Contacts of the strand formed by residues 81 - 89 (chain A) in PDB entry 5KJH
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 CYS 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A THR* 4.6 3.8 - - + -
18A PHE* 3.8 25.4 - - - -
57A PHE* 4.3 1.1 - - - -
68A CYS* 3.7 27.1 - - - -
69A ARG 3.6 3.4 - - - -
70A LEU* 3.8 14.8 - - + -
79A ASN* 3.1 34.2 + - - +
80A PRO* 1.3 79.2 - - - +
82A GLU* 1.3 64.6 + - - +
83A ILE* 5.0 0.2 - - - -
548A ILE* 3.9 16.6 - - + -
269B PHE* 4.0 15.0 - - + -
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Residues in contact with GLU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A CYS* 3.1 3.9 - - - -
69A ARG* 2.8 87.1 + - + +
71A THR* 4.1 8.8 + - - -
79A ASN 6.0 0.4 - - - +
80A PRO 5.3 2.2 - - - +
81A CYS* 1.3 75.6 - - - +
83A ILE* 1.3 63.1 + - - +
84A ILE* 3.6 8.5 + - + -
249B SER* 3.8 26.2 + - - +
269B PHE* 5.5 0.9 - - - -
288B TYR* 5.5 0.7 - - - -
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Residues in contact with ILE 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PHE* 4.9 4.0 - - + -
66A VAL* 3.9 20.0 - - + -
67A ILE 3.5 5.6 - - - +
68A CYS* 3.7 18.6 - - - -
81A CYS* 5.0 0.2 - - - -
82A GLU* 1.3 72.8 - - - +
84A ILE* 1.3 58.9 + - - +
85A GLN 3.5 25.8 - - - +
86A LEU* 4.6 7.2 - - + -
249B SER* 3.5 3.5 + - - -
250B LYS* 3.0 26.0 + - + +
267B VAL* 3.7 32.3 - - + -
269B PHE* 3.8 26.5 - - + -
288B TYR* 3.5 32.5 + - + -
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Residues in contact with ILE 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A VAL* 4.2 11.4 - - + -
67A ILE* 3.0 26.9 + - + +
68A CYS 4.8 0.7 - - - +
69A ARG* 3.6 35.9 - - + +
82A GLU* 4.0 16.4 - - + +
83A ILE* 1.3 73.5 - - - +
85A GLN* 1.3 64.6 + - + +
244B PHE* 3.8 39.9 - - + -
247B MET* 3.6 32.5 - - + +
248B LYS 3.8 17.9 - - - +
250B LYS* 3.7 19.3 - - - +
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Residues in contact with GLN 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A VAL 3.8 0.2 - - - -
67A ILE* 2.8 60.6 + - + +
83A ILE* 3.5 9.1 - - - +
84A ILE* 1.3 79.3 - - - +
86A LEU* 1.3 71.1 + - - +
87A ILE* 3.8 16.6 - - + -
125A VAL* 2.8 28.5 + - + +
126A THR 4.2 2.6 + - - -
127A GLU 4.7 0.2 - - - -
128A GLY* 3.8 17.2 - - - +
247B MET* 4.1 15.4 - - + +
250B LYS* 2.8 33.2 + - - +
291B VAL* 3.6 10.5 - - - +
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Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PHE* 3.8 17.0 - - + -
64A HIS* 4.0 12.1 - - + -
65A ALA 3.5 6.5 - - - +
66A VAL* 3.7 30.7 - - + -
83A ILE* 4.6 9.0 - - + -
85A GLN* 1.3 79.8 + - - +
87A ILE* 1.3 60.8 + - - +
250B LYS* 4.8 4.5 - - + +
265B MET* 3.8 28.7 - - + -
267B VAL* 6.1 0.9 - - + -
288B TYR* 3.9 22.0 - - + -
289B PRO 4.0 9.9 - - - +
290B VAL* 3.8 18.9 - - + -
291B VAL* 2.9 28.8 + - - +
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Residues in contact with ILE 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A HIS* 3.2 9.8 - - - +
65A ALA* 2.9 42.0 + - + +
67A ILE* 4.5 2.9 - - + -
85A GLN* 3.8 27.1 - - + -
86A LEU* 1.3 77.2 - - - +
88A ARG* 1.3 70.6 + - - +
89A ASP 4.1 0.6 + - - +
123A TYR* 4.3 25.8 - - + -
125A VAL* 4.0 27.8 - - + -
128A GLY* 4.4 4.3 - - - -
291B VAL* 3.4 9.6 - - + +
293B ILE* 3.6 35.2 - - + -
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Residues in contact with ARG 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LYS* 3.6 12.8 - - + +
64A HIS* 2.9 34.2 + - + +
87A ILE* 1.3 75.7 - - - +
89A ASP* 1.4 71.2 + - - +
90A ASP* 3.2 21.2 + - - +
263B PRO* 4.1 22.7 - - - +
264B THR 5.0 0.6 + - - -
265B MET* 3.5 26.9 - - - +
290B VAL* 3.4 28.3 - - + +
291B VAL 2.8 11.5 + - - +
292B CYS* 3.7 8.9 - - - -
293B ILE* 2.9 28.6 + - - +
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Residues in contact with ASP 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LYS* 2.9 51.0 + - - +
64A HIS* 4.9 0.2 - - - +
87A ILE* 4.1 2.0 + - - +
88A ARG* 1.4 69.8 - - - +
90A ASP* 1.3 58.1 + - - +
91A GLY* 3.5 12.7 + - - -
93A GLU* 3.7 14.1 - - - +
95A ASN* 2.8 33.3 + - - +
113A ILE* 5.8 0.4 - - + -
121A LYS* 3.2 22.0 + - - +
123A TYR* 3.7 23.7 + - + +
293B ILE 3.8 4.1 - - - +
295B PRO* 4.0 8.7 - - - +
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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