Contacts of the strand formed by residues 162 - 169 (chain D) in PDB entry 3LZK
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 ILE 162 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144D VAL* 4.0 24.7 - - + -
145D ILE 4.0 3.4 - - - -
146D VAL* 4.3 3.8 - - + -
158D ALA 3.7 3.8 - - - +
159D LYS* 3.2 22.0 + - - +
160D ALA 4.3 0.9 - - - +
161D ALA* 1.3 75.8 - - - +
163D ARG* 1.3 71.6 + - - +
164D LEU 4.2 4.9 - - - +
165D VAL* 4.7 1.3 - - + -
203D PRO* 4.1 26.1 - - + +
210D TRP* 4.0 23.3 - - + -
212D GLY 4.3 6.3 - - - +
241D PHE* 4.1 14.8 - - + -
242D PRO* 4.4 4.3 - - + -
245D ILE* 3.6 31.2 - - + -
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Residues in contact with ARG 163 (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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39D LEU* 4.2 22.2 - - + -
42D TRP* 3.3 38.0 - - + +
145D ILE 2.9 11.1 + - - +
147D ASP* 2.8 49.5 + - + +
160D ALA 2.8 28.7 + - - -
161D ALA* 3.5 11.5 - - - +
162D ILE* 1.3 89.9 + - - +
164D LEU* 1.3 73.8 + - + +
202D THR* 3.6 6.8 - - - +
203D PRO* 3.2 20.3 - - - +
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Residues in contact with LEU 164 (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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3D LEU* 4.4 12.6 - - + -
35D LEU* 4.0 27.8 - - + -
39D LEU* 4.4 12.6 - - + -
42D TRP* 4.4 9.9 - - + -
144D VAL* 3.2 9.2 - - - +
145D ILE* 2.8 56.0 + - + -
162D ILE* 3.9 0.9 - - - +
163D ARG* 1.3 91.6 - - + +
165D VAL* 1.3 63.3 + - - +
200D ALA* 4.3 12.6 - - + +
201D VAL* 3.4 18.8 - - - +
202D THR* 3.6 22.0 - - + -
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Residues in contact with VAL 165 (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 ALA* 5.0 5.4 - - + -
143D ALA 3.4 12.1 - - - +
144D VAL* 4.3 13.9 - - + -
162D ILE* 4.7 1.1 - - + -
164D LEU* 1.3 77.7 - - - +
166D MSE 1.3 74.0 + - - +
167D LEU* 5.9 0.9 - - + -
199D VAL 4.4 0.2 - - - +
200D ALA* 3.3 1.9 - - - -
201D VAL* 2.8 41.8 + - + +
203D PRO* 4.5 12.8 - - + -
206D LEU* 3.7 22.7 - - + -
210D TRP* 4.3 15.0 - - + -
215D LEU* 3.9 26.2 - - + -
241D PHE* 5.7 0.9 - - + -
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Residues in contact with MSE 166 (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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74D PRO* 3.6 32.8 - - + -
75D LEU* 5.2 2.9 - - + +
142D ALA* 3.4 6.4 - - - +
143D ALA* 2.8 36.1 + - + +
145D ILE* 3.6 33.7 - - + -
165D VAL* 1.3 80.1 - - - +
167D LEU* 1.3 67.9 + - - +
196D PHE* 3.7 36.1 - - + -
197D SER* 3.3 13.9 - - - +
199D VAL 3.8 7.6 - - - +
200D ALA* 4.0 3.8 - - + -
259D ILE* 3.8 28.9 - - + -
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Residues in contact with LEU 167 (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 GLU 3.6 7.4 - - - +
142D ALA* 4.3 10.3 - - + -
165D VAL* 5.9 0.2 - - + -
166D MSE 1.3 82.2 - - - +
168D VAL* 1.3 61.9 + - - +
196D PHE* 3.2 9.8 - - - +
197D SER* 2.8 46.7 + - - +
215D LEU* 5.7 7.4 - - + -
219D LEU* 3.9 31.4 - - + -
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Residues in contact with VAL 168 (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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81D TRP* 4.0 17.7 - - + -
139D GLU 3.4 1.2 - - - +
140D GLY* 3.4 4.5 - - - -
141D GLU* 3.0 65.3 + - + +
142D ALA 4.1 9.9 - - - +
143D ALA* 4.3 7.2 - - + -
167D LEU* 1.3 77.0 - - - +
169D ASN* 1.3 73.6 + - - +
170D ASP* 3.8 3.4 - - + +
194D SER* 4.3 3.4 - - - -
195D ALA 3.4 10.3 - - - +
196D PHE* 3.5 26.9 - - + +
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Residues in contact with ASN 169 (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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127D ILE* 3.7 26.9 - - - +
138D MSE 3.3 18.0 - - - +
139D GLU 3.0 25.7 + - - -
140D GLY* 5.7 0.4 - - - -
168D VAL* 1.3 76.2 - - - +
170D ASP* 1.3 57.4 + - - +
171D VAL* 3.0 15.6 + - - +
194D SER* 3.4 1.2 - - - -
195D ALA* 2.8 41.9 + - + +
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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