Contacts of the strand formed by residues 254 - 258 (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 ARG 254 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A ARG* 3.1 42.6 + - - +
225A GLU* 3.0 32.9 + - - +
239A MET* 3.7 45.0 + - + +
240A GLU 3.4 10.3 - - - +
241A GLU* 3.0 29.0 + - - +
242A LEU* 4.3 5.4 - - - +
252A GLU 4.0 0.2 + - - -
253A GLY* 1.3 80.5 - - - +
255A MET* 1.3 61.4 + - - +
397A LEU* 3.9 10.7 - - - +
400A ASN* 5.6 2.8 - - - +
401A LYS* 3.8 18.2 - - - +
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Residues in contact with MET 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PRO* 3.4 15.0 - - + -
66A THR 4.3 0.9 - - - +
67A PHE* 3.5 44.4 - - + +
68A VAL 3.5 6.7 - - - +
69A ARG* 4.3 12.1 - - + +
239A MET* 4.2 3.4 - - - -
240A GLU* 3.1 30.8 + - - +
242A LEU* 4.5 7.6 - - + +
245A ILE* 3.6 21.1 - - + +
248A VAL* 3.2 48.0 - - + -
254A ARG* 1.3 75.9 - - - +
256A CYS* 1.3 74.0 + - - +
257A ILE* 3.5 2.4 + - - +
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Residues in contact with CYS 256 (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* 2.4 44.9 + - - +
68A VAL* 2.8 19.6 + - + +
211A VAL* 3.8 14.1 - - - -
214A MET* 3.4 26.5 - - + -
237A CYS* 3.4 26.5 - - - -
238A TYR 3.2 11.4 - - - -
239A MET* 3.9 14.9 - - + -
255A MET* 1.3 73.7 - - - +
257A ILE* 1.3 61.4 + - - +
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Residues in contact with ILE 257 (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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51A LEU* 4.4 9.0 - - + -
63A MET* 3.6 38.8 - - + +
64A LEU 3.7 1.1 - - - +
65A PRO* 3.6 28.5 - - + -
66A THR* 4.6 0.9 - - - -
237A CYS* 3.0 27.1 - - - +
238A TYR* 2.7 35.9 + - + +
240A GLU* 3.8 22.7 - - + -
245A ILE* 3.8 28.5 - - + -
255A MET* 4.7 0.2 - - + -
256A CYS* 1.3 74.4 - - - +
258A ASN* 1.3 64.3 + - - +
259A THR 3.5 3.6 + - - +
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Residues in contact with ASN 258 (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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63A MET 3.7 0.3 + - - -
64A LEU* 2.6 50.0 + - + +
66A THR* 3.9 16.6 - - + +
156A PHE 4.7 0.8 + - - -
157A PRO* 4.7 2.0 - - - +
158A CYS 5.1 1.4 + - - +
208A ASN* 3.8 22.1 - - + +
210A THR* 4.3 2.7 + - - +
235A ASN* 2.9 26.7 + - - +
236A ALA 4.4 0.3 - - - +
237A CYS* 4.2 7.2 - - + -
256A CYS 4.1 0.6 + - - -
257A ILE* 1.3 72.6 - - - +
259A THR* 1.3 63.3 + - - +
260A GLU* 3.2 31.3 + - - +
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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