Contacts of the strand formed by residues 56 - 65 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449A GLN* 2.8 19.2 + - - +
453A HIS* 3.0 20.0 + - - -
53B THR* 4.0 5.4 - - - -
54B ILE 3.0 4.7 + - - -
55B GLY* 1.3 75.6 - - - +
57B ALA* 1.3 60.6 + - - +
75B TRP* 4.2 10.1 - - + -
76B ASP 3.2 15.3 - - - +
77B THR* 4.2 4.0 - - - -
90B TYR* 3.4 35.4 - - + +
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Residues in contact with ALA 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453A HIS* 3.9 5.2 - - + -
53B THR* 4.1 6.3 - - + +
56B ALA* 1.3 74.5 - - - +
58B PHE* 1.3 61.8 + - - +
59B LEU* 4.3 3.9 + - + +
74B ILE 3.9 0.3 - - - +
75B TRP* 3.8 6.9 - - - -
76B ASP* 3.1 32.2 + - - +
302B EDO 3.9 35.2 - - - +
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Residues in contact with PHE 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453A HIS* 3.5 46.2 + - + +
454A LEU* 4.6 11.7 - - + -
457A GLN* 3.4 35.2 - - + -
473A TYR* 4.7 8.7 - + - -
476A GLN* 5.9 0.2 - - - -
57B ALA* 1.3 74.8 - - - +
59B LEU* 1.3 79.9 + - - +
60B THR* 3.9 15.3 - - - -
73B GLU* 4.3 15.5 - - + -
74B ILE 3.5 11.4 - - - -
75B TRP* 3.2 47.1 - + + -
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Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A GLN* 5.4 1.3 - - - +
38B VAL* 4.3 11.2 - - + -
39B LEU* 6.5 0.2 - - - -
42B VAL* 4.0 36.3 - - + -
43B LYS* 5.5 8.5 - - + -
57B ALA* 4.8 2.0 - - + -
58B PHE* 1.3 100.0 - - - +
60B THR* 1.3 68.7 + - - +
61B GLN 4.3 0.2 - - - -
74B ILE* 3.1 42.2 + - + +
76B ASP* 6.4 0.4 - - + -
302B EDO 3.6 29.6 - - - +
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Residues in contact with THR 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457A GLN* 4.1 17.0 + - - +
460A LYS* 5.8 2.6 + - - -
461A GLU* 5.1 4.7 - - - +
473A TYR* 4.3 8.0 + - - -
42B VAL* 5.7 2.3 - - - +
58B PHE* 3.9 17.0 - - - -
59B LEU* 1.3 80.0 + - - +
61B GLN* 1.3 63.0 + - - +
62B THR* 4.3 5.7 + - - +
71B LYS* 3.6 38.1 - - + +
72B PHE 3.4 9.8 + - - +
73B GLU* 4.5 2.4 - - - +
74B ILE 5.0 0.2 - - - +
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Residues in contact with GLN 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B PHE* 3.9 33.2 + - + +
42B VAL* 3.3 56.4 + - + +
59B LEU 4.3 0.6 - - - -
60B THR* 1.3 76.8 - - - +
62B THR* 1.3 87.7 + - - +
63B VAL* 4.0 8.7 - - + -
71B LYS* 4.0 0.2 - - - -
72B PHE* 3.1 35.6 + - - +
74B ILE* 4.3 7.9 - - + +
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Residues in contact with THR 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ILE* 5.9 1.1 - - + -
60B THR* 4.3 4.5 + - - +
61B GLN* 1.3 88.7 + - - +
63B VAL* 1.3 62.6 + - - +
69B THR* 3.6 23.3 - - + -
70B VAL 3.4 17.9 - - - +
71B LYS* 3.9 22.2 - - + +
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Residues in contact with VAL 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B PHE* 4.3 24.2 - - + +
61B GLN* 4.0 9.6 + - + -
62B THR* 1.3 80.4 - - - +
64B CYS* 1.3 61.6 + - - +
65B LEU* 5.1 0.7 - - + +
69B THR* 4.1 1.0 - - - +
70B VAL* 2.9 47.8 + - + +
72B PHE* 4.1 17.3 - - + -
172B ASN* 5.4 4.5 - - - +
176B MET* 4.7 28.9 - - + -
179B ALA* 5.6 1.8 - - + -
69D THR* 5.7 0.9 - - - -
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Residues in contact with CYS 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B VAL* 1.3 74.3 - - - +
65B LEU* 1.3 62.2 + - - +
68B THR 3.5 8.7 - - - +
69B THR* 3.9 7.2 - - + +
176B MET* 4.8 4.9 - - - +
64D CYS* 1.9 63.3 - - - -
67D ASP* 3.3 19.0 + - - +
68D THR 4.2 4.0 - - - -
69D THR* 2.8 24.4 + - - -
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Residues in contact with LEU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B VAL* 4.1 2.2 + - + +
64B CYS* 1.3 69.6 - - - +
66B ASP* 1.3 88.3 + - - +
68B THR* 2.7 39.9 - - + +
70B VAL* 3.7 30.6 - - + +
176B MET* 4.1 21.3 - - + +
179B ALA* 3.8 27.8 - - + +
180B LYS* 3.9 27.1 - - + +
67D ASP* 3.8 4.7 - - - +
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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