Contacts of the strand formed by residues 61 - 65 (chain C) in PDB entry 3Q37
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 PHE 61 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C PHE* 3.6 29.8 - + + -
32C THR* 6.4 0.4 - - - -
34C ILE* 3.7 24.0 - - + -
39C GLN* 3.9 0.4 - - - -
40C CYS* 3.3 26.0 - - + -
41C VAL 4.8 0.2 - - - -
42C VAL* 3.3 36.8 - - + -
56C LEU* 3.7 25.8 - - + +
58C ASN* 3.1 40.6 + - + +
59C PRO* 3.2 5.3 - - - +
60C LYS* 1.3 80.0 - - - +
62C GLN* 1.3 65.1 + - - +
243C PHE* 4.5 4.9 - + - -
247C ILE* 3.9 16.6 - - + -
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Residues in contact with GLN 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C GLN* 3.4 23.4 + - - +
40C CYS 2.9 7.7 + - - +
41C VAL* 3.2 5.7 - - + +
42C VAL* 3.0 25.8 + - - +
61C PHE* 1.3 77.1 - - - +
63C ILE* 1.3 69.3 + - - +
90C SER* 3.6 19.5 + - - -
91C TRP* 3.6 37.4 - - + +
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Residues in contact with ILE 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C VAL* 3.4 15.3 - - + +
44C PRO* 3.9 18.6 - - + -
49C ILE* 4.3 8.3 - - + -
52C THR* 3.7 16.8 - - + +
53C LYS* 3.3 49.8 - - + +
56C LEU* 4.1 11.7 - - + -
61C PHE 5.9 0.2 - - - -
62C GLN* 1.3 81.4 + - - +
64C ALA* 1.3 66.2 + - - +
89C ILE* 3.5 35.0 - - + +
90C SER 4.4 2.3 + - - -
91C TRP* 3.6 11.0 + - - +
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Residues in contact with ALA 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C VAL* 3.5 23.8 - - + -
42C VAL 2.8 8.3 + - - +
43C ALA* 3.1 26.6 - - + -
44C PRO* 3.3 11.1 - - - +
49C ILE* 4.0 1.5 - - - +
62C GLN 4.0 0.2 + - - -
63C ILE* 1.3 79.9 - - - +
65C ALA* 1.3 65.6 - - - +
89C ILE* 4.4 1.8 - - - -
91C TRP* 3.2 22.9 - - + +
92C VAL* 4.1 2.2 - - - +
93C VAL* 4.7 6.3 - - + -
125C ILE* 5.8 0.4 - - + -
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Residues in contact with ALA 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ALA* 4.4 0.7 - - - -
44C PRO 4.8 0.7 - - - -
46C PHE* 4.0 6.7 - - + -
49C ILE* 4.0 8.5 - - + -
64C ALA* 1.3 74.5 - - - +
66C GLN* 1.3 61.5 + - - +
67C ASN 3.3 17.3 - - - +
84C LEU* 3.7 35.2 - - + -
89C ILE* 4.1 2.2 - - + +
91C TRP 3.1 9.1 + - - +
92C VAL* 4.1 5.8 - - + -
93C VAL* 2.9 29.1 + - - +
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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