Contacts of the strand formed by residues 161 - 167 (chain D) in PDB entry 1KD1
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 161 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2670A G 3.9 7.9 - - - +
2671A U 3.3 35.1 + - - +
23D THR* 4.2 3.3 + - - +
25D ARG* 3.2 16.6 + - - -
109D LEU* 4.7 3.8 - - + -
112D THR* 4.3 17.7 - - + +
113D LEU* 4.3 19.5 - - + -
143D ILE* 3.8 22.7 - - + -
144D THR 3.2 12.6 - - - +
145D HIS* 3.9 13.2 - - + -
159D PRO 3.8 9.8 + - - +
160D ASP* 1.3 75.2 - - - +
162D MET* 1.3 64.1 + - - +
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Residues in contact with MET 162 (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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2671A U 3.9 2.9 - - - -
23D THR* 3.4 11.2 - - + -
25D ARG* 3.5 17.5 - - - +
42D ALA* 4.2 13.9 - - + -
79D MET* 5.1 5.4 - - + +
143D ILE* 4.8 0.4 - - - -
144D THR* 2.7 42.9 + - - +
146D THR* 5.0 3.6 - - - -
160D ASP 4.2 9.4 - - - +
161D VAL* 1.3 78.5 - - - +
163D GLU* 1.3 58.9 + - - +
164D THR* 3.8 2.9 + - - +
308D LEU* 3.1 35.7 - - + -
310D ARG* 3.1 52.7 - - + +
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Residues in contact with GLU 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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2671A U 2.7 30.3 + - - +
2672A C 2.9 30.0 + - - +
29D TRP* 3.6 11.8 - - - -
85D ARG* 2.8 25.5 + - - -
87D TYR* 2.3 28.1 + - - -
141D ARG* 3.0 38.1 + - + +
142D LEU 3.6 6.7 - - - +
143D ILE* 3.6 12.6 - - + +
162D MET* 1.3 71.4 - - - +
164D THR* 1.3 61.2 + - - +
310D ARG* 3.5 13.7 + - - -
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Residues in contact with THR 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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29D TRP* 3.6 10.3 - - + -
38D VAL* 3.6 19.6 - - + +
39D GLN 3.7 6.1 - - - -
40D GLY* 3.5 38.2 - - - +
41D PHE 5.3 0.2 + - - -
79D MET* 5.7 2.6 - - - +
141D ARG* 3.1 4.1 - - - +
142D LEU* 2.7 43.0 + - - +
144D THR* 4.5 8.0 + - - -
162D MET* 3.8 7.3 + - - +
163D GLU* 1.3 72.0 - - - +
165D ARG* 1.3 63.4 + - - +
166D VAL* 4.2 0.9 - - - +
310D ARG* 3.0 20.7 + - - +
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Residues in contact with ARG 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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29D TRP* 3.6 48.9 - - + -
30D PRO 3.8 9.9 + - - -
32D ASP* 3.0 40.0 + - - -
39D GLN* 2.9 53.6 + - - +
139D ASP* 3.1 43.2 + - - +
140D LEU 3.8 3.1 - - - +
141D ARG* 3.4 12.8 - - + +
164D THR* 1.3 77.1 - - - +
166D VAL* 1.3 68.2 + - - +
167D GLY* 3.8 2.6 - - - -
174D ARG* 4.1 9.1 - - - +
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Residues in contact with VAL 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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37D GLY 3.5 24.5 - - - +
38D VAL* 4.4 6.5 - - + +
84D LEU* 5.5 0.2 - - + -
140D LEU* 2.7 28.8 + - + +
141D ARG* 4.2 0.9 - - - -
142D LEU* 3.5 42.4 - - + +
164D THR 4.2 0.9 - - - +
165D ARG* 1.3 84.0 + - - +
167D GLY* 1.3 59.4 + - - +
174D ARG* 3.0 37.8 + - + +
177D HIS* 4.4 12.3 - - + -
178D ALA* 5.0 8.1 - - + -
181D ILE* 5.9 0.2 - - + -
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Residues in contact with GLY 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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32D ASP* 3.2 24.2 - - - -
33D ASP 6.0 0.4 - - - -
35D GLN 3.6 3.6 - - - +
36D PRO* 3.4 0.5 - - - +
37D GLY* 2.9 29.0 + - - +
39D GLN* 3.7 17.1 - - - +
165D ARG* 3.8 5.4 - - - -
166D VAL* 1.3 75.3 - - - +
168D GLY* 1.3 57.8 + - - -
174D ARG* 3.7 1.6 - - - -
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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