Contacts of the helix formed by residues 165 - 178 (chain I) in PDB entry 6D84
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 GLY 165 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156I GLN* 3.2 22.6 - - - +
157I ALA 3.3 16.4 - - - -
158I THR* 3.4 9.3 - - - +
163I GLY 3.7 0.6 + - - -
164I ASP* 1.3 71.7 - - - +
166I LEU* 1.3 62.6 + - - +
167I TYR 3.4 2.3 - - - +
168I GLU* 3.9 24.8 - - - +
169I GLY* 3.3 7.1 + - - -
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Residues in contact with LEU 166 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I ILE* 3.7 48.9 - - + +
36I LYS* 3.8 19.5 - - + -
37I LEU* 3.7 24.6 - - + +
124I PHE* 4.5 11.3 - - + -
158I THR* 3.7 19.3 - - + -
159I CYS 4.0 6.7 - - - +
163I GLY* 3.7 32.5 + - - +
164I ASP 3.2 1.0 - - - -
165I GLY* 1.3 77.1 - - - +
167I TYR* 1.3 61.4 + - + +
169I GLY* 3.2 3.8 + - - -
170I LEU* 3.0 29.7 + - - +
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Residues in contact with TYR 167 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36I LYS* 4.7 6.4 + - + -
37I LEU* 4.3 25.4 + - + +
40I GLY* 6.0 0.5 - - - -
58I TYR* 3.5 43.7 + + - +
163I GLY* 4.2 16.4 - - - -
165I GLY 3.4 1.0 - - - +
166I LEU* 1.3 75.6 - - + +
168I GLU* 1.3 61.9 + - + +
170I LEU* 3.6 20.5 - - + +
171I ASP* 2.8 27.9 + - - +
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Residues in contact with GLU 168 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154I TYR* 4.6 1.7 - - - -
156I GLN* 2.9 40.2 + - - +
165I GLY* 3.6 15.9 + - - +
166I LEU 3.2 0.8 - - - -
167I TYR* 1.3 76.1 - - - +
169I GLY* 1.3 60.4 + - - +
171I ASP* 3.2 7.9 + - - +
172I TRP* 3.0 28.8 + - - +
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Residues in contact with GLY 169 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122I LEU* 3.3 19.0 - - - +
124I PHE* 3.8 24.0 - - - -
154I TYR* 5.1 0.2 - - - -
156I GLN* 4.0 5.7 - - - +
165I GLY 3.3 6.0 + - - -
166I LEU 3.2 7.5 + - - -
168I GLU* 1.3 78.8 - - - +
170I LEU* 1.3 55.0 + - - +
172I TRP* 3.5 2.5 + - - +
173I LEU* 2.9 30.5 + - - +
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Residues in contact with LEU 170 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I LEU* 3.7 30.5 - - + -
56I VAL* 5.0 7.9 - - + -
58I TYR* 3.6 28.9 - - + -
63I PHE* 3.8 32.5 - - + -
89I ILE* 5.8 5.4 - - + -
124I PHE* 5.9 2.5 - - + -
166I LEU 3.0 14.2 + - - +
167I TYR* 3.6 32.8 - - + +
168I GLU 3.3 0.2 - - - -
169I GLY* 1.3 77.9 - - - +
171I ASP* 1.3 56.5 + - - +
173I LEU* 3.7 9.6 - - + +
174I SER* 2.9 30.8 + - - -
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Residues in contact with ASP 171 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58I TYR* 4.4 8.0 - - - +
59I LYS* 5.4 9.0 - - - +
167I TYR 2.8 18.3 + - - +
168I GLU* 3.2 8.9 + - - +
170I LEU* 1.3 73.7 - - - +
172I TRP* 1.3 59.2 + - - +
174I SER* 2.7 25.1 + - - -
175I ASN* 2.9 33.7 + - - +
178I ARG* 4.7 4.9 + - - -
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Residues in contact with TRP 172 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120I VAL* 4.7 5.6 - - + -
121I LEU 3.2 17.3 - - - -
122I LEU* 3.5 25.4 - - + -
152I ASN* 3.2 31.2 - - + -
153I TRP 4.0 6.7 - - - -
154I TYR* 3.5 50.2 - + + +
168I GLU 3.0 16.0 + - - +
169I GLY 4.1 1.6 - - - +
171I ASP* 1.3 76.3 - - - +
173I LEU* 1.3 61.5 + - + +
175I ASN* 3.3 12.6 + - + +
176I GLN* 2.9 65.1 + - + +
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Residues in contact with LEU 173 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I ILE* 3.7 42.4 - - + -
63I PHE* 3.7 27.8 - - + -
87I GLY* 5.7 0.4 - - - -
88I LEU 5.2 0.9 - - - +
89I ILE* 4.2 11.4 - - + -
120I VAL* 4.5 19.1 - - + -
122I LEU* 3.8 11.9 - - + -
169I GLY 2.9 19.7 + - - +
170I LEU* 3.7 11.0 - - + +
172I TRP* 1.3 82.5 - - + +
174I SER* 1.3 57.2 + - - +
176I GLN* 3.0 5.6 + - + +
177I LEU* 2.9 44.1 + - + +
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Residues in contact with SER 174 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58I TYR* 5.7 0.2 - - - -
59I LYS* 4.8 11.8 - - - +
61I ILE* 5.6 4.0 - - - -
63I PHE* 3.6 21.3 - - - -
170I LEU 2.9 16.3 + - - -
171I ASP* 2.7 28.8 + - - -
173I LEU* 1.3 76.1 - - - +
175I ASN* 1.3 55.8 + - - +
177I LEU* 3.7 7.3 - - - +
178I ARG* 3.1 53.4 + - - +
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Residues in contact with ASN 175 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171I ASP* 2.9 35.1 + - - +
172I TRP* 3.6 15.0 - - + +
173I LEU 3.3 0.2 - - - -
174I SER* 1.3 76.1 - - - +
176I GLN* 1.3 64.2 + - - +
178I ARG* 2.9 48.0 - - - +
179I ASN* 4.3 3.3 - - - +
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Residues in contact with GLN 176 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86I GLN* 5.5 1.4 - - - +
120I VAL* 4.3 18.9 - - + +
152I ASN* 3.3 38.2 - - - +
172I TRP* 2.9 62.4 + - + +
173I LEU* 3.0 10.9 + - + +
175I ASN* 1.3 81.0 - - - +
177I LEU* 1.3 65.9 + - + +
178I ARG 4.2 1.2 - - - +
179I ASN* 4.3 8.4 + - - +
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Residues in contact with LEU 177 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I MET* 3.7 30.5 - - + +
19I ARG 5.2 1.1 - - - +
20I ILE* 5.9 0.4 - - + -
61I ILE* 4.0 16.8 - - + -
63I PHE* 3.6 33.0 - - + -
86I GLN* 3.3 36.6 - - - +
87I GLY* 6.1 0.2 - - - -
120I VAL* 6.2 1.6 - - + -
173I LEU* 2.9 31.6 + - + +
174I SER* 3.2 6.2 + - - +
176I GLN* 1.3 80.4 - - + +
178I ARG* 1.3 65.2 + - + +
179I ASN* 3.7 7.4 + - - -
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Residues in contact with ARG 178 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59I LYS* 4.9 13.3 + - - +
61I ILE* 5.5 14.7 - - + +
171I ASP* 4.7 5.3 + - - -
174I SER* 3.1 50.3 + - - +
175I ASN* 2.9 51.1 + - - +
177I LEU* 1.3 81.2 - - + +
179I ASN* 1.3 64.6 + - - +
180I GLN* 3.4 42.8 + - + +
181I LYS 4.2 11.7 + - - -
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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