Contacts of the strand formed by residues 151 - 156 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147D LYS* 3.5 6.6 - - - -
148D ASP* 2.9 44.8 + - + +
149D GLY 3.3 0.4 - - - -
150D PHE* 1.3 78.8 - - - +
152D LEU* 1.3 62.2 + - - +
153D VAL* 3.9 3.3 + - + +
191D HIS* 3.1 31.5 + - + +
193D GLU 3.7 1.3 - - - -
194D THR* 3.5 19.8 - - + +
195D MET* 4.7 1.3 - - - -
194E TRP* 4.0 32.0 - + + +
205E LEU* 5.2 2.2 - - + -
206E THR 2.7 34.9 + - - -
207E TRP 3.2 18.0 + - - -
208E LEU* 3.9 14.1 - - + +
214E TYR* 5.5 0.4 - - - -
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Residues in contact with LEU 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D ILE* 3.7 21.1 - - + -
146D THR 3.6 11.4 - - - +
147D LYS* 5.1 0.9 - - - +
150D PHE 3.7 1.2 + - - -
151D HIS* 1.3 73.6 - - - +
153D VAL* 1.3 69.4 + - - +
169D TYR* 4.8 6.5 - - + -
191D HIS* 3.8 2.3 - - - -
192D LEU* 2.8 39.5 + - + -
193D GLU* 2.9 23.3 + - + +
195D MET* 4.0 14.8 - - + -
201D TYR* 4.0 26.2 - - + -
203D VAL* 3.7 23.8 - - + -
224D VAL* 4.2 19.7 - - + -
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Residues in contact with VAL 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D ILE* 3.5 7.0 - - - +
146D THR* 2.9 52.1 + - - +
148D ASP* 5.6 2.2 - - + +
151D HIS 4.5 6.5 - - - +
152D LEU* 1.3 83.4 - - - +
154D ILE* 1.3 65.3 + - - +
189D PRO* 4.2 23.1 - - + -
190D VAL 3.2 14.8 - - - +
191D HIS* 3.8 5.6 - - + -
192D LEU* 4.3 2.7 - - - +
193E THR 4.7 2.9 - - - +
194E TRP* 3.6 37.5 - - + +
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Residues in contact with ILE 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143D MET* 3.6 42.2 - - + -
144D GLU 3.4 10.8 - - - +
145D ILE* 5.0 4.7 - - + -
153D VAL* 1.3 76.7 - - - +
155D GLU* 1.3 63.4 + - - +
156D LEU* 4.0 29.8 - - + +
167D VAL* 4.6 11.9 - - + -
183D VAL* 4.8 4.7 - - + -
188D ILE 3.3 1.7 - - - +
189D PRO* 3.3 2.8 - - - +
190D VAL* 2.8 46.0 + - + +
192D LEU* 3.9 28.7 - - + -
203D VAL* 4.5 7.0 - - + -
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Residues in contact with GLU 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D GLY 4.9 0.2 - - - -
143D MET 3.9 0.3 - - - -
144D GLU* 2.8 67.6 + - + +
153D VAL* 6.1 0.2 - - + -
154D ILE* 1.3 76.2 - - - +
156D LEU* 1.3 66.2 + - - +
186D GLY 3.8 12.0 - - - +
187D GLY* 3.2 20.8 - - - +
188D ILE 3.8 9.0 - - - +
189D PRO* 3.5 23.4 - - + +
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Residues in contact with LEU 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D PRO* 4.7 1.8 - - + -
142D GLY 3.6 12.1 - - - +
143D MET* 4.7 2.7 - - + -
154D ILE* 4.0 24.2 - - + +
155D GLU* 1.3 80.3 - - - +
157D GLU* 1.3 64.2 + - - +
158D ASP 3.4 0.9 + - - -
165D PHE* 3.6 45.8 - - + -
167D VAL* 5.7 1.6 - - + -
183D VAL* 3.6 36.6 - - + -
185D SER 4.8 1.3 + - - +
186D GLY* 2.5 32.9 + - - +
188D ILE 4.6 1.4 + - - +
205D ALA* 3.9 25.6 - - + -
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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