Contacts of the strand formed by residues 45 - 51 (chain G) in PDB entry 4WFH
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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35F TYR* 5.3 1.1 - - + -
43F PRO* 4.2 24.0 - - + -
86F TYR* 3.5 42.8 - - + -
97F PHE* 3.3 55.1 + - + +
37G VAL* 4.0 14.8 - - + -
38G LYS 3.6 2.2 - - - -
39G GLN* 3.7 36.3 - - + +
44G ASN* 1.3 76.4 - - - +
46G GLU* 1.3 61.9 + - - +
95G TYR* 4.5 3.4 - - + -
106G TRP* 4.6 1.3 - - + -
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Residues in contact with GLU 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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37G VAL* 3.2 6.9 - - - +
38G LYS* 2.8 70.4 + - + +
40G ARG* 5.7 2.8 + - - +
44G ASN* 4.5 15.8 - - - +
45G LEU* 1.3 77.0 - - - +
47G TRP* 1.3 63.8 + - - +
48G ILE 3.4 0.3 + - - -
61G ASN* 5.7 3.0 + - - +
63G LYS* 3.6 28.8 - - - +
64G PHE* 4.2 17.2 - - + -
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Residues in contact with TRP 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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82B GLN* 3.9 16.4 - - - -
94F PRO* 3.7 23.3 - - + -
95F PRO* 3.5 44.6 - - + +
97F PHE* 4.4 13.8 - - + -
35G ASN* 3.0 28.1 + - + -
36G TRP 3.8 4.3 - - - -
37G VAL* 4.5 6.1 - - + -
45G LEU 4.2 1.4 + - - -
46G GLU* 1.3 71.2 - - - +
48G ILE* 1.3 57.9 + - - +
49G GLY* 3.4 31.8 + - - -
50G LEU* 3.6 18.8 - - + -
59G THR* 4.0 10.8 - - - -
60G TYR 3.9 2.7 - - - -
61G ASN* 2.9 58.7 + - + +
64G PHE* 4.1 2.8 - - - -
103G PHE* 3.7 15.5 - + - -
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Residues in contact with ILE 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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36G TRP* 2.8 21.5 + - + +
37G VAL 3.8 15.3 - - - +
38G LYS* 3.8 7.4 - - + +
46G GLU 4.0 6.3 - - - +
47G TRP* 1.3 75.4 - - - +
49G GLY* 1.3 58.6 + - - +
60G TYR* 3.6 8.4 - - + +
61G ASN* 2.9 25.4 + - - +
64G PHE* 4.0 27.1 - - + +
68G ALA* 3.8 29.8 - - + -
70G LEU* 5.3 3.4 - - + -
81G MET* 3.8 18.6 - - - -
83G LEU* 5.6 0.9 - - + -
94G TYR* 3.6 35.0 - - + -
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Residues in contact with GLY 49 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35G ASN* 3.3 3.8 - - - -
36G TRP 3.1 23.2 + - - -
47G TRP* 3.4 22.0 + - - -
48G ILE* 1.3 82.6 - - - +
50G LEU* 1.3 60.8 + - - -
59G THR 3.2 13.7 - - - -
60G TYR* 4.1 1.6 - - - -
70G LEU* 3.6 12.0 - - - +
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Residues in contact with LEU 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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80B SER* 4.1 17.7 - - - -
82B GLN* 3.5 30.7 - - - +
90F TRP* 3.7 23.3 - - + -
33G ILE* 3.9 13.2 - - + -
34G MET 3.1 13.0 - - - +
35G ASN* 3.4 11.4 - - - +
47G TRP* 3.9 2.9 - - + -
49G GLY* 1.3 74.3 - - - -
51G ILE* 1.3 72.7 + - - +
52G ASN 4.4 0.2 - - - +
57G TYR* 4.3 9.4 - - + +
58G THR* 3.2 7.3 - - - -
59G THR* 3.0 42.3 + - - +
70G LEU* 3.6 7.5 - - - +
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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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33G ILE* 3.7 3.3 - - - +
34G MET* 2.8 43.9 + - + +
36G TRP* 5.5 2.9 - - - +
50G LEU* 1.3 79.6 - - - +
52G ASN* 1.3 69.8 + - - +
53G PRO* 3.5 2.5 - - - +
56G GLY* 4.1 9.4 - - - +
57G TYR 3.1 12.1 - - - +
58G THR* 3.5 11.4 - - + -
70G LEU* 3.6 21.5 - - + +
71G THR* 3.6 33.7 - - - +
72G VAL* 3.6 29.8 - - + +
79G ALA* 5.3 2.2 - - + -
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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