Contacts of the helix formed by residues 178 - 193 (chain A) in PDB entry 2KOD
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 SER 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A ALA* 1.3 75.7 - - - +
179A GLN* 1.3 59.2 + - - +
180A GLU* 3.5 13.0 + - - +
181A VAL* 2.7 36.4 + - - +
182A LYS* 3.4 2.8 + - - +
180B GLU* 3.7 32.8 + - - +
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Residues in contact with GLN 179 (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 LEU* 5.4 2.9 - - - +
177A ALA 3.7 2.7 + - - +
178A SER* 1.3 74.6 + - - +
180A GLU* 1.3 63.2 + - - +
182A LYS* 2.8 52.2 + - - +
183A ASN* 3.1 23.8 + - - +
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Residues in contact with GLU 180 (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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178A SER* 3.0 12.6 + - - +
179A GLN* 1.3 79.1 - - - +
181A VAL* 1.3 60.7 + - - +
183A ASN* 3.4 19.6 + - - +
184A TRP* 3.3 20.7 + - + +
178B SER* 3.6 34.3 - - - +
180B GLU* 4.1 17.3 - - + -
181B VAL* 4.8 6.7 - - + -
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Residues in contact with VAL 181 (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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177A ALA* 4.2 16.2 - - + -
178A SER* 2.7 30.8 + - - +
180A GLU* 1.3 74.8 - - - +
182A LYS* 1.3 55.2 + - - +
184A TRP* 3.0 7.1 + - + -
185A MET* 2.4 70.9 + - + +
180B GLU* 4.8 12.3 - - + +
181B VAL* 5.3 6.5 - - + -
184B TRP* 4.3 33.0 - - + -
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Residues in contact with LYS 182 (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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169A TYR* 3.4 32.5 - - - -
172A LEU* 3.4 36.6 - - + +
178A SER 3.4 2.4 + - - +
179A GLN* 2.8 44.6 + - - +
181A VAL* 1.3 79.5 - - - +
183A ASN* 1.3 58.3 + - - +
185A MET* 4.5 2.7 - - - -
186A THR* 2.3 55.1 + - - +
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Residues in contact with ASN 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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179A GLN* 3.1 24.6 + - - +
180A GLU* 3.6 24.4 + - - +
181A VAL 3.2 0.2 - - - -
182A LYS* 1.3 78.5 - - - +
184A TRP* 1.3 56.0 + - - +
186A THR* 5.0 0.4 - - - -
187A GLU* 2.6 49.1 - - - +
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Residues in contact with TRP 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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180A GLU 3.3 9.1 + - - +
181A VAL* 3.0 7.9 + - + +
183A ASN* 1.3 78.3 - - - +
185A MET* 1.3 76.9 + - + +
187A GLU* 3.0 5.9 + - - +
188A THR* 2.6 70.2 + - + +
189A LEU* 3.4 24.2 - - + -
146B SER* 5.4 6.2 - - - -
148B THR* 4.5 10.8 - - + -
151B LEU* 5.2 3.1 - - + -
175B GLU* 4.3 11.2 + - - -
176B GLN 5.7 1.7 + - - -
177B ALA* 4.8 12.0 - - + +
181B VAL* 4.2 28.3 - - + -
184B TRP* 4.7 17.3 - + - -
185B MET* 3.1 35.6 - - + +
189B LEU* 4.8 6.3 - - + -
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Residues in contact with MET 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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150A ILE* 3.6 29.4 - - + -
168A PHE* 4.2 7.9 - - + -
172A LEU* 6.3 0.2 - - - -
175A GLU* 3.7 23.8 - - - +
181A VAL* 2.4 44.9 + - + +
182A LYS* 4.4 2.7 - - - +
184A TRP* 1.3 81.1 - - + +
186A THR* 1.3 56.8 + - - +
187A GLU 2.8 10.8 + - - -
188A THR 3.0 0.2 + - - -
189A LEU* 2.9 42.8 + - + -
190A LEU 3.2 4.7 + - - -
184B TRP* 3.1 44.2 - - + -
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Residues in contact with THR 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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168A PHE* 3.8 22.5 - - + -
169A TYR* 3.3 42.8 - - + +
172A LEU* 4.5 0.5 - - - +
182A LYS* 2.3 48.9 + - + +
183A ASN* 4.8 0.7 - - - -
185A MET* 1.3 71.8 - - - +
187A GLU* 1.3 60.9 + - - +
190A LEU* 3.0 35.7 - - + +
211A LEU* 5.0 0.9 - - + -
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Residues in contact with GLU 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 ASN* 2.6 35.1 - - - +
184A TRP* 3.0 6.2 + - - +
185A MET 2.8 0.8 - - - -
186A THR* 1.3 84.7 - - - +
188A THR* 1.3 58.7 + - - +
190A LEU* 4.6 3.8 - - - -
191A VAL* 4.2 3.4 - - - +
145B TYR* 3.2 32.7 - - + +
146B SER* 3.3 9.2 + - - +
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Residues in contact with THR 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 TRP* 2.6 60.7 + - + -
187A GLU* 1.3 78.2 - - - +
189A LEU* 1.3 72.8 + - + +
190A LEU 3.1 4.0 + - - -
191A VAL 3.5 2.3 + - - -
192A GLN* 3.3 21.3 + - - +
145B TYR* 3.6 13.2 - - + -
146B SER* 3.4 31.0 + - - +
147B PRO* 5.2 0.2 - - + -
148B THR* 4.6 0.2 - - + -
151B LEU* 4.1 15.9 - - + -
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Residues in contact with LEU 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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150A ILE* 4.7 3.6 - - + -
151A LEU* 3.6 31.9 - - + -
164A TYR* 3.1 13.4 + - - -
168A PHE* 4.5 6.5 - - + -
184A TRP* 3.4 33.4 - - + -
185A MET* 2.9 34.2 + - + +
188A THR* 1.3 80.0 - - + +
190A LEU* 1.3 63.6 + - - +
191A VAL 3.3 0.2 - - - -
192A GLN* 3.7 25.4 - - - +
193A ASN* 3.3 21.8 + - - +
151B LEU* 5.3 5.4 - - + -
184B TRP* 4.7 7.4 - - + -
189B LEU* 5.3 6.5 - - + -
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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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161A PHE* 3.9 22.7 - - + -
164A TYR* 3.1 38.8 + - + -
165A VAL* 4.9 3.4 - - + -
168A PHE* 3.5 41.9 - - + -
169A TYR* 4.6 4.7 - - + -
185A MET 3.2 3.6 + - - -
186A THR* 3.0 35.9 - - + +
187A GLU* 4.2 1.1 - - - +
188A THR 3.1 0.6 - - - -
189A LEU* 1.3 79.1 - - - +
191A VAL* 1.3 64.5 + - + +
194A ALA* 3.9 2.8 + - - +
211A LEU* 4.0 22.9 - - + -
214A MET* 4.2 14.1 - - + -
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Residues in contact with VAL 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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161A PHE* 5.4 1.3 - - + -
187A GLU* 4.2 8.3 - - - +
188A THR 3.5 1.0 + - - -
190A LEU* 1.3 85.3 - - + +
192A GLN* 1.3 65.2 + - - +
194A ALA* 3.2 15.7 - - + +
199A LYS* 4.1 33.9 + - + +
202A LEU* 4.5 22.2 - - + -
203A LYS* 5.2 0.7 - - + -
214A MET* 4.6 18.8 - - + -
145B TYR* 3.4 50.5 - - + -
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Residues in contact with GLN 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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151A LEU* 5.8 2.2 - - - +
188A THR 3.3 17.1 + - - +
189A LEU* 3.8 26.2 - - - +
190A LEU 3.4 0.4 - - - -
191A VAL* 1.3 77.4 - - - +
193A ASN* 1.3 70.2 + - - +
194A ALA 2.9 14.3 + - - +
199A LYS* 4.7 9.1 + - - +
145B TYR* 4.3 10.5 + - + +
151B LEU* 3.3 42.3 - - - +
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Residues in contact with ASN 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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150A ILE* 4.0 9.7 + - - +
151A LEU* 3.9 27.3 + - - +
153A ILE 3.1 25.8 + - - +
154A ARG* 2.8 36.0 + - + +
155A GLN 3.1 8.0 + - - -
164A TYR* 3.6 16.0 + - - +
168A PHE* 6.1 0.6 - - - -
189A LEU* 3.3 15.5 + - - +
192A GLN* 1.3 89.4 + - - +
194A ALA* 1.3 63.8 + - - +
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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