Contacts of the helix formed by residues 182 - 191 (chain C) in PDB entry 1DT0
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 182 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78C ASN 3.4 25.1 - - - +
79C CYS 2.9 11.9 + - - +
80C LEU 4.4 0.3 - - - +
81C SER* 2.8 28.0 + - - +
84C ALA* 4.4 4.3 - - - +
181C VAL* 1.3 72.1 - - - +
183C TRP* 1.3 55.3 + - - +
184C ALA* 3.5 22.9 - - - +
185C PHE* 2.9 29.1 + - - +
186C VAL* 3.2 13.6 + - - +
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Residues in contact with TRP 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C ALA* 5.5 0.4 - - - +
85C GLY 3.2 27.5 + - - -
86C GLY 3.4 15.8 + - - -
87C GLN* 3.7 13.9 - - - +
88C PRO* 3.8 35.2 - - + +
92C LEU* 3.9 4.5 - - + +
96C ILE* 4.6 5.6 - - + -
103C PHE* 3.3 32.3 - + - -
106C PHE* 3.9 17.5 - + - -
125C LEU* 4.8 2.5 - - + -
153C LEU* 4.1 13.5 - - + -
178C TRP* 4.2 11.8 + + - -
181C VAL* 3.5 24.1 + - + +
182C ASN* 1.3 68.2 - - - +
184C ALA* 1.3 55.1 + - - +
186C VAL* 3.2 35.7 + - + +
187C ALA* 2.7 35.3 + - - +
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Residues in contact with ALA 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C ASN* 3.1 14.5 - - - +
183C TRP* 1.3 77.9 - - - +
185C PHE* 1.3 57.0 + - - +
187C ALA* 3.4 7.9 + - - +
188C GLU* 3.0 35.9 + - - +
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Residues in contact with PHE 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C PHE* 3.6 29.6 - + - -
78C ASN* 3.5 48.5 - - + +
79C CYS* 4.0 15.5 - - - -
152C LEU 4.6 1.1 - - - -
182C ASN* 2.9 27.3 + - - +
184C ALA* 1.3 79.1 - - - +
186C VAL* 1.3 66.1 + - - +
188C GLU* 3.1 17.4 + - - +
189C GLN* 3.1 53.5 + - + +
195C TYR 3.9 19.7 - - - -
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Residues in contact with VAL 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C CYS 5.5 0.7 - - - +
92C LEU* 3.7 17.3 - - + -
125C LEU* 4.5 4.5 - - + -
152C LEU* 3.5 39.8 - - + +
153C LEU* 3.9 21.8 - - + -
181C VAL* 4.1 0.4 - - + -
182C ASN 3.2 15.5 + - - +
183C TRP* 3.2 36.5 + - + +
185C PHE* 1.3 77.8 - - + +
187C ALA* 1.3 58.4 + - - +
189C GLN* 3.1 4.4 + - - +
190C PHE* 2.8 27.0 + - - +
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Residues in contact with ALA 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C PRO* 6.2 0.2 - - + -
89C THR 5.7 2.7 - - - +
92C LEU* 3.9 19.5 - - + +
183C TRP 2.7 21.1 + - - +
184C ALA* 3.4 9.0 - - - +
186C VAL* 1.3 73.5 - - - +
188C GLU* 1.3 62.8 + - + +
190C PHE* 2.9 22.9 + - - +
191C GLU 3.2 9.4 + - - +
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Residues in contact with GLU 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C ALA* 3.0 22.5 + - - +
185C PHE* 3.1 20.5 + - - +
187C ALA* 1.3 76.1 - - - +
189C GLN* 1.3 68.6 + - - +
191C GLU 4.9 3.1 - - - -
192C GLY* 3.5 19.3 + - - -
193C LYS* 3.4 37.9 + - + +
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Residues in contact with GLN 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C PHE* 4.0 6.0 - - + -
127C LYS* 4.7 0.9 + - - -
150C THR* 4.1 3.6 - - - +
151C PRO 3.5 23.7 - - - +
152C LEU* 3.7 23.0 - - - +
185C PHE* 3.1 57.6 + - + +
186C VAL 3.3 4.9 - - - +
187C ALA 3.1 0.6 - - - -
188C GLU* 1.3 86.4 + - - +
190C PHE* 1.3 69.1 + - - +
191C GLU* 3.3 1.7 + - - -
192C GLY 4.5 0.3 + - - -
193C LYS 4.1 5.5 + - - -
194C THR* 3.5 24.5 - - + +
195C TYR 3.0 28.3 + - - +
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Residues in contact with PHE 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C ALA* 3.5 35.4 - - + -
92C LEU* 3.7 34.1 - - + -
95C ALA* 3.5 31.2 - - + -
127C LYS* 3.0 35.8 + - + +
131C GLY 4.7 5.8 - - - -
133C LEU* 4.0 11.4 - - + -
152C LEU* 3.6 12.3 - - + -
186C VAL 2.8 13.5 + - - +
187C ALA* 2.9 11.4 + - - +
189C GLN* 1.3 78.2 - - - +
191C GLU* 1.3 96.4 + - + +
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Residues in contact with GLU 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C ALA* 5.7 1.8 - - + -
127C LYS* 3.0 24.5 + - - +
131C GLY* 5.3 4.2 - - - +
187C ALA 3.2 7.6 + - - +
188C GLU* 3.8 3.9 - - - -
189C GLN 4.1 0.2 - - - -
190C PHE* 1.3 126.7 - - + +
192C GLY* 1.3 57.8 + - - +
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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