Contacts of the helix formed by residues 182 - 194 (chain D) in PDB entry 5KZ5
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 182 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99D ALA 5.3 2.0 - - - +
102D THR* 4.6 11.9 - - + -
103D LEU* 5.1 7.6 - - + -
106D LEU* 4.8 9.9 - - + -
145D ILE* 4.3 16.2 - - + -
154D ILE* 3.7 38.1 - - + -
156D LEU* 4.4 11.2 - - + +
166D TYR* 3.4 36.0 - - + -
173D TRP* 3.5 30.7 - - + +
181D SER* 1.3 71.0 - - - +
183D HIS* 1.4 64.5 + - - +
185D LEU* 3.6 2.1 + - - +
186D LEU* 3.3 33.4 + - + +
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Residues in contact with HIS 183 (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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911 ARG* 3.5 29.9 - - - +
102D THR* 4.4 5.2 - - + -
106D LEU* 4.2 15.0 - - + +
173D TRP* 3.8 7.7 - + - -
181D SER* 3.4 22.1 - - - -
182D LEU* 1.4 77.6 - - - +
184D GLU* 1.4 69.5 + - + +
186D LEU* 3.4 1.1 + - - -
187D ALA* 2.8 33.6 + - - +
201D SER* 3.6 33.8 + - - -
203D LEU* 3.4 24.7 - - + +
206D SER* 3.3 34.6 + - - -
207D GLY 5.7 0.2 - - - -
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Residues in contact with GLU 184 (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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179D GLY 4.7 3.6 - - - +
180D VAL* 3.7 23.9 - - + +
181D SER* 3.3 25.1 + - - +
183D HIS* 1.4 89.8 - - + +
185D LEU* 1.4 55.7 + - - +
187D ALA* 3.7 5.4 - - - +
188D ALA* 3.0 28.2 + - - +
201D SER* 4.7 6.1 - - - +
119d THR* 4.8 15.5 + - - +
121d LYS* 4.1 13.1 - - - +
124d ASP* 4.3 13.4 - - - +
127d LYS* 5.8 6.0 + - - +
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Residues in contact with LEU 185 (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 TYR* 6.0 0.2 - - + -
156D LEU* 3.7 27.1 - - + -
158D SER* 4.4 4.0 - - - +
161D SER* 4.2 17.3 - - - +
164D LYS* 3.8 23.6 - - + +
166D TYR* 4.2 3.8 - - - +
180D VAL* 4.0 5.5 - - + +
181D SER 3.2 15.2 + - - +
182D LEU 4.1 3.8 - - - +
184D GLU* 1.4 71.7 - - - +
186D LEU* 1.4 65.4 + - + +
188D ALA* 3.4 6.2 + - + +
189D GLU* 3.2 43.5 + - + +
192D LYS* 6.3 0.2 - - - +
92E GLU 5.7 3.8 - - - +
93E THR* 6.4 0.9 - - + -
121d LYS* 3.7 23.1 - - - +
123d THR* 5.1 10.5 - - + +
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Residues in contact with LEU 186 (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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901 SER* 3.6 23.1 - - - +
911 ARG* 3.8 22.2 - - + -
106D LEU* 4.7 12.3 - - + -
110D PHE* 5.0 5.6 - - + -
143D TYR* 3.7 36.3 - - + -
145D ILE* 5.0 17.5 - - + -
156D LEU* 5.0 11.4 - - + -
182D LEU* 3.3 24.2 + - + +
183D HIS 3.9 0.4 - - - +
185D LEU* 1.4 74.1 - - + +
187D ALA* 1.3 59.4 + - - +
189D GLU* 3.3 13.5 + - + +
190D LEU* 3.0 34.7 + - + +
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Residues in contact with ALA 187 (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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911 ARG* 3.7 4.8 + - + +
921 THR* 3.1 26.3 - - + +
183D HIS 2.8 19.4 + - - +
184D GLU* 3.7 7.0 - - - +
186D LEU* 1.3 76.7 - - - +
188D ALA* 1.4 59.6 + - - +
190D LEU* 3.4 2.6 + - - +
191D THR* 2.8 30.8 + - - +
199D ASP* 6.1 0.4 - - - -
200D LEU 3.4 16.8 - - - +
201D SER* 4.4 3.1 - - - +
127d LYS* 5.2 6.5 - - - +
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Residues in contact with ALA 188 (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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184D GLU 3.0 17.4 + - - +
185D LEU* 3.7 7.4 - - + +
187D ALA* 1.4 76.8 - - - +
189D GLU* 1.4 62.0 + - + +
191D THR 3.2 2.1 + - - -
192D LYS* 3.1 31.6 + - - +
121d LYS* 5.5 1.8 - - - +
123d THR* 4.3 11.9 - - - +
124d ASP* 4.3 13.5 - - - +
127d LYS* 3.6 33.4 - - + +
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Residues in contact with GLU 189 (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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951 TYR* 4.9 4.3 - - + -
143D TYR* 3.2 39.4 + - + +
158D SER* 3.9 3.6 + - - -
160D SER* 3.5 23.7 + - - -
161D SER* 5.5 0.3 + - - -
185D LEU* 3.2 33.6 + - + +
186D LEU* 3.3 15.9 + - - +
188D ALA* 1.4 75.0 - - + +
190D LEU* 1.4 64.7 + - + +
192D LYS* 3.5 26.9 + - + +
193D ALA* 3.3 21.8 + - - +
133d PRO* 5.3 5.0 - - + +
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Residues in contact with LEU 190 (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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901 SER* 3.4 18.6 - - - +
911 ARG 3.1 22.4 - - - +
921 THR* 3.3 19.7 - - - +
931 HIS* 3.8 2.2 - - - -
941 ALA 3.4 29.0 - - - +
951 TYR* 3.3 55.0 - - + +
186D LEU* 3.0 23.5 + - + +
187D ALA 3.6 4.3 - - - +
189D GLU* 1.4 76.6 - - + +
191D THR* 1.3 55.9 + - - +
193D ALA* 3.3 5.9 + - - +
194D LEU* 2.9 29.7 + - - +
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Residues in contact with THR 191 (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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921 THR* 3.9 8.7 - - - +
187D ALA* 2.8 18.7 + - - +
188D ALA 3.2 5.4 + - - -
190D LEU* 1.3 75.0 - - - +
192D LYS* 1.4 60.1 + - - +
194D LEU* 3.3 13.3 + - - -
195D LYS* 3.3 4.3 + - - -
196D THR 3.3 26.8 + - - +
197D LYS* 3.9 4.7 - - + -
198D LEU* 3.0 34.9 + - - +
127d LYS* 3.4 35.6 - - + +
130d CYS* 5.1 0.3 - - - -
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Residues in contact with LYS 192 (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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831 ASN* 4.7 1.7 - - - +
185D LEU* 6.3 0.4 - - - +
188D ALA* 3.1 21.1 + - - +
189D GLU* 3.7 24.0 - - - +
190D LEU 3.4 0.2 - - - -
191D THR* 1.4 74.6 - - - +
193D ALA* 1.4 62.4 + - - +
195D LYS* 3.5 9.7 + - - +
123d THR* 3.3 50.5 - - - +
126d ALA* 4.3 3.4 - - - -
127d LYS* 3.6 19.7 + - - +
130d CYS* 3.5 19.4 - - - +
131d LEU 3.3 32.5 - - - +
132d PRO* 3.9 17.8 - - + +
133d PRO* 3.8 24.3 - - + +
136d LEU* 5.9 0.2 - - - -
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Residues in contact with ALA 193 (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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821 ILE 5.6 0.9 - - - +
831 ASN* 3.0 28.4 - - - +
951 TYR* 2.8 58.6 - - + +
140D LEU* 5.3 4.7 - - + -
189D GLU 3.3 8.8 + - - +
190D LEU 3.3 7.8 + - - +
192D LYS* 1.4 77.5 - - - +
194D LEU* 1.3 59.6 + - - +
195D LYS 3.5 0.7 + - - -
132d PRO* 4.9 5.3 - - + +
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Residues in contact with LEU 194 (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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921 THR* 5.6 2.9 - - + +
931 HIS 4.6 2.5 - - - +
941 ALA* 3.3 35.0 - - + +
951 TYR 4.1 0.2 - - - -
961 GLY* 3.9 2.9 - - - +
971 TRP* 3.0 53.6 + - + +
1001 GLU* 4.6 0.7 - - - +
118D TYR* 3.6 23.3 - - + +
190D LEU 2.9 16.7 + - - +
191D THR* 3.3 9.2 + - - +
193D ALA* 1.3 72.9 - - - +
195D LYS* 1.4 66.1 - - - +
196D THR* 3.5 28.3 - - + +
198D LEU* 3.7 25.6 - - + -
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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