Contacts of the strand formed by residues 52 - 62 (chain H) 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 GLU 52 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48H ILE* 4.3 0.9 - - - -
49H GLN* 2.9 39.6 + - - +
50H ASN 3.6 2.9 + - - +
51H GLY* 1.3 72.6 - - - -
53H VAL* 1.3 64.2 + - - +
54H VAL* 3.2 23.8 + - + +
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Residues in contact with VAL 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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46H GLU* 3.9 44.0 - - + +
47H GLU 3.6 5.4 - - - +
48H ILE* 4.1 22.9 - - + +
51H GLY 5.5 0.7 - - - +
52H GLU* 1.3 74.2 - - - +
54H VAL* 1.3 61.2 + - - +
55H ARG 3.8 13.1 + - - +
56H LYS* 5.0 5.8 - - + -
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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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25H ARG* 3.9 13.0 - - - +
47H GLU* 2.9 21.8 + - - +
49H GLN* 3.2 44.9 - - + +
52H GLU* 3.4 40.8 - - + +
53H VAL* 1.3 71.7 - - - +
55H ARG* 1.3 72.4 + - - +
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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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25H ARG* 5.0 5.7 - - - +
46H GLU* 3.4 5.4 - - - +
47H GLU* 2.9 53.5 + - + +
53H VAL* 3.5 6.2 + - - +
54H VAL* 1.3 87.5 + - - +
56H LYS* 1.3 75.0 + - - +
57H VAL* 4.4 15.2 - - + +
18N ILE* 4.6 15.1 - - - +
20N ARG* 4.7 6.9 - - - +
26N GLU* 3.3 34.1 + - - -
69N PHE* 4.3 18.8 - - - -
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Residues in contact with LYS 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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45H ALA 3.6 5.6 - - - +
46H GLU* 2.7 41.8 + - + +
53H VAL* 5.0 7.0 - - + -
55H ARG* 1.3 84.1 - - - +
57H VAL* 1.3 72.7 + - - +
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Residues in contact with VAL 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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27H PHE* 4.4 11.9 - - + -
44H ASP* 3.7 2.1 - - - -
45H ALA* 3.2 31.5 + - + +
46H GLU* 5.9 0.2 - - - -
55H ARG* 4.4 18.4 - - + +
56H LYS* 1.3 85.3 - - - +
58H GLY* 1.3 65.5 + - - +
59H SER* 4.2 2.6 - - - +
60H VAL* 3.4 30.1 - - + -
18N ILE* 6.1 5.2 - - + -
69N PHE* 5.8 3.6 - - + -
71N SER* 3.3 25.1 - - - +
72N PRO 5.3 2.7 - - - +
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Residues in contact with GLY 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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43H LEU* 3.5 6.6 - - - +
44H ASP* 3.0 25.8 + - - +
57H VAL* 1.3 73.5 - - - +
59H SER* 1.3 65.4 + - - +
71N SER* 5.0 0.2 + - - -
72N PRO* 5.4 6.0 + - - +
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Residues in contact with SER 59 (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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41H VAL* 5.2 5.2 - - - -
42H LEU 3.0 15.5 - - - -
43H LEU* 3.7 15.3 - - - +
45H ALA* 5.7 0.4 - - - +
57H VAL* 3.1 3.6 - - - -
58H GLY* 1.3 82.0 - - - +
60H VAL* 1.3 64.4 - - - +
8N VAL* 5.3 9.4 - - - +
71N SER* 2.9 22.5 + - - -
72N PRO* 3.3 27.5 - - - +
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Residues in contact with VAL 60 (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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27H PHE* 3.9 31.9 - - + -
40H LEU 3.5 0.3 - - - +
41H VAL* 3.2 27.6 - - - +
42H LEU* 3.1 30.7 + - + +
45H ALA* 4.9 1.8 - - + -
57H VAL* 3.4 24.5 - - + -
59H SER* 1.3 79.0 - - - +
61H VAL* 1.3 69.0 + - - +
62H ILE* 4.1 11.7 - - + -
8N VAL* 6.2 0.2 - - - -
69N PHE* 4.4 8.1 - - + -
70N VAL 3.6 4.9 - - - +
71N SER* 3.6 14.6 - - - -
72N PRO* 5.2 0.2 - - - -
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Residues in contact with VAL 61 (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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39H ASN* 5.1 1.1 - - + -
40H LEU 3.2 10.3 - - - +
41H VAL* 4.7 3.8 - - + -
60H VAL* 1.3 78.4 - - - +
62H ILE* 1.3 64.2 + - - +
63H ARG 4.2 0.3 + - - -
5N PRO* 4.1 25.6 - - + +
8N VAL* 4.2 30.5 - - + -
9N LEU* 4.4 16.4 - - + -
38N MET* 4.7 21.5 - - + -
69N PHE* 3.2 8.0 - - - +
70N VAL* 3.0 40.7 + - + +
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Residues in contact with ILE 62 (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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19H VAL* 4.2 16.8 - - + -
21H LEU* 4.5 12.1 - - + -
27H PHE* 4.1 26.2 - - + -
38H MET 4.3 0.2 - - - +
39H ASN* 3.3 4.0 - - - -
40H LEU* 3.0 35.1 + - + +
42H LEU* 4.3 21.3 - - + -
60H VAL* 4.3 13.7 - - + +
61H VAL* 1.3 80.3 - - - +
63H ARG* 1.3 75.6 + - - +
64H GLY* 3.0 3.8 + - - -
66H THR* 4.7 4.0 - - + -
67H VAL* 3.9 20.4 - - + -
68N VAL 3.7 8.5 - - - +
69N PHE* 4.4 9.2 - - + -
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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