Contacts of the helix formed by residues 194 - 198 (chain A) in PDB entry 1DWQ
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 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A ALA 3.5 22.2 - - - -
91A ASP* 3.8 2.9 - - - -
94A VAL* 3.8 10.5 - - - -
191A THR* 3.1 13.6 + - - -
193A LYS* 1.3 75.9 - - - +
195A TYR* 1.3 67.6 + - - +
197A SER* 2.7 20.3 + - - -
198A ILE* 3.3 11.5 - - - +
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Residues in contact with TYR 195 (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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86A ILE* 4.6 3.1 - - + -
87A ALA* 3.6 35.4 - - + +
90A ALA* 3.7 15.3 - - + +
91A ASP* 2.9 22.0 + - - +
102A PHE* 3.6 22.8 - + - -
107A LEU* 3.9 2.8 - - - +
108A PRO* 2.8 54.7 + - + +
109A ASP* 4.1 4.5 - - - -
110A THR* 4.1 7.9 - - + -
190A PHE* 3.6 22.2 - - + -
191A THR 3.2 3.3 + - - +
194A GLY* 1.3 74.0 - - - +
196A GLY* 1.3 64.9 + - - +
197A SER 3.0 1.6 + - - -
198A ILE* 3.1 8.6 + - + +
200A LYS* 2.9 40.9 + - - -
223A TYR* 4.3 2.5 - + - -
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Residues in contact with GLY 196 (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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110A THR* 4.0 2.4 - - - +
191A THR 2.7 18.4 + - - -
192A GLU* 3.1 35.2 + - - +
194A GLY 3.2 0.2 - - - -
195A TYR* 1.3 74.1 - - - +
197A SER* 1.3 56.9 + - - +
198A ILE 4.4 0.2 - - - +
200A LYS* 3.4 9.5 + - - -
223A TYR* 3.6 19.2 + - - -
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Residues in contact with SER 197 (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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94A VAL* 3.4 9.3 - - - +
192A GLU 2.9 6.2 + - - -
193A LYS* 2.5 30.2 + - - -
194A GLY 2.7 10.4 + - - -
196A GLY* 1.3 75.6 - - - +
198A ILE* 1.3 63.6 + - - +
199A LYS* 3.7 5.0 + - - +
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Residues in contact with ILE 198 (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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86A ILE* 4.7 4.0 - - + -
90A ALA* 3.4 25.6 - - + -
94A VAL* 3.4 26.5 - - + +
97A ILE* 3.7 31.0 - - + +
100A GLY* 3.9 15.9 - - - +
102A PHE* 5.6 0.2 - - + -
194A GLY 3.3 19.9 + - - +
195A TYR* 3.1 18.8 + - + +
196A GLY 4.4 0.2 - - - +
197A SER* 1.3 77.5 - - - +
199A LYS* 1.3 73.7 + - - +
200A LYS* 2.8 34.2 + - + +
226A ASP* 4.0 3.6 - - - +
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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