Contacts of the helix formed by residues 62 - 75 (chain F) in PDB entry 1KR2
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 PRO 62 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F ASP* 3.6 9.9 - - - +
61F ILE* 1.4 93.2 - - + +
63F ALA* 1.3 67.0 + - - +
64F TYR* 4.2 10.1 - - + +
65F HIS* 2.9 37.5 + - + +
66F ARG* 3.3 8.8 + - - +
261F ARG* 3.9 25.3 - - - +
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Residues in contact with ALA 63 (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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50F PRO* 6.0 0.4 - - + -
51F VAL 4.4 2.0 - - - +
53F ASP* 2.8 26.4 + - - +
62F PRO* 1.3 70.1 - - - +
64F TYR* 1.3 53.9 + - - +
66F ARG* 3.3 25.4 - - - +
67F VAL* 2.7 40.4 + - + +
87F SER* 4.3 27.8 - - - +
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Residues in contact with TYR 64 (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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62F PRO* 3.0 10.0 - - + +
63F ALA* 1.3 78.8 - - - +
65F HIS* 1.3 71.3 + + + +
67F VAL* 3.8 5.1 - - - +
68F ILE* 2.8 63.5 + - + +
247F TYR* 4.3 7.9 - - - -
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Residues in contact with HIS 65 (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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61F ILE* 3.8 15.3 - - + +
62F PRO* 2.9 32.3 + - + +
64F TYR* 1.3 88.2 - + + +
66F ARG* 1.3 60.1 + - - +
68F ILE* 3.2 4.0 + - - +
69F MET* 2.8 40.2 + - + +
247F TYR* 2.6 40.6 + + - -
251F HIS* 5.1 4.9 - - - +
253F LEU* 3.3 27.7 - - + +
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Residues in contact with ARG 66 (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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16F SER* 3.0 29.7 + - - +
17F PHE* 3.3 21.1 - - + +
18F ASN* 3.7 13.2 - - - +
20F ILE* 5.6 0.3 - - - +
50F PRO* 4.0 14.3 - - + +
51F VAL 3.1 29.9 + - - +
53F ASP* 2.8 28.5 + - - +
60F LEU* 3.0 29.9 - - - +
61F ILE* 2.8 26.9 + - + -
62F PRO 3.3 4.1 + - - +
63F ALA* 3.1 14.6 + - - +
65F HIS* 1.3 75.7 - - - +
67F VAL* 1.3 63.4 + - - +
69F MET* 3.9 11.8 - - + +
70F ALA* 3.0 25.1 + - - +
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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
----------------------------------------------------------
50F PRO* 4.4 17.5 - - + -
63F ALA 2.7 26.2 + - - +
64F TYR* 3.8 5.8 - - - +
66F ARG* 1.3 73.1 - - - +
68F ILE* 1.3 65.6 + - + +
70F ALA* 3.2 4.1 + - - +
71F GLU* 2.9 42.8 + - + +
82F VAL* 4.3 3.1 - - + -
84F THR* 3.4 28.9 - - + -
87F SER* 3.6 32.1 - - - +
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Residues in contact with ILE 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64F TYR* 2.8 58.0 + - + +
65F HIS 3.2 4.9 + - - +
67F VAL* 1.3 79.9 - - + +
69F MET* 1.3 57.1 + - - +
71F GLU* 3.3 20.9 + - - +
72F LEU* 2.9 38.5 + - + +
247F TYR* 3.8 30.1 - - + +
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Residues in contact with MET 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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17F PHE 4.6 0.2 - - - +
19F PRO* 3.7 13.5 - - + -
20F ILE* 3.9 9.2 - - + -
61F ILE* 4.1 10.5 - - + -
65F HIS* 2.8 28.1 + - + +
66F ARG* 3.9 17.0 - - + +
68F ILE* 1.3 69.0 - - - +
70F ALA* 1.3 61.2 + - - +
72F LEU* 3.1 9.4 + - - +
73F ALA* 2.8 30.7 + - - +
244F VAL* 3.6 19.1 - - + +
247F TYR* 3.8 19.7 - - + -
248F ILE* 3.6 35.0 - - - -
253F LEU* 3.9 8.1 - - - -
254F TYR* 3.6 23.6 - - + +
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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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17F PHE* 5.5 1.3 - - + -
20F ILE* 4.0 19.6 - - + +
48F ILE* 4.1 19.5 - - + -
50F PRO* 4.4 5.2 - - + -
66F ARG 3.0 18.5 + - - +
67F VAL 3.5 4.3 - - - +
69F MET* 1.3 78.2 - - - +
71F GLU* 1.3 63.1 + - - +
73F ALA* 3.2 3.3 + - - +
74F THR* 2.9 27.9 + - - +
82F VAL* 3.5 21.1 - - + -
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Residues in contact with GLU 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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67F VAL* 2.9 33.5 + - + +
68F ILE* 3.6 23.1 - - + +
69F MET 3.2 0.2 - - - -
70F ALA* 1.3 76.5 - - - +
72F LEU* 1.3 58.1 + - + +
74F THR* 3.3 7.9 + - - -
75F LYS* 2.9 30.0 + - - +
82F VAL* 3.8 19.9 - - + +
84F THR* 4.2 10.4 - - - +
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Residues in contact with LEU 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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68F ILE* 2.9 25.3 + - + +
69F MET* 3.1 11.0 + - - +
71F GLU* 1.3 77.0 - - + +
73F ALA* 1.3 64.7 + - - +
74F THR 3.3 0.5 + - - -
75F LYS* 3.4 22.1 + - + +
76F ASN* 5.0 0.5 + - - +
241F PRO* 5.3 1.2 - - - +
243F LEU* 3.6 55.4 - - + +
244F VAL* 4.2 6.1 - - + -
247F TYR* 3.7 31.2 - - + -
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Residues in contact with ALA 73 (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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238E TYR* 4.3 11.6 + - - -
20F ILE* 3.7 28.9 - - + -
25F LEU* 3.9 25.4 - - + +
69F MET 2.8 16.8 + - - +
70F ALA 3.2 5.4 + - - +
72F LEU* 1.3 78.9 - - - +
74F THR* 1.3 58.2 + - - +
75F LYS 3.9 0.2 + - - -
76F ASN* 5.0 1.9 + - - +
77F SER 5.4 0.2 + - - -
241F PRO* 4.0 19.8 - - + +
244F VAL* 3.9 2.6 - - + +
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Residues in contact with THR 74 (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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238E TYR* 5.7 0.4 - - - +
25F LEU* 4.1 9.6 - - + -
48F ILE* 3.6 30.7 - - + -
70F ALA 2.9 16.1 + - - +
71F GLU* 3.4 6.1 + - - -
72F LEU 3.2 0.2 - - - -
73F ALA* 1.3 76.6 - - - +
75F LYS* 1.3 56.7 + - - +
76F ASN 3.1 3.6 - - - -
77F SER* 2.6 36.4 + - - +
80F VAL* 3.6 32.5 + - + +
81F GLU* 4.5 2.3 - - - -
82F VAL* 3.7 13.5 + - + +
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Residues in contact with LYS 75 (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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71F GLU 2.9 12.4 + - - +
72F LEU* 3.4 20.2 + - + +
73F ALA 3.5 0.2 - - - -
74F THR* 1.3 76.8 - - - +
76F ASN* 1.3 72.6 + - - +
77F SER 3.5 3.5 + - - +
243F LEU* 4.1 23.4 - - + +
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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