Contacts of the strand formed by residues 76 - 81 (chain M) in PDB entry 6RQT
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 TYR 76 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572B PRO* 3.3 35.4 - - + +
575B HIS* 4.7 7.6 - - - +
576B THR* 5.7 0.2 + - - -
23M VAL* 5.4 4.5 - - + -
74M ASN* 3.6 11.1 + - - -
75M GLN* 1.3 81.2 - - - +
77M VAL* 1.3 61.2 + - - +
93M ALA* 2.7 47.6 + - + +
95M VAL* 3.8 36.3 - - + +
55N LEU* 4.7 18.4 - - + -
56N ILE 3.4 19.5 - - - +
57N LYS* 3.5 32.7 - - + +
58N PHE* 4.6 1.1 - - - -
107N MET* 4.9 9.2 - - + +
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Residues in contact with VAL 77 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75M GLN* 3.8 2.6 + - + +
76M TYR* 1.3 81.0 - - - +
78M VAL* 1.3 66.6 + - - +
90M LEU* 3.8 30.5 - - + -
91M TYR 3.2 12.6 - - - +
92M LYS* 3.7 19.7 - - + -
93M ALA* 3.8 4.9 - - - -
55N LEU* 3.4 4.5 - - - +
56N ILE* 3.0 43.1 + - + +
58N PHE* 3.5 33.7 - - + -
64N ILE* 5.0 1.3 - - + -
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Residues in contact with VAL 78 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21M VAL* 5.2 6.3 - - + -
77M VAL* 1.3 77.5 - - - +
79M GLY* 1.3 62.8 + - - +
80M LEU* 5.8 5.2 - - + -
89M GLN 3.5 0.9 - - - +
90M LEU* 3.9 0.7 - - - -
91M TYR* 2.6 65.7 + - + +
93M ALA* 4.2 7.8 - - + +
38N PHE* 6.0 2.0 - - + -
53N VAL* 4.3 11.7 - - + -
54N TRP 3.2 26.7 - - - +
55N LEU* 3.7 13.0 - - + +
109N LEU* 5.8 8.1 - - + -
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Residues in contact with GLY 79 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78M VAL* 1.3 71.0 - - - +
80M LEU* 1.3 70.7 + - - +
88M ILE* 5.1 5.2 - - - -
89M GLN 3.3 11.9 - - - -
90M LEU* 5.1 0.7 - - - -
53N VAL* 3.4 1.4 - - - -
54N TRP* 2.4 61.9 + - - -
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Residues in contact with LEU 80 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78M VAL* 5.7 5.4 - - + -
79M GLY* 1.3 80.7 - - - +
81M PHE* 1.3 62.6 + - - +
87M SER 3.7 0.2 - - - +
88M ILE* 3.3 12.2 - - - +
89M GLN* 2.9 48.5 + - + +
91M TYR* 6.0 6.7 - - + -
38N PHE* 5.0 7.4 - - + -
39N PRO* 3.2 48.7 - - + +
40N LEU* 5.1 4.0 - - + -
51N GLN* 3.4 12.6 - - + +
52N GLN 3.9 16.8 - - - +
53N VAL* 4.0 19.3 - - + -
54N TRP* 4.3 0.2 - - - +
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Residues in contact with PHE 81 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80M LEU* 1.3 77.4 - - - +
82M ASN* 1.3 71.5 + - - +
85M LYS* 5.9 1.1 - - - -
86M LYS* 4.1 28.3 - - + -
87M SER 4.1 13.0 - - - +
88M ILE* 3.6 30.1 - - + -
50N GLN 3.9 1.0 - - - +
51N GLN* 3.3 24.7 - - - +
52N GLN* 3.8 26.5 + - + +
54N TRP* 3.4 47.3 - + + -
134N ASP* 4.7 1.3 - - - -
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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