Contacts of the strand formed by residues 56 - 64 (chain H) in PDB entry 4KYI
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 ALA 56 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449G GLN* 2.5 19.1 + - + +
453G HIS* 2.9 20.0 + - - -
53H THR* 4.5 4.5 - - - -
54H ILE 3.2 4.3 + - - +
55H GLY* 1.3 75.3 - - - +
57H ALA* 1.3 60.1 + - - +
75H TRP* 4.2 14.6 - - + -
76H ASP 3.2 16.2 - - - +
77H THR* 4.4 1.1 - - + -
90H TYR* 3.3 34.1 - - + +
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Residues in contact with ALA 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453G HIS* 4.0 3.8 - - - -
53H THR* 4.2 8.4 - - + +
56H ALA* 1.3 75.9 - - - +
58H PHE* 1.3 61.9 + - - +
59H LEU* 4.2 10.7 + - + -
74H ILE 3.6 0.3 - - - +
75H TRP* 3.5 4.9 - - - -
76H ASP* 2.7 57.9 + - + +
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Residues in contact with PHE 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453G HIS* 3.5 44.9 + - + +
454G LEU* 4.6 12.3 - - + -
457G GLN* 3.4 35.4 + - + -
473G TYR* 5.4 5.6 - + - -
57H ALA* 1.3 75.6 - - - +
59H LEU* 1.3 70.9 - - - +
60H THR* 3.8 12.6 - - - -
73H GLU* 4.0 25.1 - - + -
74H ILE 3.3 15.0 - - - -
75H TRP* 3.3 40.8 - + + -
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Residues in contact with LEU 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457G GLN* 5.3 0.7 - - - +
38H VAL* 3.6 35.4 - - + -
39H LEU* 5.8 2.9 - - + -
42H VAL* 3.9 27.1 - - + -
43H LYS* 5.8 4.7 - - - -
57H ALA* 4.4 14.8 - - + +
58H PHE* 1.3 92.3 - - - +
60H THR* 1.3 70.5 + - - +
72H PHE 3.9 0.3 - - - +
74H ILE* 3.1 36.3 + - + +
76H ASP* 4.7 6.5 - - + -
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Residues in contact with THR 60 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457G GLN* 3.0 31.7 + - - +
460G LYS* 5.4 5.9 + - - -
461G GLU* 4.9 2.0 - - - +
473G TYR* 5.4 3.1 + - - +
42H VAL* 5.2 3.9 - - - +
58H PHE* 3.8 9.5 - - - -
59H LEU* 1.3 80.6 + - - +
61H GLN* 1.3 75.0 + - - +
62H THR* 5.3 0.9 - - + -
71H LYS* 3.6 35.0 - - + -
72H PHE 3.5 11.6 + - - +
73H GLU* 5.2 2.6 - - + +
74H ILE* 5.1 0.7 - - - -
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Residues in contact with GLN 61 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41H PHE* 3.6 52.0 + - + -
42H VAL* 3.8 31.3 + - + +
60H THR* 1.3 83.5 - - - +
62H THR* 1.3 73.3 + - - +
63H VAL* 4.1 5.3 + - + +
70H VAL 4.0 0.9 - - - +
71H LYS* 3.8 0.2 - - - -
72H PHE* 3.0 35.4 + - - +
74H ILE* 4.5 7.8 - - + +
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Residues in contact with THR 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F THR* 5.7 0.5 + - - -
60H THR* 5.3 0.7 - - + -
61H GLN* 1.3 79.9 + - - +
63H VAL* 1.3 66.6 + - - +
64H CYS* 6.0 0.2 - - - -
69H THR* 4.0 19.3 - - + -
70H VAL 3.4 6.3 - - - -
71H LYS* 3.6 40.2 - - + -
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Residues in contact with VAL 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F THR* 5.6 0.9 - - - -
41H PHE* 3.8 29.2 - - + -
61H GLN* 4.5 7.0 - - + +
62H THR* 1.3 78.1 - - - +
64H CYS* 1.3 65.1 + - - +
69H THR* 3.7 3.1 - - - -
70H VAL* 3.0 50.3 + - + +
72H PHE* 4.0 20.2 - - + -
172H ASN* 5.4 2.7 - - - +
176H MET* 3.6 28.5 - - - -
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Residues in contact with CYS 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F CYS* 2.0 56.5 - - + -
67F ASP* 3.8 32.0 - - - +
68F THR 4.6 0.2 - - - +
69F THR* 2.7 33.0 + - - +
63H VAL* 1.3 76.3 - - - +
65H LEU* 1.3 59.2 + - - +
66H ASP 4.0 1.1 - - - +
68H THR 3.2 3.1 - - - -
69H THR* 5.6 0.4 - - - -
176H MET* 3.3 17.8 - - - +
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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