Contacts of the strand formed by residues 43 - 54 (chain G) in PDB entry 5IXM
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 GLY 43 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37G HIS 3.9 0.3 - - - +
38G TYR* 3.8 6.4 - - - -
39G MET* 2.9 40.1 + - - +
42G ARG* 1.3 78.1 - - - +
44G LEU* 1.3 61.3 + - - -
45G GLN 3.9 1.4 + - - -
66G LEU* 3.7 9.0 - - - -
68G ASN 5.7 1.8 - - - -
69G ASP 5.7 0.2 - - - -
70G ARG* 3.9 15.7 - - - +
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Residues in contact with LEU 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G PRO* 4.2 10.3 - - + -
37G HIS 3.9 4.9 - - - +
38G TYR* 3.9 31.2 - - + +
43G GLY* 1.3 70.1 - - - -
45G GLN* 1.3 70.0 + - - +
46G TRP* 3.9 34.2 + - + +
66G LEU* 3.3 5.7 - - - +
67G PRO* 3.2 26.8 - - + +
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Residues in contact with GLN 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G PRO* 3.4 4.9 - - - +
37G HIS* 2.8 52.5 + - + +
39G MET* 3.7 15.0 - - + -
43G GLY 3.9 0.2 + - - -
44G LEU* 1.3 76.3 - - - +
46G TRP* 1.3 70.6 + - - +
47G GLN* 3.0 31.6 + - - +
64G ASP* 4.2 6.5 + - - +
65G TRP 3.6 8.5 - - - +
66G LEU* 3.6 18.5 - - + +
84G ARG* 5.7 0.6 + - - +
113G TYR* 3.5 23.6 + - - -
117G LEU* 3.5 27.4 - - - +
118G THR 4.9 2.2 + - - +
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Residues in contact with TRP 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34G ILE* 4.5 17.3 - - + -
35G THR 3.7 2.2 - - - -
36G PRO* 3.8 37.7 - - + -
44G LEU* 3.9 36.1 + - + +
45G GLN* 1.3 79.6 - - - +
47G GLN* 1.3 62.9 + - - +
48G ASN* 4.1 11.0 + - - +
63G LEU 3.6 2.6 - - - +
64G ASP* 3.3 4.0 - - - -
65G TRP* 2.9 70.7 + + + +
67G PRO* 4.7 4.4 - - + +
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Residues in contact with GLN 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G LEU* 4.7 6.6 - - - +
33G THR* 3.4 6.4 - - - +
34G ILE* 3.5 1.0 - - - -
35G THR* 2.9 58.2 + - - +
37G HIS* 3.8 16.7 + - + -
45G GLN* 3.0 26.7 + - - +
46G TRP* 1.3 75.8 - - - +
48G ASN* 1.3 62.2 + - - +
49G GLU* 5.5 0.4 - - - +
64G ASP* 3.5 28.8 + - - +
118G THR 3.9 14.6 + - - -
119G SER* 5.6 0.6 - - - +
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Residues in contact with ASN 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G THR 3.5 4.9 - - - +
34G ILE* 4.0 22.4 - - + +
46G TRP* 4.2 15.0 + - - +
47G GLN* 1.3 77.1 + - - +
49G GLU* 1.3 60.8 + - - +
62G ALA* 3.2 5.5 - - - +
63G LEU* 2.9 66.9 + - + +
64G ASP* 4.1 1.4 + - - +
65G TRP* 5.3 4.0 - - - +
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Residues in contact with GLU 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31G ASP* 4.1 1.5 - - - +
32G ALA* 3.3 4.2 - - - +
33G THR* 2.8 53.9 + - + +
47G GLN 5.5 0.4 - - - +
48G ASN* 1.3 75.5 - - - +
50G PHE* 1.3 62.2 + - - +
51G ARG* 4.2 17.6 + - + +
60G THR* 3.6 13.5 - - + +
61G MET 3.6 9.2 - - - +
62G ALA* 4.8 2.9 - - + -
120G GLN* 4.4 13.1 - - - +
121G TYR* 2.9 26.2 + - - +
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Residues in contact with PHE 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G ILE* 4.7 5.6 - - + -
30G PHE* 3.3 39.3 - + + -
31G ASP 2.9 33.9 - - - -
32G ALA* 4.5 8.5 - - + -
48G ASN 5.8 0.2 - - - -
49G GLU* 1.3 74.3 - - - +
51G ARG* 1.3 61.7 + - - +
52G TYR* 4.1 23.2 + + + -
60G THR* 3.5 1.2 - - - -
61G MET* 2.9 61.7 + - + +
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Residues in contact with ARG 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G TYR* 4.8 5.3 + - - -
29G ASN 4.7 0.2 - - - -
30G PHE 3.7 0.2 - - - -
31G ASP* 2.8 77.8 + - + +
33G THR* 5.6 1.4 + - - -
49G GLU* 4.4 17.2 - - + +
50G PHE* 1.3 76.2 - - - +
52G TYR* 1.3 61.8 + - - +
59G GLY 3.6 5.4 - - - +
60G THR* 4.0 21.3 - - + +
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Residues in contact with TYR 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G ASN 3.5 11.9 - - - +
30G PHE* 4.4 16.8 - + + -
50G PHE* 4.1 22.4 - + + -
51G ARG* 1.3 76.1 - - - +
53G LEU* 1.3 63.8 + - - +
54G LEU* 4.1 20.2 - - + -
57G GLY 3.9 7.4 - - - -
58G SER* 3.4 3.8 - - - -
59G GLY* 2.9 61.4 + - - +
60G THR 4.1 2.5 - - - -
61G MET* 4.2 13.0 - - + -
89G TRP* 2.9 32.3 + + - -
91G HIS* 2.8 35.5 + + - +
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Residues in contact with LEU 53 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G PRO 5.8 2.2 - - - +
29G ASN* 3.1 38.3 + - + +
52G TYR* 1.3 77.7 - - - +
54G LEU* 1.3 73.9 + - - +
57G GLY 4.1 1.6 - - - -
58G SER* 3.7 22.9 - - - +
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Residues in contact with LEU 54 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G ASN* 3.4 28.7 - - - +
30G PHE* 3.8 25.6 - - + -
52G TYR* 4.1 22.2 - - + -
53G LEU* 1.3 84.3 - - - +
55G ALA* 1.3 61.8 + - - +
56G PRO* 3.4 19.3 - - + -
57G GLY* 2.9 31.0 + - - +
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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