Contacts of the strand formed by residues 66 - 72 (chain F) in PDB entry 2HAK
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 LYS 66 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F THR* 3.4 29.1 + - + +
60F GLY 3.7 10.1 - - - +
61F LYS* 4.4 15.3 - - + +
65F ALA* 1.3 74.4 - - - +
67F VAL* 1.3 67.3 + - - +
68F LYS* 3.9 21.8 - - + +
81F VAL 3.6 0.5 - - - +
82F LYS* 3.2 5.2 - - - +
83F ILE* 2.8 52.8 + - + +
202F VAL* 4.9 0.7 - - - -
66H LYS* 3.3 28.7 - - - +
68H LYS* 6.0 0.4 - - - +
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Residues in contact with VAL 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F THR* 3.3 4.1 - - - +
59F ILE* 2.4 58.3 + - + -
60F GLY 2.5 24.0 + - - +
66F LYS* 1.3 79.2 - - - +
68F LYS* 1.3 63.4 - - - +
80F ALA* 4.2 11.7 - - + -
81F VAL 3.4 9.6 - - - +
82F LYS* 3.3 29.4 - - + +
129F MET* 6.0 3.6 - - - -
202F VAL* 3.8 20.2 - - + -
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Residues in contact with LYS 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F PRO* 6.5 0.9 - - - -
55F LEU* 4.1 26.9 - - + -
56F GLN 3.2 19.6 + - - +
57F LYS* 3.6 5.1 - - - +
58F THR* 2.4 38.4 + - + +
59F ILE* 4.1 3.4 - - - -
66F LYS* 3.9 20.8 + - + +
67F VAL* 1.3 74.7 - - - +
69F LEU* 1.3 67.8 + - - +
80F ALA* 3.5 3.6 - - - -
81F VAL* 2.7 43.5 + - - +
83F ILE* 3.8 26.0 - - + -
66H LYS* 5.9 0.4 - - - +
68H LYS* 6.1 1.9 - - - +
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Residues in contact with LEU 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F GLN* 2.7 42.7 + - + +
57F LYS* 3.0 39.0 + - + +
59F ILE* 3.8 20.0 - - + +
68F LYS* 1.3 76.0 - - - +
70F ALA* 1.3 62.9 + - - +
78F GLU* 3.7 23.6 - - + +
79F VAL 3.4 13.5 - - - +
131F TYR* 3.8 44.6 - - + +
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Residues in contact with ALA 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F TYR* 4.4 5.4 - - + -
54F ARG 3.2 15.9 - - - +
55F LEU* 3.8 11.4 - - + -
56F GLN* 2.9 9.6 - - - +
69F LEU* 1.3 77.0 - - - +
71F ARG* 1.3 56.2 + - - +
78F GLU* 3.3 4.2 - - - +
79F VAL* 2.6 43.8 + - + +
81F VAL* 3.7 29.2 - - + -
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Residues in contact with ARG 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F TYR* 3.6 3.5 - - - -
54F ARG* 2.9 64.2 + - + +
56F GLN* 2.9 13.4 + - - +
70F ALA* 1.3 74.7 - - - +
72F HIS* 1.3 72.7 + - - +
73F VAL* 3.4 4.1 + - - +
76F GLY* 3.1 30.3 + - - +
77F ARG 3.4 3.4 - - - -
78F GLU* 2.9 33.2 + - - +
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Residues in contact with HIS 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F ASN* 3.5 27.8 + - + +
53F TYR* 3.5 39.8 + + + -
70F ALA 4.2 0.2 + - - -
71F ARG* 1.3 70.1 - - - +
73F VAL* 1.3 58.0 + - - +
74F LEU* 3.4 25.5 - - + +
75F THR* 2.8 34.9 + - + +
76F GLY* 2.6 35.0 + - - -
77F ARG 2.8 17.9 + - - +
79F VAL* 5.0 0.6 - - + +
117F GLU* 4.7 2.0 + - - -
353F GLU 4.9 0.2 + - - -
356F ALA* 4.8 0.4 - - - +
357F THR* 3.5 23.8 + - - -
360F LEU* 3.4 19.8 - - + +
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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