Contacts of the helix formed by residues 168 - 178 (chain M) in PDB entry 6K4Y
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 MET 168 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147M ASN* 4.4 3.5 + - - +
166M LYS 3.9 2.6 + - - +
167M MET* 1.3 81.8 - - - +
169M GLU* 1.3 65.3 + - - +
170M HIS* 3.0 32.7 + - + -
171M HIS* 3.4 26.3 + - + +
172M ILE* 3.3 20.4 + - - +
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Residues in contact with GLU 169 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167M MET 3.9 0.4 + - - -
168M MET* 1.3 75.2 - - - +
170M HIS* 1.3 58.6 + - - +
172M ILE* 3.1 25.5 + - - +
173M GLN* 2.9 53.5 + - - +
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Residues in contact with HIS 170 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168M MET* 3.0 37.7 - - + +
169M GLU* 1.3 75.6 - - - +
171M HIS* 1.3 99.1 + + - +
173M GLN* 3.4 18.1 + - - +
174M LYS* 2.9 39.5 + - + +
211M LEU 5.3 3.6 - - - -
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Residues in contact with HIS 171 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147M ASN* 3.2 42.8 + - + +
167M MET* 3.7 15.9 - - + -
168M MET* 3.4 46.1 + - + +
169M GLU 3.3 0.4 - - - -
170M HIS* 1.3 103.3 + + - +
172M ILE* 1.3 56.4 + - - +
174M LYS* 3.0 4.8 + - - +
175M PHE* 2.9 35.7 + - + -
211M LEU* 3.3 46.4 - - + +
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Residues in contact with ILE 172 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167M MET* 3.7 25.4 - - + +
168M MET 3.3 18.6 - - - +
169M GLU* 3.1 30.9 + - - +
171M HIS* 1.3 74.6 - - - +
173M GLN* 1.3 58.1 + - - +
175M PHE* 3.3 5.7 + - - +
176M THR* 2.9 37.2 + - + +
182M CYS* 4.5 26.7 - - + -
184M ILE* 5.3 6.7 - - + -
190M VAL* 4.5 21.1 - - + -
192M LEU* 4.6 8.5 - - + +
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Residues in contact with GLN 173 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169M GLU* 2.9 45.3 + - - +
170M HIS* 3.5 17.9 - - - +
171M HIS 3.2 0.2 - - - -
172M ILE* 1.3 76.0 - - + +
174M LYS* 1.3 57.2 + - + +
176M THR* 3.0 11.9 + - - +
177M ASP* 2.9 34.7 + - - +
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Residues in contact with LYS 174 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170M HIS* 2.9 26.4 + - + +
171M HIS* 3.0 9.6 + - - +
173M GLN* 1.3 77.1 - - + +
175M PHE* 1.3 57.4 + - - +
177M ASP* 3.3 29.8 + - - +
178M ILE 4.0 2.4 + - - -
207M VAL* 3.3 24.2 - - + +
210M GLU* 3.3 50.0 + - - +
211M LEU* 3.7 27.6 - - + +
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Residues in contact with PHE 175 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149M ILE* 4.9 7.0 - - + -
152M PHE* 6.0 0.2 - + - -
162M ILE* 5.3 7.6 - - + -
167M MET* 4.9 1.6 - - - -
171M HIS* 2.9 31.3 + - + +
172M ILE 3.3 3.3 + - - +
174M LYS* 1.3 73.7 - - - +
176M THR* 1.3 62.4 + - - +
177M ASP 3.2 1.3 - - - -
178M ILE* 3.3 21.0 - - + +
180M MET* 3.2 48.3 + - + +
192M LEU* 4.2 26.0 - - + -
204M VAL* 3.5 31.2 - - + -
207M VAL* 3.6 12.6 - - + -
208M ALA* 3.5 29.4 - - + -
211M LEU* 3.6 27.6 - - + -
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Residues in contact with THR 176 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172M ILE* 2.9 29.3 + - + +
173M GLN* 3.0 18.9 + - - +
175M PHE* 1.3 73.7 - - + +
177M ASP* 1.3 65.0 + - - +
178M ILE 3.3 0.7 - - - -
179M GLY* 3.3 12.3 + - - +
180M MET 3.4 23.1 - - - +
182M CYS* 5.5 6.5 - - + -
192M LEU* 5.8 1.6 - - + -
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Residues in contact with ASP 177 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173M GLN* 2.9 22.8 + - - +
174M LYS* 3.3 25.1 + - - +
175M PHE 3.2 0.4 - - - -
176M THR* 1.3 80.0 + - - +
178M ILE* 1.3 61.9 + - + +
179M GLY 3.2 1.8 + - - -
207M VAL* 5.8 0.7 - - + -
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Residues in contact with ILE 178 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174M LYS 4.2 0.9 - - - +
175M PHE* 3.3 26.9 - - + +
177M ASP* 1.3 79.2 - - + +
179M GLY* 1.3 62.3 + - - +
180M MET* 3.9 3.8 - - + -
194M ILE* 3.9 12.0 - - + +
200M ASN* 5.2 0.7 - - - +
203M ALA* 3.5 44.9 - - + +
204M VAL* 3.7 22.7 - - + -
206M THR* 6.0 0.4 - - + -
207M VAL* 3.7 24.9 - - + -
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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