Contacts of the strand formed by residues 67 - 72 (chain N) in PDB entry 1I5L
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 N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63H ARG* 3.4 31.3 + - + +
66H THR* 4.2 3.6 + - - -
19N VAL* 3.9 30.3 - - + -
20N ARG 4.1 2.5 - - - -
21N LEU* 4.3 1.8 - - + -
22N LYS* 4.8 3.5 + - - -
38N MET* 4.6 7.9 - - + +
40N LEU* 4.3 9.6 - - + -
62N ILE* 3.9 21.1 - - + -
63N ARG 4.0 2.2 - - - +
64N GLY* 2.9 19.3 + - - +
65N ASP 4.7 2.3 - - - +
66N THR* 1.3 79.7 - - - +
68N VAL* 1.3 65.6 + - - +
69N PHE* 3.5 20.6 - - - +
70N VAL* 4.1 9.0 - - + -
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Residues in contact with VAL 68 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H LEU* 4.4 9.6 - - + -
62H ILE* 3.7 5.7 - - - +
63H ARG* 3.3 22.3 + - - +
66H THR* 3.9 32.5 + - + +
20N ARG* 2.8 30.1 + - + +
21N LEU 3.8 18.8 - - - +
22N LYS* 3.8 15.3 - - + +
67N VAL* 1.3 77.7 - - - +
69N PHE* 1.3 76.5 + - + +
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Residues in contact with PHE 69 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21H LEU* 5.7 0.2 - - + -
27H PHE* 3.8 32.3 - + - -
47H GLU* 4.3 16.4 - - - -
55H ARG* 4.3 22.0 - - - -
57H VAL* 5.8 3.6 - - + -
60H VAL* 4.4 7.9 - - + -
61H VAL 3.2 17.0 - - - +
62H ILE* 4.4 9.2 - - + -
63H ARG 5.0 0.4 - - - +
18N ILE* 4.6 9.0 - - + -
19N VAL* 3.4 4.5 - - - +
20N ARG* 3.0 62.5 + - + -
67N VAL* 3.5 4.6 - - - +
68N VAL* 1.3 91.2 - - + +
70N VAL* 1.3 74.0 + - - +
71N SER* 4.3 15.9 - - - -
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Residues in contact with VAL 70 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60H VAL* 3.6 1.2 - - - -
61H VAL* 3.0 39.0 + - + +
9N LEU* 4.0 29.6 - - + -
12N SER* 6.4 0.7 - - - -
17N VAL* 4.3 24.7 - - + -
18N ILE 3.4 6.7 - - - +
19N VAL* 4.3 4.5 - - + -
31N LEU* 5.3 4.9 - - + -
38N MET* 5.6 6.7 - - + -
40N LEU* 3.8 28.9 - - + -
67N VAL* 4.1 11.4 - - + -
69N PHE* 1.3 78.6 - - - +
71N SER* 1.3 64.8 + - - +
72N PRO* 4.5 1.9 - - + +
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Residues in contact with SER 71 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57H VAL* 3.3 25.4 - - - +
59H SER 2.9 19.5 + - - -
60H VAL* 3.6 13.0 - - - -
17N VAL* 3.5 4.3 - - - -
18N ILE* 2.9 39.7 + - - +
69N PHE* 4.3 11.7 - - - -
70N VAL* 1.3 77.2 - - - +
72N PRO* 1.3 72.0 + - - +
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Residues in contact with PRO 72 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57H VAL* 5.3 3.8 - - - +
58H GLY* 5.4 4.3 + - - -
59H SER* 3.3 37.5 - - - +
61H VAL* 6.4 1.1 - - + -
8N VAL* 6.2 3.4 - - + -
12N SER* 4.7 16.8 - - - +
15N SER* 5.7 1.1 - - - +
16N PRO 4.0 9.6 - - - +
17N VAL* 4.2 5.2 - - + -
18N ILE* 5.2 2.8 - - - +
70N VAL* 4.5 2.5 - - + +
71N SER* 1.3 94.1 + - - +
73N ALA* 1.3 60.2 + - - +
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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