Contacts of the helix formed by residues 90 - 102 (chain D) in PDB entry 2P4K
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 LYS 90 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88D GLU* 3.3 37.3 + - - +
89D PRO* 1.3 91.7 + - - +
91D GLY* 1.3 72.0 + - - +
92D GLU 3.5 1.0 + - - -
93D LEU* 3.6 6.6 + - - +
94D LEU* 3.4 29.8 + - + +
190D THR* 4.8 8.7 + - - +
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Residues in contact with GLY 91 (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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90D LYS* 1.3 78.7 - - - +
92D GLU* 1.3 59.5 + - - -
94D LEU* 3.0 5.7 + - - +
95D GLU* 3.0 35.0 + - - +
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Residues in contact with GLU 92 (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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90D LYS 3.5 0.6 + - - -
91D GLY* 1.3 68.0 - - - -
93D LEU* 1.3 61.1 + - - +
95D GLU* 3.3 8.4 + - - +
96D ALA* 2.8 29.1 + - - +
193D TYR* 4.0 19.7 + - + +
194D MET* 3.9 30.8 - - + +
197D LYS* 4.7 8.3 - - - +
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Residues in contact with LEU 93 (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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89D PRO* 3.9 15.9 - - + -
90D LYS 3.6 4.3 + - - +
91D GLY 3.3 0.8 - - - -
92D GLU* 1.3 79.3 - - - +
94D LEU* 1.3 64.6 + - - +
96D ALA* 3.1 2.9 + - - +
97D ILE* 2.9 39.8 + - + +
126D LEU* 5.0 2.2 - - + -
135D LEU* 4.4 11.9 - - + -
155D LEU* 4.8 4.7 - - + -
186D TRP* 4.0 7.2 - - + -
189D VAL* 3.7 27.4 - - + -
190D THR* 3.6 35.2 - - + +
193D TYR* 3.9 40.2 - - + -
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Residues in contact with LEU 94 (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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88D GLU* 4.2 14.1 - - - +
89D PRO* 3.6 34.4 - - + +
90D LYS* 3.4 35.7 + - + +
91D GLY 3.0 10.9 + - - +
93D LEU* 1.3 77.9 - - - +
95D GLU* 1.3 68.7 + - - +
97D ILE* 3.2 5.6 + - + +
98D LYS* 3.0 56.0 + - + +
104D PHE* 4.3 17.9 - - + -
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Residues in contact with GLU 95 (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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91D GLY* 3.0 24.5 + - - +
92D GLU* 3.8 8.3 - - - +
93D LEU 3.1 0.2 - - - -
94D LEU* 1.3 84.9 - - - +
96D ALA* 1.3 55.3 - - - +
98D LYS* 3.3 33.7 + - - +
99D ARG* 2.9 29.7 + - - +
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Residues in contact with ALA 96 (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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92D GLU 2.8 17.9 + - - +
93D LEU 3.4 4.9 - - - +
95D GLU* 1.3 74.5 - - - +
97D ILE* 1.3 60.8 + - - +
99D ARG* 3.6 23.3 - - - +
100D ASP* 2.8 35.3 + - - +
135D LEU* 3.7 16.6 - - + -
193D TYR* 3.6 24.7 - - + +
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Residues in contact with ILE 97 (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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89D PRO* 3.9 25.6 - - + -
93D LEU* 2.9 30.1 + - + +
94D LEU* 3.6 8.7 - - + +
96D ALA* 1.3 77.0 - - - +
98D LYS* 1.3 56.9 + - + +
101D PHE* 2.9 34.7 + - + +
102D GLY 3.6 0.5 + - - -
103D SER 3.8 8.9 + - - +
104D PHE* 3.9 20.4 - - + -
107D PHE* 3.5 37.5 - - + -
126D LEU* 4.9 4.3 - - + -
135D LEU* 3.8 18.6 - - + -
186D TRP* 4.4 10.8 - - + -
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Residues in contact with LYS 98 (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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94D LEU* 3.0 44.0 + - + +
95D GLU* 3.4 31.1 + - - +
97D ILE* 1.3 76.8 - - - +
99D ARG* 1.3 59.0 + - - +
102D GLY* 2.9 39.7 + - - +
103D SER* 4.0 14.6 - - - +
104D PHE* 4.6 6.1 - - - +
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Residues in contact with ARG 99 (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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95D GLU 2.9 17.9 + - - +
96D ALA* 3.2 25.1 + - - +
98D LYS* 1.3 79.1 - - - +
100D ASP* 1.3 93.0 + - - +
102D GLY* 4.5 0.9 + - - -
128D PHE* 5.3 1.6 - - - -
133D GLY 4.1 6.5 + - - -
134D HIS* 4.0 15.1 - - - +
135D LEU* 4.5 1.2 - - - +
193D TYR* 4.6 8.5 + - - -
197D LYS* 5.1 8.3 - - - +
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Residues in contact with ASP 100 (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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132B ARG* 3.3 45.3 + - - +
96D ALA 2.8 17.0 + - - +
99D ARG* 1.3 116.0 + - - +
101D PHE* 1.3 74.8 + - + +
102D GLY 3.8 0.2 - - - -
134D HIS* 3.7 9.1 + - - +
135D LEU* 2.9 22.4 + - + +
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Residues in contact with PHE 101 (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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131B GLU* 5.7 0.9 - - - -
132B ARG* 4.2 20.9 - - - -
97D ILE* 2.9 25.9 + - - +
100D ASP* 1.3 77.6 - - + +
102D GLY* 1.3 57.4 + - - +
103D SER 3.3 2.2 - - - +
106D LYS* 3.2 21.5 - - - +
107D PHE* 3.9 38.4 - + + +
110D LYS* 3.2 31.8 + - + +
126D LEU* 4.0 12.1 - - + -
135D LEU* 3.8 42.6 - - + -
136D GLN 4.2 0.7 - - - -
137D ILE* 3.7 33.7 - - + -
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Residues in contact with GLY 102 (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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97D ILE 3.6 0.2 + - - -
98D LYS* 2.9 29.8 + - - +
99D ARG 4.5 1.0 + - - -
100D ASP 3.8 0.8 - - - -
101D PHE* 1.3 75.5 - - - +
103D SER* 1.3 62.0 + - - +
106D LYS* 4.4 10.3 - - - -
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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