Contacts of the strand formed by residues 43 - 54 (chain G) in PDB entry 5IYB
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 THR 4.0 0.2 - - - +
38G CYS* 4.4 0.4 - - - -
39G THR* 2.8 43.7 + - - -
40G GLY 4.5 0.6 - - - -
41G LYS 3.8 0.4 - - - -
42G TYR* 1.3 77.7 - - - +
44G PHE* 1.3 67.7 + - - -
45G VAL* 3.4 3.8 + - - +
77G PHE 3.4 8.1 - - - -
78G ARG* 4.7 2.0 - - - +
157G ILE* 4.2 20.0 - - - -
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Residues in contact with PHE 44 (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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60D VAL* 4.7 15.3 - - + -
36G GLY 5.1 2.7 - - - -
37G THR 3.7 4.5 - - - +
38G CYS* 3.4 39.0 - - + -
42G TYR 4.9 0.4 - - - -
43G GLY* 1.3 70.9 - - - -
45G VAL* 1.3 59.6 + - - +
46G ILE* 3.2 23.5 + - + +
76G VAL* 3.8 2.1 - - - -
77G PHE* 3.3 32.6 + + + -
103G PRO* 3.4 31.6 - - + -
104G MET* 3.6 36.3 - - + -
156G ASP* 5.2 4.0 - - + -
157G ILE* 3.8 23.4 - - + +
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Residues in contact with VAL 45 (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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60D VAL* 5.9 0.2 - - - -
7G LEU* 5.7 6.5 - - + -
34G VAL* 3.9 28.0 - - + +
35G GLU* 3.9 6.0 - - - -
36G GLY* 2.8 32.7 + - - -
37G THR* 3.1 20.6 + - - +
39G THR* 4.3 18.8 - - + +
42G TYR* 5.6 2.0 - - + -
43G GLY 4.1 6.7 - - - +
44G PHE* 1.3 69.4 - - - +
46G ILE* 1.3 61.9 + - - +
47G ALA 4.6 8.3 - - - +
48G VAL* 5.2 2.0 - - + -
72G TYR* 5.7 4.3 - - + +
74G ALA* 5.1 13.2 - - + -
75G ILE 4.2 4.9 - - - +
76G VAL* 4.8 12.1 - - + -
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Residues in contact with ILE 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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37D VAL* 5.1 2.0 - - + -
41D LEU* 3.7 27.4 - - + -
60D VAL* 4.8 6.3 - - + -
61D PHE* 4.3 15.5 - - + +
64D THR* 4.0 40.2 - - + +
2G PHE* 5.2 3.4 - - + -
35G GLU* 3.8 12.4 - - - +
36G GLY* 4.9 1.5 + - - -
44G PHE* 3.5 31.2 - - + +
45G VAL* 1.3 74.8 - - - +
47G ALA* 1.3 62.7 + - - +
75G ILE* 3.0 29.0 + - + +
76G VAL 4.6 0.2 - - - -
77G PHE* 4.4 16.4 - - + +
103G PRO* 4.8 3.1 - - + -
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Residues in contact with ALA 47 (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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41D LEU* 4.1 20.6 - - + -
44D ARG* 4.6 11.2 - - + -
61D PHE* 5.4 0.2 - - + -
35G GLU* 3.8 17.3 - - - +
45G VAL* 3.6 3.6 - - - -
46G ILE* 1.3 83.2 - - - +
48G VAL* 1.3 67.5 + - - +
49G THR* 3.6 1.0 + - + -
74G ALA* 3.3 3.4 - - - +
75G ILE* 2.7 45.3 + - + +
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Residues in contact with VAL 48 (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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44D ARG* 5.1 6.2 - - - -
30G LEU* 3.9 20.0 - - + -
31G PHE* 3.5 30.7 - - + -
34G VAL* 4.2 13.0 - - + -
35G GLU* 4.5 8.4 + - + -
45G VAL* 5.2 3.6 - - + -
47G ALA* 1.3 75.0 - - - +
49G THR* 1.3 64.4 + - - +
50G THR 3.7 20.4 - - - +
51G ILE* 3.7 21.3 - - + -
72G TYR* 3.8 26.0 - - + -
73G LYS 3.7 7.2 - - - +
74G ALA* 3.9 3.4 - - + -
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Residues in contact with THR 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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40D LEU* 5.0 13.5 - - + -
4G HIS* 2.9 38.4 + - + +
31G PHE* 5.6 1.7 - - - -
47G ALA* 3.6 1.3 + - + +
48G VAL* 1.3 77.3 - - - +
50G THR* 1.3 76.8 + - - +
73G LYS 2.6 27.0 + - - +
75G ILE* 3.6 25.8 - - + +
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Residues in contact with THR 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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4G HIS* 5.3 0.2 - - - -
48G VAL* 3.6 1.9 - - - +
49G THR* 1.3 90.7 + - - +
51G ILE* 1.3 69.3 + - - +
52G ASP* 5.1 1.1 + - - -
72G TYR* 3.4 6.8 - - - +
73G LYS* 2.9 52.7 + - - +
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Residues in contact with ILE 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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27G LYS* 4.2 36.1 - - + +
30G LEU* 4.5 16.8 - - + -
31G PHE* 4.8 9.6 - - + -
48G VAL* 3.7 26.2 - - + -
50G THR* 1.3 75.0 - - - +
52G ASP* 1.3 64.0 + - - +
53G ASN* 4.3 3.6 - - - +
54G ILE* 4.1 20.6 - - + -
70G VAL* 4.0 15.7 - - + -
71G LYS 3.9 9.9 - - - +
72G TYR* 4.1 6.3 - - + -
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Residues in contact with ASP 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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50G THR* 3.7 5.8 + - - -
51G ILE* 1.3 76.3 - - - +
53G ASN* 1.3 74.3 + - - +
71G LYS* 2.7 36.0 + - + +
72G TYR* 4.2 6.1 - - - +
73G LYS* 4.7 16.3 - - + +
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Residues in contact with ASN 53 (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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51G ILE* 3.6 2.4 - - - -
52G ASP* 1.3 90.1 - - - +
54G ILE* 1.3 91.4 + - - +
55G GLY* 4.1 6.9 + - - +
70G VAL* 3.4 4.2 - - - +
71G LYS* 2.6 57.7 + - + +
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Residues in contact with ILE 54 (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 LEU* 4.1 27.8 - - + +
26G VAL* 4.4 17.7 - - + -
27G LYS* 4.6 18.6 - - + -
51G ILE* 4.1 13.7 - - + -
53G ASN* 1.3 89.5 + - - +
55G GLY* 1.3 74.3 + - - +
68G TYR* 3.6 27.1 - - + -
69G PRO 3.6 7.6 - - - +
70G VAL* 4.0 17.5 - - + -
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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