Contacts of the strand formed by residues 168 - 176 (chain D) in PDB entry 4KZX
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 VAL 168 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157D MET* 3.6 25.1 - - + -
158D ILE* 4.4 3.8 - - + +
164D VAL* 3.1 43.5 + - + +
165D ASN* 4.5 4.5 - - - +
166D TYR 3.8 0.2 - - - -
167D TYR* 1.3 77.4 - - + +
169D ASP* 1.3 62.5 + - - +
170D THR* 4.2 9.7 + - - +
187D LYS* 4.7 7.0 - - + -
188D ILE 3.1 11.0 - - - +
189D MET* 2.9 37.2 - - - -
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Residues in contact with ASP 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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96D LEU 4.6 13.4 - - - +
97D CYS* 4.8 4.3 - - - -
98D ALA* 3.9 23.2 + - + +
99D ILE* 5.3 4.8 + - - +
167D TYR 4.1 0.8 + - - -
168D VAL* 1.3 72.7 - - - +
170D THR* 1.4 92.0 + - - +
186D VAL 3.9 0.3 - - - +
187D LYS* 3.4 1.6 - - - +
188D ILE* 2.9 34.2 + - + +
190D LEU* 4.9 4.7 - - + +
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Residues in contact with THR 170 (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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98D ALA* 4.2 1.6 - - - -
99D ILE* 5.3 1.0 - - - +
168D VAL* 4.2 6.1 + - - +
169D ASP* 1.4 88.6 + - - +
171D ALA* 1.4 81.5 + - - +
172D VAL* 5.1 6.5 - - + -
185D LYS* 5.3 7.9 - - + -
186D VAL 3.1 15.3 - - - +
187D LYS* 3.0 34.1 - - + +
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Residues in contact with ALA 171 (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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98D ALA* 4.3 10.1 - - + -
99D ILE* 4.1 29.4 - - + -
102D ALA* 4.5 11.1 - - + +
170D THR* 1.4 81.2 - - - +
172D VAL* 1.3 65.8 + - - +
173D ARG* 4.5 9.9 - - - +
184D ILE 3.7 0.9 - - - +
185D LYS* 3.4 3.8 - - - -
186D VAL* 2.9 30.7 + - + +
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Residues in contact with VAL 172 (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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170D THR* 5.1 4.7 - - + -
171D ALA* 1.3 78.9 - - - +
173D ARG* 1.3 93.3 + - - +
174D HIS* 4.2 22.4 + - + +
183D GLY* 5.3 3.6 - - - -
184D ILE 3.3 9.6 - - - +
185D LYS* 3.8 36.8 - - + +
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Residues in contact with ARG 173 (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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26D THR* 3.8 26.6 + - - +
34D TYR* 5.5 0.8 + - - -
99D ILE* 4.1 29.9 - - - +
102D ALA* 3.8 23.8 - - + +
103D GLU* 2.8 34.8 + - - +
106D ARG* 5.8 9.9 - - + +
171D ALA* 4.2 6.7 - - - +
172D VAL* 1.3 95.3 + - - +
174D HIS* 1.3 68.5 + - - +
175D VAL* 3.8 1.1 + - + -
182D LEU 3.7 0.2 - - - +
183D GLY* 3.5 4.0 - - - -
184D ILE* 2.9 47.0 + - + +
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Residues in contact with HIS 174 (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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106D ARG* 4.2 11.4 + - - -
172D VAL* 4.2 22.3 + - + +
173D ARG* 1.3 80.9 + - - +
175D VAL* 1.3 58.8 + - - +
176D LEU* 3.2 17.6 - - + +
181D VAL* 3.9 15.3 - - + +
182D LEU 3.6 5.0 + - - -
183D GLY* 5.2 4.6 - - - -
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Residues in contact with VAL 175 (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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106D ARG* 3.8 40.2 - - + +
109D LEU* 4.9 7.2 - - + -
110D LEU* 5.6 2.9 - - + +
173D ARG* 3.8 0.8 + - + -
174D HIS* 1.3 71.6 - - - +
176D LEU* 1.3 65.5 + - - +
177D LEU* 3.5 24.4 + - + -
181D VAL* 3.2 3.0 - - - +
182D LEU* 2.9 63.3 + - + +
184D ILE* 4.2 19.7 - - + -
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Residues in contact with LEU 176 (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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106D ARG* 3.5 25.9 + - - +
110D LEU* 5.7 3.3 - - - +
174D HIS* 3.2 23.3 - - + +
175D VAL* 1.3 69.0 - - - +
177D LEU* 1.3 72.8 + - - +
178D ARG* 4.6 0.5 + - - -
180D GLY 3.9 4.3 - - - +
181D VAL* 3.9 17.7 - - + -
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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