Contacts of the helix formed by residues 197 - 201 (chain A) in PDB entry 2KUL
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 ASP 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A GLY 4.3 1.7 + - - +
83A GLU* 3.3 5.3 + - - -
175A HIS* 2.8 27.0 + - - -
181A SER 5.3 1.8 - - - +
182A ASN* 2.8 21.7 + - - +
196A VAL* 1.3 91.0 - - + +
198A TYR* 1.3 57.9 + - - +
199A GLY 3.1 6.1 + - - +
200A LEU* 3.5 7.8 + - - +
350A LYS 4.7 0.4 - - - +
351A ALA* 3.1 18.0 - - + +
352A LYS* 2.6 64.6 + - - +
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Residues in contact with TYR 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A PRO* 5.0 0.4 - - - -
82A THR* 4.3 10.9 - - + +
83A GLU* 2.8 52.5 + - + +
86A PHE* 3.5 34.5 - + + -
87A TYR* 5.1 11.9 - + - -
110A VAL* 3.6 27.5 - - + +
111A PRO* 5.5 0.4 - - + -
164A ILE* 4.2 7.0 - - + +
168A ILE* 5.6 7.0 - - + -
175A HIS* 4.6 6.7 - + - -
195A LEU* 3.1 45.6 + - + +
196A VAL* 3.7 11.9 - - + -
197A ASP* 1.3 71.0 - - - +
199A GLY* 1.3 62.6 + - - +
200A LEU 3.2 2.0 - - - -
201A ALA* 3.2 28.1 - - + +
354A ILE* 4.4 0.9 - - - +
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Residues in contact with GLY 199 (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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79A PRO* 3.9 10.7 - - - +
83A GLU* 4.5 0.2 + - - -
197A ASP* 3.1 4.0 + - - +
198A TYR* 1.3 78.1 - - - +
200A LEU* 1.3 59.1 + - - +
201A ALA 3.1 5.8 + - - +
222A ASP* 5.2 0.7 - - - +
351A ALA* 5.9 0.2 - - - +
352A LYS 3.0 27.6 + - - -
353A THR 3.5 1.0 - - - +
354A ILE* 3.0 41.1 - - - +
355A THR 4.5 0.7 + - - -
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Residues in contact with LEU 200 (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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174A VAL 3.1 11.3 - - - +
175A HIS* 3.2 24.4 - - + +
177A ASP* 3.5 38.8 - - + +
179A LYS* 5.9 0.2 - - + -
182A ASN* 4.6 1.1 - - - +
197A ASP* 3.5 17.9 + - - +
198A TYR 3.2 0.8 - - - -
199A GLY* 1.3 79.4 - - - +
201A ALA* 1.3 57.2 + - - +
202A TYR 3.7 0.6 + - - -
222A ASP* 3.1 31.9 - - + +
223A GLY* 3.4 23.8 - - - +
352A LYS* 3.4 40.4 - - + +
353A THR 4.5 4.7 - - - +
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Residues in contact with ALA 201 (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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82A THR* 4.5 12.8 - - + +
173A TYR* 3.9 26.5 - - + -
174A VAL 3.1 12.1 - - - +
175A HIS* 5.1 1.6 - - + -
198A TYR* 3.2 29.8 - - + +
199A GLY 3.1 5.8 + - - -
200A LEU* 1.3 74.8 - - - +
202A TYR* 1.3 61.4 + - - +
203A ARG 4.2 0.7 + - - -
354A ILE* 4.6 10.5 - - - +
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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