Contacts of the strand formed by residues 74 - 80 (chain R) in PDB entry 6QXT
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 PRO 74 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66R ILE* 5.8 6.5 - - + -
67R PHE 3.6 11.2 - - - +
68R CYS* 4.2 4.7 - - + -
72R ARG 3.5 3.4 - - - +
73R LEU* 1.3 74.6 - - - +
75R THR* 1.3 61.4 + - - +
76R ALA 5.8 1.1 - - - +
189R ALA* 5.3 5.1 - - - +
190R ARG* 5.3 7.5 - - + -
193R VAL* 4.0 27.1 - - + -
81S TYR* 4.4 11.0 - - + +
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Residues in contact with THR 75 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67R PHE* 3.0 11.5 + - - -
68R CYS 5.0 0.7 - - - -
69R ASP* 4.8 15.5 - - - -
73R LEU 3.4 5.3 + - - -
74R PRO* 1.3 73.6 - - - +
76R ALA* 1.3 55.8 + - - +
56S LYS* 5.7 5.2 - - - -
59S VAL* 4.4 18.4 - - - -
80S PRO* 3.4 4.4 - - - +
81S TYR* 2.5 39.6 + - - +
82S TYR 4.2 1.4 + - - -
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Residues in contact with ALA 76 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66R ILE* 4.1 0.9 - - - +
67R PHE* 3.1 37.7 + - + +
74R PRO* 5.8 0.9 - - - +
75R THR* 1.3 78.3 - - - +
77R PHE* 1.3 62.3 + - - +
59S VAL* 4.6 13.0 - - + -
78S LEU* 4.7 10.5 - - + -
79S THR 3.3 19.5 - - - +
80S PRO* 3.7 11.9 - - + -
81S TYR* 4.1 1.3 - - - +
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Residues in contact with PHE 77 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64R LEU* 6.5 0.4 - - + -
65R VAL 3.4 15.0 - - - +
66R ILE* 4.9 3.8 - - + -
67R PHE* 5.0 0.4 - - - +
76R ALA* 1.3 76.3 - - - +
78R LEU* 1.3 66.8 + - - +
79R THR* 3.5 0.7 + - - -
78S LEU* 3.8 2.8 - - - -
79S THR* 2.9 35.7 + - - +
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Residues in contact with LEU 78 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64R LEU* 5.6 2.4 - - - -
65R VAL* 3.1 36.9 + - + +
77R PHE* 1.3 74.1 - - - +
79R THR* 1.3 60.1 + - - +
80R PRO 4.1 1.9 - - - -
76S ALA* 4.9 11.0 - - + -
77S PHE 4.0 5.2 - - - +
78S LEU* 4.7 3.4 - - - +
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Residues in contact with THR 79 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77R PHE 3.5 0.4 + - - -
78R LEU* 1.3 72.6 - - - +
80R PRO* 1.3 64.4 - - - +
81R TYR 3.9 0.3 + - - -
76S ALA* 3.4 3.3 - - - -
77S PHE* 2.8 39.9 + - - +
79S THR* 4.3 18.8 - - - -
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Residues in contact with PRO 80 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59R VAL* 5.1 15.5 - - + +
78R LEU 4.1 2.4 - - - -
79R THR* 1.3 76.2 - - - +
81R TYR* 1.3 64.3 + - - +
82R TYR* 3.5 19.9 + - - +
83R ALA 4.9 5.8 - - - +
84R ARG* 5.1 12.3 - - - +
75S THR 3.8 2.5 - - - +
76S ALA* 3.7 17.1 - - + -
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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