Contacts of the helix formed by residues 156 - 172 (chain D) in PDB entry 1KLG
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 ALA 156 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D VAL 3.7 1.8 + - - -
155D THR* 1.3 71.0 - - - +
157D GLN* 1.3 64.8 + - - +
159D LEU* 3.0 4.0 + - - -
160D ASP* 2.7 25.8 + - - +
188D PHE* 3.6 19.9 - - + -
196D PHE* 3.9 22.9 - - + -
198D TYR* 3.7 29.6 - - + +
221D LYS* 2.9 15.1 + - + +
222D THR* 4.5 0.6 - - - +
223D VAL* 5.1 4.2 - - + +
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Residues in contact with GLN 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D TYR 4.1 0.4 - - - -
86D GLY* 2.8 12.2 - - - -
87D SER* 2.7 36.0 + - - +
111D MET* 4.5 0.8 - - - +
112D TYR 2.8 27.1 + - - +
114D GLY 3.5 10.6 + - - +
155D THR* 3.7 11.6 - - - +
156D ALA* 1.3 79.1 - - - +
158D GLU* 1.3 62.9 + - - +
160D ASP* 3.2 1.0 + - - +
161D ILE* 2.9 38.7 + - + +
217D TYR* 3.2 56.1 - - + +
221D LYS 4.8 0.2 + - - -
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Residues in contact with GLU 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D TYR* 3.5 41.7 - - + +
116D THR* 5.9 0.2 - - - +
149D THR* 3.1 13.9 + - - -
150D ASP* 4.1 1.0 - - - +
151D LYS* 2.9 31.7 + - - -
154D VAL* 3.2 19.8 - - + +
155D THR* 3.0 22.5 + - - +
157D GLN* 1.3 76.4 - - - +
159D LEU* 1.3 65.9 + - + +
161D ILE* 3.5 2.1 + - - +
162D LYS* 2.7 54.4 + - + +
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Residues in contact with LEU 159 (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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131D VAL* 4.3 11.7 - - + -
147D VAL* 3.8 26.8 - - + +
148D GLN 5.1 2.0 - - - +
149D THR* 4.4 15.5 - - - -
154D VAL* 3.8 33.0 - - + -
155D THR 3.5 3.1 + - - +
156D ALA 3.0 6.5 + - - +
158D GLU* 1.3 74.7 - - + +
160D ASP* 1.3 68.4 + - - +
162D LYS* 3.0 7.1 + - + +
163D ALA* 2.7 24.2 + - - +
186D ILE* 5.3 0.2 - - - -
188D PHE* 3.9 23.8 - - + -
223D VAL* 4.1 3.8 - - + -
228D VAL* 4.0 23.3 - - + -
230D ILE* 4.0 10.8 - - + -
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Residues in contact with ASP 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156D ALA 2.7 21.6 + - - +
157D GLN* 3.4 7.0 - - - +
159D LEU* 1.3 70.9 - - - +
161D ILE* 1.3 64.7 + - - +
163D ALA* 2.8 13.3 + - - +
164D ARG* 2.7 54.0 + - - +
186D ILE* 3.5 30.1 - - + +
188D PHE* 4.0 6.1 - - + -
198D TYR* 3.7 9.0 - - + -
217D TYR* 2.6 30.4 + - + +
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Residues in contact with ILE 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D LEU 5.0 1.1 - - - +
28D TYR* 3.7 36.8 - - + +
31D HIS 4.1 19.1 - - - +
32D TYR* 4.6 3.6 - - + -
85D TYR* 4.1 21.1 - - + +
86D GLY* 3.5 12.1 - - - +
87D SER* 3.5 32.1 - - - +
157D GLN* 2.9 39.4 + - + +
158D GLU 3.6 3.8 - - - +
160D ASP* 1.3 73.2 - - - +
162D LYS* 1.3 61.1 + - + +
164D ARG* 3.3 1.7 + - - +
165D ASN* 2.9 29.4 + - + +
217D TYR* 4.6 0.7 - - - +
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Residues in contact with LYS 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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85D TYR* 3.4 35.5 - - - +
147D VAL* 4.1 18.8 - - + +
148D GLN 2.8 31.5 + - - +
149D THR* 3.8 4.0 - - - +
150D ASP* 5.0 2.0 + - - +
158D GLU* 2.7 41.9 + - + +
159D LEU* 3.0 11.4 + - + +
161D ILE* 1.3 80.3 - - + +
163D ALA* 1.3 63.6 + - - +
165D ASN* 3.8 7.0 + - - +
166D PHE* 3.3 19.4 + - - +
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Residues in contact with ALA 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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133D VAL* 4.7 15.3 - - + -
145D PHE* 4.2 6.6 - - + -
147D VAL* 4.0 15.0 - - + +
159D LEU 2.7 16.3 + - - +
160D ASP 2.8 8.6 + - - +
162D LYS* 1.3 73.1 - - - +
164D ARG* 1.3 64.5 + - + +
166D PHE* 3.2 7.3 + - - +
167D LEU* 3.1 25.1 + - - +
186D ILE* 4.0 20.6 - - + -
230D ILE* 5.1 1.3 - - + -
232D VAL* 4.9 4.9 - - + -
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Residues in contact with ARG 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D MET* 4.2 0.4 - - - -
28D TYR* 3.1 50.0 + - + -
160D ASP* 2.7 48.7 + - - +
161D ILE 3.9 2.9 - - - +
163D ALA* 1.3 75.1 - - + +
165D ASN* 1.3 65.0 + - - +
167D LEU* 3.2 4.0 + - + +
168D ILE* 2.9 31.8 + - - +
173D LEU* 4.0 10.3 - - + +
174D TYR* 3.1 28.9 + - + -
186D ILE* 4.3 0.9 - - + +
198D TYR* 4.2 4.0 - - - +
199D ASP 3.8 5.7 + - - -
200D MET* 3.8 34.6 + - + +
213D TYR* 2.7 30.1 + - - -
216D MET* 3.6 9.1 - - - +
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Residues in contact with ASN 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D TYR 3.3 16.9 + - - +
29D ASP* 3.7 4.7 - - - +
30D ASP* 2.8 34.7 + - - +
161D ILE* 2.9 18.0 + - + +
162D LYS* 3.8 8.0 + - - +
163D ALA 3.3 0.2 - - - -
164D ARG* 1.3 77.3 - - - +
166D PHE* 1.3 64.6 - - - +
168D ILE* 3.3 9.3 + - - +
169D ASN* 3.1 34.9 + - - +
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Residues in contact with PHE 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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143D ILE* 4.0 17.0 - - + -
145D PHE* 3.3 59.9 - + + -
146D GLU 5.8 0.2 - - - -
147D VAL* 5.7 0.2 - - + -
162D LYS 3.3 9.4 + - - +
163D ALA 3.2 8.9 + - - +
164D ARG 3.2 0.2 - - - -
165D ASN* 1.3 84.0 - - - +
167D LEU* 1.3 62.3 + - + +
169D ASN* 3.2 6.5 + - - +
170D LYS* 2.9 66.2 + - + +
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Residues in contact with LEU 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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135D VAL* 3.9 25.8 - - + -
143D ILE* 4.3 9.2 - - + -
145D PHE* 4.1 5.6 - - + -
163D ALA* 3.1 18.4 + - + +
164D ARG 3.2 3.6 + - - +
166D PHE* 1.3 87.6 - - + +
168D ILE* 1.3 61.1 + - - +
170D LYS* 4.9 0.2 - - - -
171D LYS* 2.8 40.3 + - + +
172D ASN 3.1 5.9 + - - -
173D LEU* 3.1 28.7 + - + -
200D MET* 4.6 2.2 - - + -
232D VAL* 3.8 39.3 - - + -
234D LEU* 5.1 6.5 - - + -
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Residues in contact with ILE 168 (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 LYS* 3.8 35.7 - - + +
28D TYR* 3.6 41.3 - - + +
29D ASP* 3.9 13.7 - - - +
164D ARG 2.9 25.0 + - - +
165D ASN* 3.5 5.2 - - - +
166D PHE 3.2 0.2 - - - -
167D LEU* 1.3 76.0 - - - +
169D ASN* 1.3 64.2 + - - +
172D ASN* 3.1 26.7 + - - +
173D LEU* 3.7 11.0 - - + +
174D TYR* 3.7 34.3 - - + +
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Residues in contact with ASN 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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29D ASP* 4.5 10.8 + - - +
165D ASN* 3.1 36.2 + - - +
166D PHE* 3.2 8.0 + - - +
168D ILE* 1.3 85.1 - - - +
170D LYS* 1.3 76.7 + - - +
171D LYS 3.9 0.2 + - - -
172D ASN* 4.5 5.6 + - - +
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Residues in contact with LYS 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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143D ILE* 5.4 2.7 - - + -
166D PHE* 2.9 59.5 + - + +
167D LEU* 4.9 0.7 - - - -
169D ASN* 1.3 90.7 - - + +
171D LYS* 1.3 73.7 + - + +
172D ASN* 3.8 1.3 - - - -
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Residues in contact with LYS 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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135D VAL* 5.9 2.7 - - + -
137D GLU* 3.4 25.3 + - - +
142D THR* 4.7 2.6 + - - -
143D ILE* 4.0 31.4 - - + +
167D LEU* 2.8 30.5 + - + +
170D LYS* 1.3 85.0 - - - +
172D ASN* 1.3 76.9 + - - +
173D LEU 3.2 2.6 + - - +
180D PRO* 4.2 4.0 - - - +
181D TYR* 3.6 33.5 + - + +
234D LEU* 5.8 2.0 - - + -
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Residues in contact with ASN 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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167D LEU 3.1 2.4 + - - -
168D ILE 3.1 17.7 + - - +
169D ASN 4.8 4.7 - - - +
170D LYS 3.8 0.6 - - - -
171D LYS* 1.3 81.5 + - - +
173D LEU* 1.3 67.0 + - - +
174D TYR* 3.0 9.9 + - - -
175D GLU* 4.0 26.2 + - + +
180D PRO* 3.0 25.4 - - + +
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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
------------------------------------------------------------
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