Contacts of the strand formed by residues 45 - 51 (chain H) in PDB entry 1I9J
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 LEU 45 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37H VAL* 4.5 8.7 - - + -
38H ARG 3.4 3.6 - - - +
39H GLN* 3.5 37.9 - - + +
43H LYS 3.7 0.2 + - - -
44H ARG* 1.3 76.0 - - - +
46H GLU* 1.3 63.5 + - - +
94H TYR* 5.3 1.8 - - + -
108H TRP* 4.8 4.3 - - + -
41L TYR* 5.8 0.7 - - + -
49L PRO* 4.2 25.4 - - + -
92L TYR* 3.9 37.3 - - + -
103L PHE* 3.6 60.8 + - + +
104L GLY 5.4 1.2 + - - -
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Residues in contact with GLU 46 (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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37H VAL* 4.0 4.0 - - - +
38H ARG* 2.8 73.2 + - + +
40H THR* 5.4 5.3 - - + +
44H ARG* 5.2 1.1 - - + +
45H LEU* 1.3 77.1 - - - +
47H TRP* 1.3 75.5 + - - +
48H VAL* 3.4 3.4 + - + +
60H SER* 5.4 2.0 + - - -
62H SER* 3.1 24.5 + - - -
103L PHE* 4.5 1.3 - - - -
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Residues in contact with TRP 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35H SER* 4.3 6.5 - - - -
36H TRP 4.1 6.1 - - - -
37H VAL* 4.2 12.8 - - + -
46H GLU* 1.3 84.2 - - - +
48H VAL* 1.3 61.9 + - - +
49H ALA* 3.4 13.8 - - - -
50H SER* 2.7 29.9 + - - -
58H TYR* 3.5 47.6 - - + -
59H TYR 3.7 19.7 - - - -
60H SER* 3.1 29.2 + - - -
105H LEU* 6.4 0.2 - - + -
1010H TES 3.9 19.3 - - + +
94L PHE* 5.2 2.7 - + + -
99L VAL* 4.0 10.5 - - + -
100L PRO* 3.6 20.6 - - + -
101L PRO* 3.4 45.8 + - + +
102L THR* 6.2 0.2 - - - +
103L PHE* 4.4 10.5 - - + -
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Residues in contact with VAL 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H TRP* 2.8 24.0 + - + +
37H VAL 4.1 0.2 - - - -
38H ARG* 3.6 35.0 - - + +
46H GLU* 3.5 15.3 - - + +
47H TRP* 1.3 75.2 - - - +
49H ALA* 1.3 63.0 + - - +
59H TYR* 3.9 4.0 - - - -
60H SER* 3.6 13.6 + - - -
63H VAL* 3.7 19.3 - - + +
67H PHE* 3.6 34.1 - - + -
80H LEU* 4.2 16.2 - - + -
93H TYR* 4.4 4.9 - - + -
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Residues in contact with ALA 49 (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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35H SER* 3.0 6.9 - - - -
36H TRP* 2.8 27.5 + - + +
47H TRP* 3.4 8.4 + - - +
48H VAL* 1.3 91.2 - - + +
50H SER* 1.3 61.9 + - - +
58H TYR 3.3 7.6 - - - -
59H TYR* 3.4 29.2 - - + -
69H ILE* 3.9 16.6 - - + -
80H LEU* 4.7 5.2 - - + -
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Residues in contact with SER 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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33H ALA* 5.5 0.9 - - - -
34H LEU 3.3 7.4 - - - -
35H SER* 2.5 23.7 + - - -
47H TRP* 2.7 27.3 + - - +
49H ALA* 1.3 71.3 - - - +
51H ILE* 1.3 62.9 + - - +
52H VAL 5.4 0.4 - - - -
56H ASN 4.7 0.2 - - - -
57H THR* 3.2 5.0 - - - -
58H TYR* 2.9 34.9 + - - -
69H ILE* 3.9 6.3 - - - +
1010H TES 3.7 27.6 - - - +
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Residues in contact with ILE 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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32H TYR 4.2 1.0 - - - +
33H ALA* 3.3 2.6 - - - -
34H LEU* 2.9 38.4 + - + +
50H SER* 1.3 76.7 - - - +
52H VAL* 1.3 71.0 + - - +
55H GLY* 3.6 26.0 - - - +
56H ASN 3.3 4.3 - - - +
57H THR* 3.8 14.6 - - + -
69H ILE* 4.1 6.5 - - + -
70H SER* 4.6 6.1 - - - -
71H ARG* 3.4 45.6 + - + +
78H LEU* 4.1 23.3 - - + -
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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