Contacts of the helix formed by residues 171 - 183 (chain K) in PDB entry 6C0W
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 ASN 171 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116K LEU* 4.1 21.6 - - - +
137K TRP* 3.7 39.7 - - + +
138K GLY 5.3 1.9 + - - +
168K LEU* 4.0 22.0 - - - +
169K ARG 3.1 12.5 + - - +
170K ARG* 1.3 81.9 + - - +
172K THR* 1.3 58.8 + - - +
173K PRO 3.6 1.3 - - - -
174K LEU* 3.8 12.7 - - + +
175K LEU* 2.9 31.4 + - - +
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Residues in contact with THR 172 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86K PHE* 4.5 19.5 - - + -
168K LEU 5.2 1.0 + - - -
169K ARG* 4.5 18.1 - - - +
170K ARG 3.4 2.2 - - - -
171K ASN* 1.3 75.5 - - - +
173K PRO* 1.4 69.2 - - + +
175K LEU* 3.4 4.9 + - - +
176K GLY* 2.9 24.6 + - - -
190K LYS* 3.9 24.9 - - - +
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Residues in contact with PRO 173 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170K ARG* 4.1 13.5 - - - +
171K ASN 3.9 0.9 - - - -
172K THR* 1.4 91.4 - - + +
174K LEU* 1.3 60.3 + - + +
176K GLY* 4.3 2.0 - - - +
177K GLN* 2.9 43.5 + - + +
190K LYS* 6.2 0.2 - - - +
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Residues in contact with LEU 174 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112K LEU* 4.2 8.1 - - + -
115K ALA* 4.0 29.2 - - + -
116K LEU* 5.2 7.9 - - + -
137K TRP* 4.1 22.2 - - + -
170K ARG 4.9 2.7 - - - +
171K ASN* 3.8 21.1 - - - +
172K THR 3.3 0.6 - - - -
173K PRO* 1.3 82.6 - - + +
175K LEU* 1.3 58.4 + - - +
177K GLN* 3.9 7.0 - - + +
178K ALA* 2.9 35.3 + - + +
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Residues in contact with LEU 175 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86K PHE* 5.6 10.3 - - + -
108K PHE* 3.6 31.2 - - + -
112K LEU* 5.0 4.3 - - + -
135K ILE* 4.8 9.2 - - + -
137K TRP* 3.6 28.0 - - + -
150K THR* 5.6 6.7 - - + -
152K VAL* 4.3 23.1 - - + -
163K THR* 5.8 4.0 - - + +
171K ASN 2.9 20.4 + - - +
172K THR* 3.9 4.7 - - - +
174K LEU* 1.3 76.3 - - - +
176K GLY* 1.3 60.1 + - - +
178K ALA* 4.4 3.6 - - + -
179K LEU* 2.9 43.1 + - + +
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Residues in contact with GLY 176 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86K PHE* 5.6 3.1 - - - -
172K THR 2.9 16.9 + - - -
173K PRO* 3.4 3.1 + - - -
175K LEU* 1.3 80.8 - - - +
177K GLN* 1.3 52.3 + - - +
179K LEU* 3.8 1.9 - - - -
180K THR* 2.6 38.6 + - - -
188K ILE* 3.7 28.6 - - - +
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Residues in contact with GLN 177 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173K PRO* 2.9 27.4 + - + +
174K LEU* 4.2 8.0 - - + +
176K GLY* 1.3 76.4 - - - +
178K ALA* 1.3 57.8 + - - +
180K THR* 3.8 5.7 - - - -
181K ILE* 2.9 44.6 + - + +
188K ILE* 5.5 6.5 - - + -
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Residues in contact with ALA 178 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108K PHE* 4.2 8.4 - - + -
111K ILE* 3.8 27.3 - - + +
112K LEU* 4.9 11.9 - - + +
115K ALA* 5.7 1.8 - - + -
174K LEU* 2.9 30.4 + - + +
175K LEU* 4.0 4.9 - - - +
177K GLN* 1.3 76.3 - - - +
179K LEU* 1.3 57.8 + - - +
181K ILE* 3.9 2.4 - - - -
182K ALA* 2.8 29.1 + - - +
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Residues in contact with LEU 179 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88K MET* 3.7 28.7 - - + -
104K PHE* 4.6 12.2 - - + -
108K PHE* 4.0 23.1 - - + -
133K ILE* 5.5 4.5 - - + -
152K VAL* 4.1 26.2 - - + -
154K TYR* 5.1 9.4 - - + -
161K ALA* 5.2 7.6 - - + -
175K LEU* 2.9 32.5 + - + +
176K GLY* 4.0 4.3 - - - +
178K ALA* 1.3 76.1 - - - +
180K THR* 1.3 58.8 + - - +
182K ALA* 3.7 5.3 - - - -
183K SER* 2.9 29.3 + - - -
188K ILE* 5.1 7.0 - - + -
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Residues in contact with THR 180 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88K MET* 3.8 4.9 - - - -
176K GLY 2.6 22.9 + - - -
177K GLN* 3.3 6.9 + - - -
179K LEU* 1.3 76.4 - - - +
181K ILE* 1.3 63.1 + - + +
183K SER* 2.9 28.6 + - - +
185K HIS* 3.2 17.4 - - + +
186K HIS* 3.6 42.0 - - - +
187K GLN 3.8 9.9 - - - +
188K ILE* 3.5 23.3 - - + +
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Residues in contact with ILE 181 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107K SER* 5.7 0.2 - - - -
111K ILE* 3.8 22.0 - - + +
177K GLN* 2.9 29.0 + - + +
178K ALA* 4.3 4.0 - - - +
180K THR* 1.3 76.3 - - + +
182K ALA* 1.3 59.8 + - - +
183K SER 2.9 11.7 - - - +
185K HIS 4.8 4.0 - - - +
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Residues in contact with ALA 182 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99K PHE* 5.2 0.9 - - - -
104K PHE* 3.5 18.7 - - + -
107K SER* 4.0 14.2 - - - -
108K PHE* 3.7 41.1 - - + +
111K ILE* 3.8 11.4 - - + +
178K ALA 2.8 23.2 + - - +
179K LEU* 3.7 4.7 - - - +
180K THR 3.3 0.2 - - - -
181K ILE* 1.3 77.5 - - - +
183K SER* 1.3 57.8 + - - +
184K LYS* 4.9 5.5 - - - +
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Residues in contact with SER 183 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88K MET* 2.8 37.7 - - - -
99K PHE* 5.5 1.8 - - - -
104K PHE* 3.7 17.7 - - - -
154K TYR* 4.5 4.5 - - - -
179K LEU 2.9 13.7 + - - -
180K THR 2.9 12.5 + - - +
181K ILE* 2.9 17.0 - - - +
182K ALA* 1.3 76.9 - - - +
184K LYS* 1.3 66.2 + - - +
185K HIS* 3.1 15.5 + - - +
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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