Contacts of the strand formed by residues 61 - 69 (chain B) in PDB entry 5HKE
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 TYR 61 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B TYR* 3.8 7.6 - - - -
37B PHE* 4.4 12.1 - + - -
38B LYS* 3.8 24.8 + - + -
39B PHE* 5.0 1.2 - - - -
57B VAL* 3.3 6.7 - - - +
58B ALA 2.9 32.1 + - - +
59B ASN 4.2 3.6 - - - +
60B ASP* 1.3 78.8 - - - +
62B PRO* 1.3 87.3 - - + +
63B LEU* 3.3 18.0 + - + +
100B PHE* 3.8 27.8 - + - -
101B GLU* 3.6 21.1 - - + +
104B PRO* 3.5 25.5 - - + +
130B PHE* 3.7 18.2 - + + -
309B LEU* 4.3 0.4 - - - -
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Residues in contact with PRO 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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29B ILE* 3.9 24.2 - - + -
31B THR* 3.8 13.9 - - - +
35B TYR* 3.4 19.7 - - + +
37B PHE* 3.9 17.7 - - + -
56B ILE 3.9 3.8 - - - +
57B VAL* 4.5 0.7 - - + -
61B TYR* 1.3 105.0 - - + +
63B LEU* 1.3 59.0 + - - +
64B TYR* 3.3 29.0 + - + -
100B PHE 4.9 0.9 - - - +
104B PRO* 4.6 4.2 - - + +
309B LEU* 4.1 9.8 - - + -
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Residues in contact with LEU 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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29B ILE* 4.6 0.4 - - - +
55B GLY* 3.3 2.8 - - - -
56B ILE* 2.8 49.4 + - + +
58B ALA* 3.9 17.5 - - + -
61B TYR* 3.7 25.8 - - + +
62B PRO* 1.3 69.8 - - - +
64B TYR* 1.3 64.6 + - - +
65B PHE* 3.6 4.2 + - - -
100B PHE* 3.8 29.4 - - + +
130B PHE* 3.8 18.4 - - + -
134B LEU* 3.8 29.2 - - + -
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Residues in contact with TYR 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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29B ILE* 2.8 43.5 + - + +
31B THR* 2.8 34.5 + - - -
51B LEU* 3.7 32.7 - - + +
53B GLY* 3.5 15.5 - - - -
54B VAL 3.6 11.0 - - - -
55B GLY 4.6 0.2 - - - -
62B PRO* 3.3 22.1 + - + -
63B LEU* 1.3 74.1 - - - +
65B PHE* 1.3 62.5 + - - +
66B ASP 3.4 20.2 - - - +
67B ALA* 3.8 4.0 - - + -
77B GLY* 6.0 0.2 - - - -
100B PHE 5.5 2.0 + - - -
103B ILE* 3.5 34.2 - - + +
104B PRO* 4.9 6.7 - - + +
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Residues in contact with PHE 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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16B ARG* 3.0 17.1 + - - +
18B LEU* 4.1 29.2 - - + -
20B LEU* 5.1 9.4 - - + -
25B GLY 5.7 0.2 - - - -
26B GLU* 3.9 20.4 - - + -
54B VAL 2.8 6.8 + - - +
55B GLY* 3.6 30.1 - - - -
56B ILE* 4.5 15.9 - - + -
63B LEU 3.6 3.5 + - - -
64B TYR* 1.3 75.2 - - - +
66B ASP* 1.3 59.9 + - - +
77B GLY* 3.0 31.1 + - - +
103B ILE* 4.2 1.6 - - - -
274B TYR* 3.4 26.9 - + - +
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Residues in contact with ASP 66 (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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14B PHE* 4.9 2.2 - - + -
16B ARG* 2.9 26.3 + - + -
53B GLY* 3.3 0.2 - - - -
54B VAL* 3.0 30.1 + - - +
64B TYR* 3.4 4.9 - - - -
65B PHE* 1.3 76.8 - - - +
67B ALA* 1.3 65.5 + - - +
75B MET 3.2 13.0 - - - +
76B ALA* 3.8 14.4 - - + +
103B ILE* 4.3 2.2 - - - -
274B TYR* 2.7 24.9 + - - -
276B ASN* 2.9 17.5 + - - -
278B TYR* 2.6 31.0 + - + +
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Residues in contact with ALA 67 (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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14B PHE* 3.9 1.6 - - - -
51B LEU* 4.7 2.5 - - + -
52B ILE 3.4 14.1 - - - +
53B GLY* 3.9 0.2 - - - -
64B TYR* 3.8 26.2 - - + -
66B ASP* 1.3 78.1 - - - +
68B ILE* 1.3 68.1 + - - +
74B GLY* 3.4 2.6 - - - -
75B MET 3.0 30.9 + - - +
103B ILE* 4.2 5.1 - - + +
107B LEU* 3.4 18.0 - - + +
278B TYR* 3.6 6.4 + - - -
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Residues in contact with ILE 68 (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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14B PHE* 4.0 3.8 - - + -
51B LEU* 3.2 5.9 - - - +
52B ILE* 2.8 51.9 + - + +
67B ALA* 1.3 78.2 - - - +
69B ASN* 1.3 69.9 + - - +
72B GLY* 5.0 0.4 - - - -
73B LEU 3.1 10.8 - - - +
74B GLY* 3.8 7.6 - - - -
107B LEU* 4.0 4.5 - - - -
278B TYR* 3.5 38.6 - - + -
279B ASP 4.4 3.4 - - - +
280B LEU* 3.6 25.4 - - + -
283B LYS* 3.8 34.5 - - + -
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Residues in contact with ASN 69 (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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49B LYS* 3.7 9.9 - - + +
50B SER 3.1 13.7 - - - +
51B LEU* 3.6 6.1 - - + -
68B ILE* 1.3 83.6 - - - +
70B GLU* 1.3 61.1 + - - +
71B ASP* 2.9 17.4 + - - +
72B GLY* 3.0 18.2 + - - -
73B LEU* 2.9 36.2 + - - +
107B LEU* 2.8 29.2 + - + +
110B CYS 2.8 28.9 + - - -
283B LYS* 4.1 2.3 - - - +
300B LEU* 4.1 4.1 - - - +
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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