Contacts of the strand formed by residues 49 - 58 (chain H) in PDB entry 1I3R
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 ARG 49 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67F ASP* 5.2 2.2 + - - -
69F ASP* 3.5 35.8 + - - +
70F VAL* 4.1 3.4 - - - +
42H HIS 3.6 0.2 - - - +
44H TYR* 3.0 74.2 + - + -
46H GLY 4.1 0.2 - - - +
48H GLN* 1.3 81.4 - - + +
50H VAL* 1.3 70.2 + - - +
51H ARG* 4.2 16.2 - - - +
69H ASP* 3.7 24.4 + - - -
106H ARG* 4.1 0.7 - - - +
316H NAG 3.5 32.0 - - - +
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Residues in contact with VAL 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42H HIS 3.2 10.1 - - - +
43H PHE* 3.6 35.9 - - + -
47H THR* 3.8 8.1 - - - +
49H ARG* 1.3 87.3 + - - +
51H ARG* 1.3 70.3 + - - +
68H SER* 4.5 2.3 + - - -
69H ASP* 4.8 5.2 - - - +
101H VAL* 3.9 32.1 - - + +
105H CYS* 3.9 14.8 - - + -
106H ARG* 3.6 33.1 + - + +
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Residues in contact with ARG 51 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F ARG* 3.0 40.6 - - - +
65F ARG* 5.5 3.2 - - - +
67F ASP* 4.1 3.6 + - - -
40H GLU 3.6 1.4 - - - +
41H CYS* 3.7 1.0 - - - -
42H HIS* 2.8 60.5 + - + +
44H TYR* 4.9 4.3 + - + -
49H ARG* 4.2 20.6 - - - +
50H VAL* 1.3 78.2 - - - +
52H LEU* 1.3 65.2 - - - +
53H LEU* 4.0 28.5 - - - +
65H ARG* 5.0 6.3 - - - +
67H ASP* 2.9 40.0 + - - +
68H SER* 3.6 5.8 - - - +
69H ASP* 3.7 19.8 + - - +
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Residues in contact with LEU 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H PHE* 3.7 41.1 - - + -
39H SER* 4.4 0.2 - - - -
40H GLU 3.3 15.3 - - - +
41H CYS* 4.7 1.1 - - - +
51H ARG* 1.3 76.2 - - - +
53H LEU* 1.3 69.9 + - - +
54H VAL* 3.9 23.8 - - + -
66H PHE* 3.2 10.7 - - + +
67H ASP* 3.6 1.7 - - - -
68H SER* 2.7 48.3 + - - +
97H LYS* 4.3 6.5 - - - +
100H GLU* 4.1 18.2 - - + +
101H VAL* 3.8 19.5 - - + +
105H CYS* 4.3 7.0 - - - -
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Residues in contact with LEU 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H LYS 3.6 1.2 - - - +
40H GLU* 2.8 61.3 + - - +
42H HIS* 4.2 12.3 - - + +
51H ARG* 4.0 28.2 + - - +
52H LEU* 1.3 73.2 - - - +
54H VAL* 1.3 72.0 + - - +
55H ARG* 3.9 18.1 + - + +
65H ARG* 4.1 37.2 - - + +
66H PHE 3.4 9.9 - - - +
67H ASP* 4.3 6.5 - - + -
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Residues in contact with VAL 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H PHE* 5.4 0.7 - - + -
10H GLU* 4.7 1.1 - - - +
37H CYS* 4.0 8.1 - - - -
38H LYS 3.4 2.5 - - - -
39H SER* 3.7 21.5 - - - +
52H LEU* 3.9 22.0 - - + -
53H LEU* 1.3 76.0 - - - +
55H ARG* 1.3 63.5 + - - +
56H TYR* 3.5 32.5 - - + +
65H ARG* 2.9 12.1 - - - +
66H PHE* 2.9 44.2 + - + +
97H LYS* 4.0 23.3 - - - +
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Residues in contact with ARG 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141G ASP 2.7 30.1 + - - -
142G ASP* 4.5 4.0 - - - +
37H CYS* 3.4 5.2 - - - -
38H LYS* 2.8 46.8 + - + +
40H GLU* 3.3 35.8 + - - -
53H LEU* 3.9 20.2 - - + +
54H VAL* 1.3 79.9 - - - +
56H TYR* 1.3 63.4 + - - +
57H PHE* 3.6 29.7 - - + -
62H GLU* 2.9 35.6 + - - +
64H LEU 3.6 3.1 - - - -
65H ARG* 3.9 8.9 - - + +
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Residues in contact with TYR 56 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66G ASN* 6.2 0.2 - - - -
69G ASN* 5.9 0.7 - - - -
10H GLU* 2.7 34.8 + - + -
11H GLY 4.9 1.0 + - - -
13H LYS* 4.5 11.9 - - - +
35H GLU* 4.5 14.1 - - - +
36H TYR 3.6 2.7 - - - -
37H CYS* 3.6 15.7 - - + -
54H VAL* 3.5 26.6 - - + +
55H ARG* 1.3 75.4 - - - +
57H PHE* 1.3 60.3 + - - +
62H GLU* 3.2 6.8 - - - +
63H ASN* 2.8 42.5 + - - +
64H LEU* 2.9 36.5 + - + +
65H ARG* 4.9 0.4 - - - -
73H PHE* 4.1 14.7 - + - -
87H TRP* 3.6 33.8 - + - -
93H PHE* 5.7 0.5 - - - -
97H LYS* 4.6 4.2 + - - -
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Residues in contact with PHE 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142G ASP 4.0 3.4 - - - -
143G HIS* 3.5 30.7 - - + -
34H LEU 3.6 0.5 - - - +
35H GLU* 3.9 7.3 - - - +
36H TYR* 2.7 62.8 + + + +
38H LYS* 3.5 26.5 - - + -
55H ARG* 3.6 52.9 - - + -
56H TYR* 1.3 75.8 - - - +
58H TYR* 1.3 59.4 + - - +
59H ASN 4.0 9.4 - - - +
61H GLU 3.2 7.4 - - - +
62H GLU* 3.5 36.6 - - + -
63H ASN* 3.9 2.7 - - - -
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Residues in contact with TYR 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70G LEU* 4.0 16.2 - - + -
73G MET* 3.8 37.2 - - + -
74G LYS* 3.9 7.3 - - - -
77G SER* 3.3 29.0 + - - -
79G ASN* 5.1 0.3 - - - -
80G THR 4.0 5.2 + - - -
82G ASP* 4.3 2.3 - - - +
33H PHE* 3.3 26.6 - - + -
34H LEU 3.1 13.7 - - - -
35H GLU* 4.4 1.8 - - - +
57H PHE* 1.3 75.2 - - - +
59H ASN* 1.3 94.0 + - + +
60H LEU 3.1 2.4 + - - -
61H GLU* 2.9 18.8 + - - +
63H ASN* 3.6 16.5 - - - +
79H LEU* 3.8 20.6 - - + -
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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