Contacts of the strand formed by residues 40 - 47 (chain G) in PDB entry 1P8Z
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 40 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38G GLU 3.2 4.6 + - - -
39G PRO* 1.3 73.9 - - - +
41G LEU* 1.3 59.7 + - - -
42G GLN* 5.5 2.0 - - - -
71G LEU 3.7 1.3 - - - +
72G LYS* 3.0 14.4 - - - +
73G THR* 2.8 39.9 + - - -
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Residues in contact with LEU 41 (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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40G GLY* 1.3 74.1 - - - -
42G GLN* 1.3 65.4 + - - +
43G ILE* 3.9 27.1 - - + -
59G TYR* 3.2 29.1 + - + -
70G ILE* 3.4 27.4 - - + -
71G LEU 3.5 13.2 - - - +
72G LYS* 4.0 21.8 - - + -
133G TYR* 4.3 21.3 - - + +
134G PHE* 4.1 19.5 - - + -
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Residues in contact with GLN 42 (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 LYS* 2.7 32.8 + - - +
35G ALA* 3.6 4.0 - - - +
36G GLY* 2.8 29.8 + - - -
37G LYS 4.6 1.2 + - - -
38G GLU* 5.4 4.2 + - - +
40G GLY 5.5 0.9 - - - -
41G LEU* 1.3 80.1 - - - +
43G ILE* 1.3 66.1 + - - +
44G TRP* 3.8 25.3 - - + -
59G TYR* 3.5 5.4 - - - +
69G VAL 3.8 0.7 - - - +
70G ILE* 3.5 2.3 - - - +
71G LEU* 2.9 41.5 + - - +
73G THR* 4.9 1.4 + - - -
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Residues in contact with ILE 43 (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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41G LEU* 3.9 17.3 - - + -
42G GLN* 1.3 79.9 - - - +
44G TRP* 1.3 67.8 + - - +
53G PRO* 3.6 5.4 - - - +
54G VAL* 3.0 30.7 + - + +
59G TYR* 3.2 54.0 + - + -
60G GLY 4.6 0.2 - - - +
62G PHE* 4.3 9.6 - - + -
68G TYR* 3.9 25.1 - - + -
69G VAL 3.6 6.1 - - - +
70G ILE* 4.2 15.0 - - + -
134G PHE* 4.0 20.0 - - + -
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Residues in contact with TRP 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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31G GLU* 2.8 54.5 + - + +
34G LYS 5.3 0.2 - - - -
35G ALA* 4.0 18.6 - - + -
42G GLN* 3.8 37.2 - - + -
43G ILE* 1.3 75.8 - - - +
45G ARG* 1.3 61.1 + - - +
51G LEU* 3.4 29.8 - - + -
52G VAL 3.3 6.7 - - - +
53G PRO* 3.6 28.3 - - + +
54G VAL* 4.0 0.9 - - - -
68G TYR* 3.0 28.0 - - - +
69G VAL* 3.0 39.0 + - + +
71G LEU* 3.7 28.0 - - + -
108G LEU* 3.9 17.0 - - + -
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Residues in contact with ARG 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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44G TRP* 1.3 77.0 - - - +
46G VAL* 1.3 74.0 + - - +
47G GLU* 2.4 38.9 + - - +
50G ASP 3.4 0.3 - - - +
51G LEU* 3.8 1.6 - - - -
52G VAL* 2.7 36.9 + - - +
54G VAL* 4.0 6.6 - - + +
63G PHE* 3.3 29.7 - - - -
66G ASP* 3.1 29.7 + - + +
67G ALA 3.5 12.3 - - - +
68G TYR* 3.7 28.0 - - + -
144G GLY* 4.8 0.4 - - - -
145G VAL* 4.4 12.6 - - - +
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Residues in contact with VAL 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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45G ARG* 1.3 76.6 - - - +
47G GLU* 1.3 69.4 + - - +
48G LYS 4.6 0.7 - - - +
49G PHE 4.3 11.7 - - - +
50G ASP 3.2 8.1 - - - +
51G LEU* 4.7 4.9 - - + +
66G ASP* 5.0 0.5 - - - -
67G ALA* 2.9 22.4 + - + +
68G TYR* 4.7 0.2 - - - +
69G VAL* 4.9 2.2 - - + -
96G ASP* 4.8 1.1 - - - +
97G GLU* 4.0 26.9 - - + +
100G ALA* 3.9 18.6 - - + -
101G ALA* 3.8 31.2 - - + +
104G PHE* 3.9 19.5 - - + -
145G VAL* 3.7 12.5 - - - +
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Residues in contact with GLU 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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45G ARG* 2.4 53.2 + - - +
46G VAL* 1.3 81.7 - - - +
48G LYS* 1.3 76.2 + - + +
49G PHE 3.3 0.4 - - - -
50G ASP* 2.8 26.1 + - - +
52G VAL* 3.4 39.4 - - + +
145G VAL* 4.1 19.0 - - + +
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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