Contacts of the strand formed by residues 67 - 72 (chain U) in PDB entry 1H64
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 VAL 67 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63O ARG* 3.6 23.4 + - + -
66O ASN* 3.1 16.7 + - - -
19U VAL* 3.7 20.9 - - + -
20U ILE 3.9 4.5 - - - +
21U LEU* 4.3 1.6 - - + -
22U LYS* 4.1 1.7 - - - -
38U LEU 4.8 4.5 - - - +
40U VAL* 5.5 1.6 - - + -
62U ILE* 4.2 11.2 - - + +
63U ARG 3.8 15.5 - - - +
64U GLY* 2.9 18.3 + - - +
65U ASP 3.4 0.2 - - - -
66U ASN* 1.3 79.6 - - - +
68U LEU* 1.3 64.2 + - - +
69U ALA* 3.4 25.6 - - - +
70U ILE* 3.7 20.6 - - + -
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Residues in contact with LEU 68 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21O LEU* 4.1 18.6 - - + -
23O LYS* 6.5 1.6 - - + -
25O PHE* 3.7 30.7 - - + -
27O PHE* 4.7 7.6 - - + -
62O ILE* 3.7 4.9 - - - +
63O ARG* 3.0 24.4 + - - +
66O ASN* 3.6 32.8 + - + +
20U ILE* 2.6 36.6 + - + +
21U LEU 4.1 8.7 - - - +
22U LYS* 4.3 14.4 - - + +
66U ASN 3.7 2.2 + - - -
67U VAL* 1.3 73.8 - - - +
69U ALA* 1.3 62.9 + - + +
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Residues in contact with ALA 69 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27O PHE* 4.6 6.1 - - + -
60O ILE* 3.6 26.9 - - + -
61O VAL 3.1 14.8 - - - +
62O ILE* 4.0 7.9 - - + -
63O ARG* 4.7 0.9 - - - +
18U LEU 4.5 0.2 - - - -
20U ILE* 2.8 40.5 + - + +
67U VAL* 3.4 5.5 - - - +
68U LEU* 1.3 83.4 - - + +
70U ILE* 1.3 67.2 + - - +
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Residues in contact with ILE 70 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60O ILE* 3.7 1.9 - - - -
61O VAL* 2.9 39.7 + - + +
63O ARG* 6.2 0.9 - - + -
9U ILE* 3.9 31.2 - - + -
17U VAL* 4.4 20.2 - - + -
18U LEU 3.2 9.2 - - - +
19U VAL* 4.4 15.3 - - + -
31U LEU* 6.2 2.9 - - + -
38U LEU* 4.8 16.2 - - + +
40U VAL* 4.0 25.4 - - + -
67U VAL* 3.7 18.6 - - + -
69U ALA* 1.3 82.3 - - - +
71U SER* 1.3 61.7 + - - +
72U PRO* 4.1 3.7 - - + +
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Residues in contact with SER 71 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57O TYR* 3.8 31.4 - - - +
58O GLY 5.0 0.9 + - - -
59O LYS 2.7 21.3 + - - -
60O ILE* 4.2 6.1 - - - -
17U VAL* 3.4 2.9 - - - -
18U LEU* 2.8 48.8 + - - +
20U ILE* 5.8 1.7 - - - +
69U ALA 4.3 0.2 - - - -
70U ILE* 1.3 74.5 - - - +
72U PRO* 1.3 71.0 + - - +
73U THR* 3.2 1.9 + - - -
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Residues in contact with PRO 72 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58O GLY 5.9 0.7 + - - -
59O LYS* 3.5 33.6 + - + +
61O VAL* 5.6 0.2 - - + -
8U VAL* 4.5 16.2 - - + -
9U ILE* 6.6 0.2 - - + -
12U SER* 3.3 28.0 - - - +
15U LYS* 5.6 3.6 - - + -
16U ASP 3.6 7.2 - - - +
17U VAL* 3.8 7.2 - - + -
70U ILE* 4.1 7.0 - - + +
71U SER* 1.3 87.1 + - - +
73U THR* 1.3 66.2 + - - +
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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