Contacts of the strand formed by residues 202 - 207 (chain A) in PDB entry 1HKC
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 202 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A LYS* 5.0 10.6 - - + +
148A LEU 3.8 17.3 + - - +
149A PRO* 4.0 4.1 - - + +
150A VAL* 2.6 34.2 + - - +
200A ASP 4.4 0.2 + - - -
201A ALA* 1.3 73.1 + - - +
203A ILE* 1.3 61.0 + - - +
204A VAL* 2.8 21.6 + - - +
461A TYR* 3.7 26.0 - - - -
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Residues in contact with ILE 203 (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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134A LEU* 6.2 0.2 - - + -
150A VAL* 3.4 23.6 - - + +
152A PHE* 4.7 6.3 - - + -
164A ASP* 4.1 10.2 - - + +
186A VAL* 3.9 35.1 - - + +
189A LEU* 3.3 39.3 - - + -
190A ASN* 3.2 30.9 + - - +
193A ILE* 3.9 12.8 - - + -
201A ALA* 3.8 4.0 + - + -
202A ASN* 1.3 69.8 + - - +
204A VAL* 1.3 59.8 + - - +
205A ALA 4.0 16.6 - - - +
206A VAL* 4.3 3.4 - - + -
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Residues in contact with VAL 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A PRO* 4.2 2.9 - - + -
150A VAL 2.9 9.1 + - - +
163A ILE* 3.4 9.7 - - - +
164A ASP* 3.1 19.8 - - - +
202A ASN* 2.8 38.7 + - - +
203A ILE* 1.3 73.2 - - - +
205A ALA* 1.3 63.8 + - - +
457A THR* 3.2 44.4 - - + +
460A ALA* 3.9 12.1 - - + +
461A TYR* 4.2 20.0 - - + -
464A ALA* 6.1 2.2 - - + -
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Residues in contact with ALA 205 (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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150A VAL 3.8 0.4 + - - -
151A GLY* 3.9 1.3 - - - -
152A PHE* 3.1 24.6 + - - +
163A ILE* 3.5 27.8 - - + -
164A ASP* 4.3 0.9 - - - +
203A ILE* 3.4 4.8 - - - +
204A VAL* 1.3 86.4 - - + +
206A VAL* 1.3 68.2 + - - +
207A VAL* 4.3 2.9 - - + -
453A ALA 5.4 0.2 - - - +
456A VAL* 3.7 18.8 - - + -
457A THR* 4.2 13.7 - - - +
460A ALA* 4.5 1.6 - - + -
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Residues in contact with VAL 206 (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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66A THR 5.4 0.5 - - - +
152A PHE* 3.2 23.8 - - + +
154A PHE* 4.3 19.7 - - + +
158A CYS* 5.4 2.0 - - + -
160A GLN* 3.6 16.3 + - - +
163A ILE* 3.0 22.1 + - - +
164A ASP 5.0 0.4 - - - -
165A GLU 4.7 0.2 - - - +
166A ALA* 3.5 27.4 - - + -
185A VAL* 4.8 2.2 - - + -
186A VAL* 3.2 34.5 - - + -
203A ILE* 4.3 2.2 - - + -
205A ALA* 1.3 78.3 - - - +
207A VAL* 1.3 69.7 + - - +
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Residues in contact with VAL 207 (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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68A VAL* 5.2 0.4 - - + -
152A PHE 2.8 9.6 + - - +
153A THR* 3.2 21.0 - - - +
154A PHE 3.0 25.4 + - - -
160A GLN* 5.4 2.5 - - - -
163A ILE* 4.6 5.6 - - + -
205A ALA* 4.6 1.8 - - + -
206A VAL* 1.3 86.0 - - - +
208A ASN* 1.3 68.6 + - - +
211A VAL* 4.0 13.5 - - + -
212A GLY* 4.4 8.5 - - - +
452A GLY 5.4 0.4 - - - -
453A ALA* 4.1 16.8 - - + +
456A VAL* 3.6 37.7 - - + -
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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