 - - + +
216B ILE* 3.0 23.8 + - + +
217B PHE* 3.3 38.4 - - + +
218B LYS* 2.7 30.3 + - - -
219B LEU 3.5 2.4 + - - -
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Residues in contact with ILE 156 (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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139B LEU 4.1 2.5 - - - +
140B CYS* 3.5 26.2 - - - +
143B ALA* 3.6 26.5 - - + -
144B GLN* 3.7 8.1 - - + +
154B GLY 3.6 14.4 - - - +
155B LYS* 1.3 82.7 - - - +
157B ILE* 1.3 83.5 - - - +
158B PHE* 4.4 1.1 - - + +
187B ASN 2.9 13.2 + - - +
188B VAL* 3.3 15.1 - - + -
189B LEU 2.8 24.6 + - - -
217B PHE* 3.7 3.7 - - - -
219B LEU* 3.6 20.9 - - + -
221B ILE* 4.0 17.9 - - + -
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Residues in contact with ILE 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A PHE* 3.4 28.9 - - + -
156B ILE* 1.3 82.3 - - - +
158B PHE* 1.3 64.0 + - - +
159B ILE* 4.7 0.9 - - + -
189B LEU* 3.4 13.2 - - + +
205B TYR* 6.4 1.3 - - + -
206B VAL* 3.7 29.8 - - + -
209B LYS* 4.6 9.9 - - + -
210B PHE* 3.8 22.2 - - + -
217B PHE* 3.7 22.7 - - + -
219B LEU 2.9 12.2 + - - +
220B LEU* 3.5 12.7 - - + -
221B ILE 2.7 32.6 + - - +
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Residues in contact with PHE 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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85A PHE* 4.5 0.2 - - - -
136B SER* 3.9 30.7 - - - -
137B HIS* 4.8 3.4 - + - -
140B CYS* 3.5 29.4 - - - -
156B ILE* 4.8 0.4 - - + -
157B ILE* 1.3 75.0 - - - +
159B ILE* 1.3 77.3 - - - +
160B ASP* 4.1 13.7 - - + -
165B PHE* 3.8 32.1 - + + -
188B VAL* 4.1 13.2 - - + -
189B LEU 2.6 14.7 + - - +
190B TYR* 3.3 16.4 - + + -
191B ALA 3.0 25.3 + - - +
221B ILE* 3.7 17.5 - - + -
223B ASP* 4.1 18.2 - - + -
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Residues in contact with ILE 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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85A PHE* 4.0 22.2 - - + -
157B ILE* 4.7 1.8 - - + -
158B PHE* 1.3 76.6 - - - +
160B ASP* 1.3 60.3 + - - +
161B THR* 4.5 3.4 - - + -
191B ALA 3.3 7.0 - - - +
193B ALA* 4.0 25.1 - - + -
199B GLN* 4.7 5.6 - - + -
202B LEU* 4.1 26.2 - - + -
203B LEU* 4.2 29.6 - - + -
206B VAL* 4.5 4.3 - - + -
220B LEU* 4.3 11.4 - - + -
221B ILE 3.0 13.5 + - - +
222B ILE* 3.4 17.6 - - + +
223B ASP 2.9 27.2 + - - +
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Residues in contact with ASP 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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91A TYR* 5.2 0.2 + - - -
158B PHE* 4.1 7.0 - - + -
159B ILE* 1.3 72.5 - - - +
161B THR* 1.3 56.6 + - - +
162B GLU* 3.0 8.3 + - - +
163B ASN* 2.8 28.9 + - - -
164B THR* 3.3 9.0 + - - -
165B PHE* 2.8 28.7 + - - +
190B TYR* 2.4 44.2 + - + +
191B ALA 2.9 5.5 + - - +
192B ARG* 3.0 7.2 + - - -
193B ALA 2.7 31.0 + - - -
223B ASP* 3.3 7.1 - - - +
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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