Contacts of the strand formed by residues 137 - 145 (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 LEU 137 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86D ALA* 4.1 12.8 - - + -
87D TYR 3.4 17.9 - - - +
88D GLU* 4.5 0.7 - - - +
89D ASP* 3.8 7.3 - - - +
97D LEU* 4.9 6.5 - - + -
128D ILE* 4.4 11.2 - - + +
131D ALA* 3.9 4.8 + - - -
132D HIS* 3.6 46.0 - - + +
135D GLY 3.5 2.5 - - - -
136D ASP* 1.3 77.5 - - - +
138D GLY* 1.3 69.2 + - - +
140D LEU* 3.7 29.6 - - + -
171D VAL* 5.1 15.0 - - + +
175D LEU* 4.4 14.4 - - + -
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Residues in contact with GLY 138 (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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87D TYR 2.4 31.0 + - - +
88D GLU 4.6 0.2 - - - -
89D ASP* 3.7 21.8 - - - -
94D GLN* 4.0 5.6 - - - -
136D ASP 3.3 3.2 + - - -
137D LEU* 1.3 81.4 - - - +
139D ASP* 1.3 75.1 - - - +
140D LEU* 4.2 0.3 - - - +
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Residues in contact with ASP 139 (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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87D TYR* 3.5 27.4 + - - +
94D GLN* 3.2 31.0 + - - +
138D GLY* 1.3 85.8 - - - +
140D LEU* 1.3 61.9 + - - +
141D ARG* 2.7 30.4 + - - +
165D ARG* 3.1 45.4 + - - +
174D ARG* 5.1 7.4 - - - +
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Residues in contact with LEU 140 (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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84D LEU* 4.3 15.3 - - + -
85D ARG 4.0 3.1 - - - +
86D ALA* 4.2 14.6 - - + -
128D ILE* 5.0 4.7 - - + -
137D LEU* 3.7 34.8 - - + -
138D GLY 4.2 0.7 - - - +
139D ASP* 1.3 85.7 - - - +
141D ARG* 1.3 56.7 + - - +
165D ARG* 3.8 1.2 - - - +
166D VAL* 2.7 48.1 + - + +
171D VAL* 4.1 9.0 - - + +
174D ARG* 4.3 16.5 - - + +
175D LEU* 3.6 42.6 - - + +
178D ALA* 5.5 0.9 - - + -
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Residues in contact with ARG 141 (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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2672A C 3.5 8.3 + - - -
2673A U 3.0 31.3 + - - -
2674A G 5.8 0.6 + - - -
26D PHE 6.0 0.4 + - - -
29D TRP* 3.9 23.1 - - - +
84D LEU* 3.6 3.7 - - - +
85D ARG* 2.7 43.5 + - - +
87D TYR* 3.7 16.7 - - + -
94D GLN* 3.6 18.0 + - - -
139D ASP* 2.7 26.7 + - - +
140D LEU* 1.3 77.7 - - - +
142D LEU* 1.3 55.2 - - - +
163D GLU* 3.0 36.5 + - + +
164D THR 3.1 15.3 - - - +
165D ARG* 3.4 21.3 - - - +
166D VAL* 4.1 1.6 - - - +
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Residues in contact with LEU 142 (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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38D VAL* 3.6 32.3 - - + -
81D ALA* 3.7 26.0 - - + -
83D ALA 3.1 16.6 - - - +
84D LEU* 3.7 22.2 - - + -
141D ARG* 1.3 72.7 - - - +
143D ILE* 1.3 66.3 + - - +
144D THR* 3.2 7.5 + - - +
163D GLU* 4.4 0.2 - - - -
164D THR* 2.7 32.8 + - - +
166D VAL* 3.5 13.9 - - + -
178D ALA* 4.1 11.0 - - + -
181D ILE* 4.3 14.6 - - + -
182D VAL* 3.6 20.4 - - + -
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Residues in contact with ILE 143 (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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2670A G 5.8 0.4 - - - +
2671A U 3.4 30.7 - - + +
81D ALA* 3.4 4.2 - - - -
82D VAL* 3.1 26.1 + - + -
83D ALA* 2.7 30.0 + - + +
85D ARG* 4.2 21.1 - - + +
99D GLU* 4.4 11.2 - - - +
101D TRP* 4.5 19.1 - - + -
113D LEU* 6.1 0.7 - - + -
142D LEU* 1.3 71.9 - - - +
144D THR* 1.3 62.3 + - - +
161D VAL* 3.8 24.2 - - + -
162D MET 4.2 2.5 - - - +
163D GLU* 3.6 19.1 - - + +
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Residues in contact with THR 144 (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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38D VAL* 5.4 2.8 - - - +
79D MET* 3.4 46.4 - - + +
80D ARG 3.7 6.3 - - - +
81D ALA* 4.1 9.7 - - - +
82D VAL* 5.8 0.2 - - - -
142D LEU* 3.4 11.6 + - - +
143D ILE* 1.3 76.9 + - - +
145D HIS* 1.3 74.2 + - - +
161D VAL* 3.2 6.6 - - - +
162D MET* 2.7 48.8 + - + -
164D THR* 4.5 11.2 + - - -
188D HIS* 3.9 10.8 + - + -
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Residues in contact with HIS 145 (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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79D MET* 3.5 5.4 - - - +
80D ARG* 3.3 35.3 + - + +
82D VAL* 3.4 32.6 - - + +
106D HIS* 4.0 26.8 - - + +
109D LEU* 3.8 23.9 - - + +
143D ILE* 6.3 0.2 - - + -
144D THR* 1.3 80.4 - - - +
146D THR* 1.3 92.3 + - - +
147D VAL* 4.3 6.9 - - - +
159D PRO* 3.5 12.4 - - + +
160D ASP 3.2 12.6 - - - +
161D VAL* 3.9 19.3 - - + -
162D MET* 5.2 0.9 - - - -
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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