Contacts of the strand formed by residues 60 - 66 (chain A) in PDB entry 5HNK
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 60 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ASN 3.2 14.8 - - - +
22A LEU 4.5 0.4 - - - -
23A MET* 3.8 22.7 - - + +
55A ALA* 2.8 26.6 + - - +
58A TYR* 4.0 4.5 - - + +
59A SER* 1.3 71.1 - - - +
61A ARG* 1.3 61.3 + - - +
62A THR 3.7 15.5 - - - +
63A THR* 4.0 9.7 + - - +
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Residues in contact with ARG 61 (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 ARG* 3.7 24.0 - - + +
21A ASN 3.1 7.8 + - - +
59A SER 3.6 4.0 + - - -
60A ALA* 1.3 72.1 - - - +
62A THR* 1.3 77.9 + - - +
143A LEU* 3.5 21.0 + - - +
144A TYR* 3.3 29.7 - - + -
288A ILE 5.0 0.4 + - - -
289A ALA 3.2 27.3 + - - -
290A GLU 4.0 9.9 + - - -
291A GLN* 3.6 45.8 + - - +
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Residues in contact with THR 62 (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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21A ASN 3.6 1.2 + - - -
22A LEU* 3.5 18.2 - - + +
23A MET 2.9 25.8 + - - -
60A ALA* 3.7 2.7 - - - +
61A ARG* 1.3 96.8 + - - +
63A THR* 1.3 63.5 + - - +
64A ILE* 4.1 6.7 - - + -
120A PRO* 5.6 0.7 - - + -
140A ILE* 5.4 0.2 - - + -
144A TYR* 2.7 31.3 + - - +
288A ILE* 3.5 36.6 + - + +
289A ALA* 5.2 0.2 - - - -
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Residues in contact with THR 63 (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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23A MET* 3.3 31.7 - - + +
25A VAL* 4.2 6.5 - - + -
51A ILE* 3.7 18.4 - - + -
55A ALA* 3.4 25.5 - - - +
60A ALA* 4.0 4.7 + - - +
61A ARG 4.4 0.2 - - - -
62A THR* 1.3 74.3 + - - +
64A ILE* 1.3 63.3 + - - +
65A VAL* 4.2 3.4 - - + -
119A PHE* 3.7 29.0 - - + +
120A PRO* 3.5 25.3 - - - +
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Residues in contact with ILE 64 (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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22A LEU* 4.2 13.0 - - + -
23A MET 3.0 8.4 + - - +
24A ILE* 3.5 8.5 - - + +
25A VAL* 3.0 24.4 + - - +
62A THR* 4.1 11.0 - - + -
63A THR* 1.3 76.4 - - - +
65A VAL* 1.3 63.7 + - - +
66A LEU* 3.8 24.1 + - + -
120A PRO* 3.5 7.9 - - + +
122A PHE* 3.9 20.9 - - + -
136A ILE* 4.1 34.3 - - + -
140A ILE* 4.5 5.6 - - + -
285A ILE* 4.2 9.9 - - + -
288A ILE* 4.2 22.0 - - + -
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Residues in contact with VAL 65 (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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25A VAL* 3.9 11.7 - - + -
27A GLY* 4.3 4.7 - - - -
47A TYR* 4.2 17.7 - - - +
51A ILE* 4.2 13.5 - - + -
63A THR* 4.2 11.4 - - + -
64A ILE* 1.3 75.2 - - - +
66A LEU* 1.3 69.8 + - - +
112A PHE* 4.3 10.1 - - + -
115A CYS* 3.5 34.1 - - - -
119A PHE* 4.1 15.3 - - + -
120A PRO 2.9 6.3 + - - -
121A THR* 3.3 10.0 - - + +
122A PHE 3.1 24.8 + - - -
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Residues in contact with LEU 66 (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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24A ILE* 3.7 24.2 - - + -
25A VAL 2.9 14.6 + - - +
27A GLY* 2.7 34.8 + - - -
64A ILE* 3.8 22.4 - - + -
65A VAL* 1.3 75.3 - - - +
67A GLY* 1.3 57.4 + - - +
112A PHE* 3.6 3.2 - - - -
122A PHE* 3.5 18.2 - - + -
129A ALA* 3.4 38.3 - - + +
132A MET* 3.8 19.5 - - + -
133A ALA* 3.5 18.8 - - + +
136A ILE* 4.2 6.3 - - + -
156A TRP* 4.4 2.7 - - + -
281A PHE* 5.1 0.2 - - + -
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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