Contacts of the helix formed by residues 130 - 146 (chain D) in PDB entry 4K71
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 ASN 130 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D ALA 3.0 10.8 + - - +
129D ASP* 1.3 79.6 + - + +
131D GLU* 1.3 55.2 + - - +
132D GLU* 3.5 10.7 + - - +
133D THR* 3.0 44.5 + - - +
134D PHE* 2.8 36.6 + - - +
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Residues in contact with GLU 131 (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 PHE* 3.3 52.1 + - + +
128D HIS 4.5 2.7 + - - +
129D ASP 4.1 0.4 - - - -
130D ASN* 1.3 71.1 + - - +
132D GLU* 1.3 68.6 + - + +
134D PHE* 3.3 3.1 + - - +
135D LEU* 2.9 37.3 + - + +
162D LYS* 3.7 26.1 + - - +
166D THR* 4.4 2.4 + - - +
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Residues in contact with GLU 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D ASN* 3.3 8.4 + - - +
131D GLU* 1.3 86.3 - - + +
133D THR* 1.3 61.0 + - - +
135D LEU* 3.5 5.8 + - - +
136D LYS* 3.1 43.7 + - - +
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Residues in contact with THR 133 (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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36D PHE* 3.8 23.2 - - + -
40D VAL* 6.5 0.4 - - + -
130D ASN* 3.0 36.0 + - - +
132D GLU* 1.3 75.0 - - - +
134D PHE* 1.3 66.3 + - - +
136D LYS* 3.1 13.3 + - + +
137D LYS* 2.9 22.7 + - + +
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Residues in contact with PHE 134 (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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123D MET* 3.8 29.8 - - + -
126D ALA* 3.8 27.8 - - + +
127D PHE* 3.9 23.8 - + + -
130D ASN 2.8 22.3 + - - +
131D GLU 3.5 3.1 - - - +
133D THR* 1.3 73.8 - - - +
135D LEU* 1.3 68.1 + - + +
137D LYS* 3.2 19.5 + - + +
138D TYR* 3.3 25.4 + + - +
165D PHE* 3.5 51.8 - + - -
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Residues in contact with LEU 135 (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 PHE* 4.3 13.5 - - + -
131D GLU* 2.9 37.3 + - + +
132D GLU* 3.9 5.4 - - - +
134D PHE* 1.3 79.4 - - + +
136D LYS* 1.3 67.6 + - - +
138D TYR* 3.0 16.8 + - + +
139D LEU* 3.1 13.8 + - - +
158D ALA* 5.1 3.4 - - + +
161D TYR* 4.3 12.8 - - + +
162D LYS* 3.8 57.0 - - + +
165D PHE* 4.8 3.1 - - + -
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Residues in contact with LYS 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D LYS* 3.9 36.1 - - - +
21D ALA* 6.5 1.1 - - - -
24D LEU* 3.6 20.9 - - + +
36D PHE* 3.7 13.9 - - + -
40D VAL* 5.0 14.3 - - + +
43D VAL* 6.3 2.6 - - + +
44D ASN* 4.5 7.9 + - - +
132D GLU* 3.1 35.8 + - - +
133D THR* 3.4 12.3 + - - +
135D LEU* 1.3 76.0 - - - +
137D LYS* 1.3 60.9 + - - +
139D LEU* 3.2 13.4 + - + +
140D TYR* 3.1 18.5 + - - +
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Residues in contact with LYS 137 (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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36D PHE* 3.5 37.5 - - + +
37D GLU* 3.5 22.6 + - - -
133D THR* 2.9 13.3 + - + +
134D PHE* 3.4 16.6 - - + +
135D LEU 3.1 0.2 - - - -
136D LYS* 1.3 75.7 - - - +
138D TYR* 1.3 62.1 + - - +
140D TYR* 3.2 4.3 + - + +
141D GLU* 2.9 49.5 + - + +
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Residues in contact with TYR 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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115D LEU* 4.1 27.0 - - + +
117D ARG* 3.8 20.2 + - + +
123D MET* 4.8 6.5 - - - -
134D PHE* 3.3 21.2 + + - +
135D LEU* 3.0 12.9 + - + +
137D LYS* 1.3 77.8 - - + +
139D LEU* 1.3 62.8 + - - +
141D GLU* 3.1 6.8 + - + +
142D ILE* 3.1 47.1 + - + +
161D TYR* 3.3 48.0 - + + -
165D PHE* 3.9 28.3 - + - -
182D LEU* 3.6 21.6 + - + +
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Residues in contact with LEU 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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21D ALA* 3.9 38.1 - - + +
24D LEU* 4.5 10.8 - - + -
25D ILE* 4.0 11.2 - - + -
135D LEU 3.1 10.1 + - - +
136D LYS* 3.3 15.3 - - + +
138D TYR* 1.3 77.3 - - - +
140D TYR* 1.3 53.6 + - - +
142D ILE* 3.5 4.5 + - + +
143D ALA* 2.8 37.6 + - - +
154D LEU* 3.3 48.2 - - + +
155D LEU* 4.8 2.9 - - + -
158D ALA* 4.5 17.5 - - + -
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Residues in contact with TYR 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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24D LEU* 4.5 10.7 - - + +
28D ALA* 4.0 13.8 - - + +
32D GLN 5.1 0.2 - - - -
34D CYS 2.6 30.0 + - - -
35D PRO* 3.4 4.5 - - - +
36D PHE* 3.3 51.2 + + + -
39D HIS* 3.2 28.7 - + + -
136D LYS 3.1 5.3 + - - +
137D LYS* 3.2 12.8 + - + +
139D LEU* 1.3 77.0 - - - +
141D GLU* 1.3 81.1 + - + +
143D ALA* 4.0 0.3 - - - +
144D ARG* 2.9 73.1 + - + +
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Residues in contact with GLU 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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115D LEU* 4.0 37.4 - - + +
137D LYS* 2.9 37.0 + - + +
138D TYR* 3.1 10.0 + - - +
140D TYR* 1.3 95.3 - - + +
142D ILE* 1.3 61.5 + - + +
144D ARG* 2.9 20.1 + - - +
145D ARG* 2.8 59.8 + - - +
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Residues in contact with ILE 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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115D LEU* 6.4 0.4 - - + -
138D TYR* 3.1 29.4 + - + +
139D LEU* 4.0 3.6 - - - +
141D GLU* 1.3 74.6 - - + +
143D ALA* 1.3 66.8 + - - +
145D ARG* 3.3 4.3 + - - +
146D HIS* 3.1 33.4 + - + +
149D PHE* 3.7 31.9 - - + -
154D LEU* 3.9 16.6 - - + -
157D PHE* 5.5 1.8 - - + -
161D TYR* 3.3 45.5 - - + +
189D GLY* 5.7 1.3 - - - -
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Residues in contact with ALA 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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25D ILE* 4.0 17.9 - - + -
28D ALA* 3.7 20.4 - - + -
29D GLN* 3.5 13.0 - - + +
139D LEU 2.8 19.6 + - - +
142D ILE* 1.3 76.3 - - - +
144D ARG* 1.3 60.0 + - - +
146D HIS* 3.1 26.9 + - - +
147D PRO* 3.6 1.0 - - - +
149D PHE* 5.4 0.2 - - - -
154D LEU* 3.9 21.0 - - + +
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Residues in contact with ARG 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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28D ALA* 3.5 23.5 - - + +
32D GLN* 2.9 63.8 + - - +
33D GLN* 4.0 12.7 + - - +
110D PRO* 4.3 0.2 - - - +
112D LEU* 3.8 27.2 - - + +
113D PRO* 5.4 3.4 - - - +
140D TYR* 2.9 58.9 + - + +
141D GLU* 2.9 39.5 + - - +
143D ALA* 1.3 76.0 - - - +
145D ARG* 1.3 75.7 + - + +
146D HIS 3.6 0.2 + - - -
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Residues in contact with ARG 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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110D PRO* 4.0 18.9 - - + +
112D LEU* 3.1 41.3 - - + +
113D PRO* 4.5 7.9 - - - +
114D ARG* 3.3 23.8 - - - +
115D LEU* 3.4 28.4 - - - +
141D GLU* 2.8 48.1 + - - +
142D ILE* 3.3 6.3 + - - +
144D ARG* 1.3 89.3 - - - +
146D HIS* 1.3 82.6 + - + +
147D PRO* 3.8 6.1 - - - +
186D ARG* 4.8 15.9 - - - +
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Residues in contact with HIS 146 (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 GLN* 3.0 9.9 + - - -
142D ILE* 3.1 35.7 + - + +
143D ALA 3.1 4.9 - - - +
145D ARG* 1.3 101.1 + - + +
147D PRO* 1.3 63.5 - - - +
148D TYR 3.2 2.9 - - - -
149D PHE* 3.0 30.7 + + + +
186D ARG* 5.1 8.4 + - - -
189D GLY 5.0 2.7 - - - -
190D LYS* 4.1 35.1 + - + +
193D SER* 3.4 27.8 + - - +
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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