Contacts of the strand formed by residues 74 - 80 (chain o) 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 o).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66o ILE* 5.8 6.3 - - + -
67o PHE 3.5 11.2 - - - +
68o CYS* 4.2 4.7 - - + -
72o ARG 3.5 3.2 - - - -
73o LEU* 1.3 73.7 - - - +
75o THR* 1.3 62.1 + - - +
76o ALA 5.9 0.4 - - - +
189o ALA* 5.3 5.7 - - + +
190o ARG* 5.3 8.3 - - + -
193o VAL* 4.0 26.5 - - + -
81p TYR* 4.3 11.8 - - + +
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Residues in contact with THR 75 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67o PHE* 3.0 15.2 + - - -
68o CYS* 4.9 1.6 - - - -
69o ASP* 4.7 14.4 - - - -
73o LEU 3.3 5.3 + - - -
74o PRO* 1.3 73.9 - - - +
76o ALA* 1.3 53.3 + - - -
56p LYS* 5.7 4.7 - - - -
59p VAL* 4.5 18.4 - - - -
80p PRO* 3.4 4.0 - - - +
81p TYR* 2.5 39.1 + - - +
82p TYR 4.3 1.4 + - - +
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Residues in contact with ALA 76 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66o ILE* 4.0 0.5 - - - -
67o PHE* 2.9 38.6 + - + +
74o PRO* 5.9 0.2 - - - +
75o THR* 1.3 79.4 - - - +
77o PHE* 1.3 62.6 + - - +
59p VAL* 4.6 13.0 - - + -
78p LEU* 4.8 11.2 - - + -
79p THR 3.3 20.0 - - - +
80p PRO* 3.7 11.0 - - + -
81p TYR* 4.2 1.3 - - - +
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Residues in contact with PHE 77 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64o LEU* 6.5 0.9 - - + -
65o VAL 3.3 15.0 - - - +
66o ILE* 4.7 4.5 - - + -
76o ALA* 1.3 75.2 - - - +
78o LEU* 1.3 66.0 + - - +
79o THR 3.5 0.3 + - - -
78p LEU* 3.9 2.6 - - - -
79p THR* 3.0 36.3 + - - +
81p TYR 5.3 0.2 - - - +
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Residues in contact with LEU 78 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64o LEU* 5.7 2.3 - - - -
65o VAL* 3.1 36.6 + - + +
77o PHE* 1.3 74.4 - - - +
79o THR* 1.3 60.3 + - - +
80o PRO 4.0 1.7 - - - -
76p ALA* 4.9 11.0 - - + -
77p PHE 4.0 4.9 - - - +
78p LEU* 4.7 3.4 - - - +
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Residues in contact with THR 79 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77o PHE 3.5 0.6 + - - -
78o LEU* 1.3 74.3 - - - +
80o PRO* 1.3 64.8 - - - +
76p ALA* 3.4 3.0 - - - -
77p PHE* 2.9 39.6 + - - +
79p THR* 4.3 17.9 - - - -
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Residues in contact with PRO 80 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59o VAL* 5.1 15.7 - - + +
78o LEU 4.0 2.8 - - - -
79o THR* 1.3 75.9 - - - +
81o TYR* 1.3 62.3 + - - +
82o TYR* 3.3 19.0 + - - +
83o ALA 5.0 5.2 - - - +
84o ARG* 5.1 11.6 - - - +
75p THR 3.9 2.5 - - - +
76p ALA* 3.7 16.9 - - + -
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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