Contacts of the strand formed by residues 151 - 156 (chain B) in PDB entry 4DOH
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 HIS 151 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146B THR 3.6 0.3 - - - +
147B LYS* 3.3 7.5 - - - -
148B ASP* 3.0 47.9 + - + +
149B GLY 3.1 3.4 - - - -
150B PHE* 1.3 79.4 - - - +
152B LEU* 1.3 62.6 + - - +
153B VAL* 3.7 4.0 + - + +
191B HIS* 3.0 31.6 + + + -
193B GLU 3.7 1.3 - - - -
194B THR* 3.6 21.4 + - + +
195B MET* 4.8 1.3 - - - -
194R TRP* 4.0 23.0 - + - +
205R LEU* 5.4 2.5 - - + -
206R THR 2.8 34.4 + - - -
207R TRP 3.6 14.1 + - - -
208R LEU* 3.8 12.7 - - + +
214R TYR* 5.9 0.9 - + - -
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Residues in contact with LEU 152 (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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145B ILE* 3.4 30.5 - - + -
146B THR 3.5 6.3 - - - +
147B LYS* 5.1 0.9 - - + +
150B PHE 3.7 1.8 + - - -
151B HIS* 1.3 70.0 - - - +
153B VAL* 1.3 61.1 + - - +
169B TYR* 4.6 7.9 - - + -
191B HIS* 3.7 1.9 - - - -
192B LEU* 2.7 47.0 + - + +
193B GLU* 2.9 23.8 + - + +
195B MET* 4.0 16.1 - - + -
201B TYR* 4.2 23.3 - - + -
203B VAL* 3.8 26.5 - - + -
224B VAL* 4.0 16.6 - - + -
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Residues in contact with VAL 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B ILE* 3.4 7.8 - - - +
146B THR* 2.8 51.3 + - - +
148B ASP* 5.1 3.6 - - + +
151B HIS* 3.9 11.4 - - + +
152B LEU* 1.3 81.7 - - - +
154B ILE* 1.3 66.6 + - - +
155B GLU* 5.9 0.4 - - + -
189B PRO* 4.0 27.1 - - + -
190B VAL 3.3 13.0 - - - +
191B HIS* 4.2 5.4 - - + -
192B LEU* 4.4 1.3 - - - +
193R THR 5.0 1.3 - - - +
194R TRP* 3.9 35.4 - - + +
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Residues in contact with ILE 154 (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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143B MET* 3.4 47.1 - - + -
144B GLU 3.6 9.4 - - - +
145B ILE* 4.7 3.6 - - + -
153B VAL* 1.3 77.8 - - - +
155B GLU* 1.3 64.3 + - - +
156B LEU* 3.9 29.1 - - + +
167B VAL* 4.5 11.7 - - + -
183B VAL* 4.7 4.9 - - + -
188B ILE 3.6 1.6 - - - +
189B PRO* 3.4 0.3 - - - +
190B VAL* 2.8 49.6 + - + +
192B LEU* 3.8 33.7 - - + -
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Residues in contact with GLU 155 (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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143B MET 3.9 0.9 - - - -
144B GLU* 3.2 59.1 + - - +
153B VAL* 5.9 0.2 - - + -
154B ILE* 1.3 78.1 - - - +
156B LEU* 1.3 64.9 + - - +
186B GLY 3.8 5.7 - - - +
187B GLY* 2.7 22.5 - - - +
188B ILE 3.2 21.1 - - - +
189B PRO* 4.2 17.7 - - + +
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Residues in contact with LEU 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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141B PRO* 4.6 1.8 - - + -
142B GLY 3.5 14.1 - - - +
143B MET* 4.2 1.8 - - + -
154B ILE* 3.9 26.7 - - + -
155B GLU* 1.3 80.8 - - - +
157B GLU* 1.3 62.9 + - - +
158B ASP 3.3 0.3 + - - -
165B PHE* 3.8 50.0 - - + -
167B VAL* 5.5 2.0 - - + -
183B VAL* 3.9 29.4 - - + -
185B SER 4.8 0.8 + - - +
186B GLY* 2.5 33.4 + - - +
188B ILE 4.4 1.6 + - - -
205B ALA* 3.7 28.9 - - + -
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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