Contacts of the helix formed by residues 182 - 194 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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914 ARG* 3.0 42.6 + - - +
154A ILE* 5.3 4.9 - - + -
166A TYR* 3.4 54.7 - - + -
173A TRP* 3.6 52.1 - - + +
174A VAL 3.7 22.7 - - - +
175A TYR* 6.6 0.2 - - - -
180A VAL 4.6 0.9 - - - +
181A SER* 1.3 73.0 - - - +
183A HIS* 1.4 62.5 + - - +
185A LEU* 3.4 7.6 + - - +
186A LEU 3.2 14.0 + - - -
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Residues in contact with HIS 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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914 ARG* 4.9 0.7 - - - +
102A THR* 5.9 1.8 - - + -
106A LEU* 5.7 11.0 - - + -
173A TRP* 3.3 33.7 + + + -
181A SER* 3.7 4.1 - - - -
182A LEU* 1.4 78.7 - - - +
184A GLU* 1.4 56.8 + - - +
186A LEU* 3.4 8.7 + - - +
187A ALA* 3.0 28.8 + - - +
200A LEU 3.7 16.7 - - - +
201A SER* 3.2 17.9 + - - +
203A LEU* 3.4 33.0 - - + +
205A TYR* 3.1 34.2 - - - +
206A SER* 2.8 29.9 + - - -
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Residues in contact with GLU 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ASN* 5.2 1.0 + - - -
180A VAL* 3.6 24.4 - - + +
181A SER* 3.3 14.2 + - - +
183A HIS* 1.4 76.1 + - - +
185A LEU* 1.4 58.8 + - - +
187A ALA* 3.4 2.1 + - - +
188A ALA* 3.0 28.2 + - - +
201A SER* 3.6 15.5 - - - +
206A SER* 3.4 32.7 + - - +
207A GLY* 4.5 3.7 + - - -
108a TRP* 4.0 22.5 - - - -
112a LYS* 5.2 1.4 + - - -
116a GLU* 4.6 9.8 - - - +
119a THR* 5.4 6.4 - - - +
124a ASP* 4.0 13.7 - - - +
127a LYS* 4.5 6.0 + - - +
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Residues in contact with LEU 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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914 ARG* 5.5 1.8 - - - +
924 THR* 5.4 6.5 - - - +
164A LYS* 3.7 26.2 - - - +
166A TYR* 4.2 13.7 - - - +
175A TYR* 4.1 17.3 - - + -
181A SER 3.1 13.0 + - - +
182A LEU* 3.6 10.1 - - - +
184A GLU* 1.4 78.3 - - - +
186A LEU* 1.4 58.9 + - - +
188A ALA* 3.5 4.2 + - - +
189A GLU* 3.4 39.6 + - - +
92B GLU 4.9 3.6 - - - +
121a LYS* 3.8 32.7 - - - +
123a THR* 3.9 19.7 - - + +
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Residues in contact with LEU 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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914 ARG* 3.7 17.5 - - - +
924 THR* 3.3 37.7 - - - +
974 TRP* 3.4 37.9 - - + -
106A LEU* 4.5 8.5 - - + -
110A PHE* 4.0 18.4 - - + -
182A LEU 3.2 13.7 + - - +
183A HIS* 3.6 7.4 - - - +
185A LEU* 1.4 76.1 - - - +
187A ALA* 1.3 61.2 + - - +
189A GLU* 3.7 10.9 + - - +
190A LEU 3.4 15.2 + - - -
200A LEU* 3.6 27.6 - - + +
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Residues in contact with ALA 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A HIS 3.0 12.8 + - - +
184A GLU 3.5 3.4 - - - +
185A LEU 3.4 0.2 - - - -
186A LEU* 1.3 74.7 - - - +
188A ALA* 1.4 63.8 + - - +
190A LEU* 3.3 5.7 + - - +
191A THR* 3.1 27.1 + - - -
198A LEU 4.3 1.2 - - - +
199A ASP* 4.5 2.0 - - - -
200A LEU* 3.5 30.5 - - - +
201A SER* 3.2 27.6 - - - +
127a LYS* 4.3 8.1 - - - +
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Residues in contact with ALA 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A GLU 3.0 17.5 + - - +
185A LEU* 3.7 6.1 - - - +
186A LEU 3.4 0.2 - - - -
187A ALA* 1.4 73.2 - - - +
189A GLU* 1.3 58.2 + - - +
191A THR 3.5 0.3 + - - -
192A LYS* 3.1 30.5 + - - +
123a THR* 3.8 26.0 - - - +
124a ASP* 3.6 20.6 - - - +
127a LYS* 3.3 23.2 - - + +
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Residues in contact with GLU 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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924 THR* 3.9 24.0 - - - +
944 ALA* 4.2 5.1 - - - +
954 TYR* 6.1 2.6 - - + -
974 TRP* 5.7 2.5 - - + -
984 GLU* 3.3 34.7 - - + +
164A LYS* 5.5 2.1 + - - -
185A LEU* 3.4 35.4 + - + +
186A LEU* 3.8 12.8 - - - +
188A ALA* 1.3 75.4 - - + +
190A LEU* 1.4 57.6 + - - +
192A LYS* 3.4 24.3 + - - +
193A ALA 3.0 24.4 + - - -
123a THR* 5.6 2.0 - - + +
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Residues in contact with LEU 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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974 TRP* 3.5 58.3 - - + +
984 GLU* 3.3 24.6 - - - +
1004 GLU* 5.6 0.9 - - + +
113A LEU* 5.2 0.7 - - + -
186A LEU 3.4 3.1 + - - +
187A ALA 3.3 9.5 + - - +
189A GLU* 1.4 79.6 - - - +
191A THR* 1.4 57.0 + - - +
194A LEU* 3.0 52.8 + - + +
198A LEU* 4.1 32.8 - - + +
199A ASP 4.4 0.7 - - - +
200A LEU* 4.0 17.3 - - + -
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Residues in contact with THR 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A ALA 3.1 10.5 + - - -
190A LEU* 1.4 74.8 - - - +
192A LYS* 1.3 64.4 + - - +
194A LEU* 4.7 0.2 - - - -
195A LYS* 3.1 23.9 + - - +
196A THR 3.8 15.8 - - - +
197A LYS* 3.8 35.2 - - + -
198A LEU 3.0 22.0 + - - +
127a LYS* 3.3 41.6 - - + +
130a CYS* 5.0 1.0 - - - -
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Residues in contact with LYS 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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984 GLU* 5.3 3.1 - - - +
188A ALA 3.1 17.6 + - - +
189A GLU* 3.5 21.8 - - - +
190A LEU 3.3 0.2 - - - -
191A THR* 1.3 78.3 - - - +
193A ALA* 1.4 61.5 + - - +
195A LYS 4.1 2.3 + - - -
456O GLN* 4.1 3.6 - - - +
123a THR* 3.7 44.0 - - - +
126a ALA* 3.7 16.6 - - + +
127a LYS* 3.9 12.8 - - - +
130a CYS* 2.7 28.0 - - - +
131a LEU 3.0 28.7 - - - +
132a PRO* 4.8 0.7 - - + -
133a PRO* 3.9 33.3 - - + +
136a LEU* 4.1 8.1 - - - +
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Residues in contact with ALA 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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844 TYR* 4.2 13.2 - - + -
984 GLU* 3.1 52.3 - - + +
994 SER* 3.5 13.8 + - - +
189A GLU 3.0 7.2 + - - +
192A LYS* 1.4 77.5 - - - +
194A LEU* 1.4 62.8 + - - +
195A LYS* 4.2 5.9 - - - +
456O GLN* 4.5 13.4 + - - +
133a PRO* 6.5 2.0 - - + -
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Residues in contact with LEU 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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984 GLU 3.2 8.7 + - - +
994 SER* 3.8 4.1 + - - +
1004 GLU* 3.1 49.4 - - + +
1014 ALA* 3.9 11.2 - - + +
1044 GLU* 6.1 0.4 - - - +
1054 ARG* 3.7 10.0 + - - -
190A LEU* 3.0 45.9 + - + +
191A THR* 5.1 0.2 - - - -
193A ALA* 1.4 76.6 - - - +
195A LYS* 1.3 67.8 - - - +
196A THR* 3.1 33.2 + - + +
198A LEU* 4.1 23.6 - - + -
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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