Contacts of the strand formed by residues 78 - 86 (chain B) in PDB entry 3QJS
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 GLN 78 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73B GLN* 3.7 0.7 - - - +
74B THR* 2.7 51.5 + - + +
75B GLY* 3.2 20.2 + - - +
77B ASN* 1.3 79.7 - - - +
79B TYR* 1.3 74.0 + - - +
80B THR* 4.7 0.2 + - - -
102B GLU* 2.5 45.2 + - + +
104B VAL* 4.3 7.6 - - + +
136B ARG* 3.5 14.6 - - - +
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Residues in contact with TYR 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B VAL* 3.4 30.7 - - + -
72B VAL 3.4 3.6 - - - +
73B GLN* 3.2 48.3 + - + -
74B THR* 4.0 2.0 - - - -
76B PRO 5.2 4.5 - - - -
77B ASN* 5.2 1.6 - - - -
78B GLN* 1.3 82.7 - - - +
80B THR* 1.3 62.6 + - - +
81B VAL* 5.2 2.2 - - + -
97B VAL* 5.7 0.2 - - + -
98B PRO* 3.6 34.6 - - + +
101B ALA* 4.1 13.2 - - + -
102B GLU 3.0 9.3 + - - +
103B ILE* 3.6 14.7 - - + +
104B VAL* 3.0 25.5 + - - +
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Residues in contact with THR 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B ALA 3.2 1.8 - - - +
71B VAL* 3.3 3.1 - - - +
72B VAL* 2.8 47.1 + - - +
74B THR* 3.2 22.5 + - - +
79B TYR* 1.3 72.4 + - - +
81B VAL* 1.3 63.8 + - - +
82B TYR* 3.5 33.4 - - + +
104B VAL* 3.4 20.5 - - + +
106B LYS* 4.0 16.8 - - + -
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Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ALA* 3.1 12.3 - - + +
71B VAL* 3.9 22.0 - - + -
79B TYR* 4.9 0.9 - - + -
80B THR* 1.3 80.5 - - - +
82B TYR* 1.3 65.6 + - - +
83B VAL* 3.4 18.4 + - + +
92B PRO* 4.7 0.7 - - + -
95B ILE* 3.6 25.8 - - + -
97B VAL* 3.9 10.5 - - + -
103B ILE* 3.7 26.0 - - + -
104B VAL 2.9 9.1 + - - -
105B PHE* 3.7 11.3 - - + -
106B LYS 2.9 23.6 + - - -
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Residues in contact with TYR 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B GLU* 5.6 0.7 - - - -
63B PRO* 3.5 52.0 - - + +
64B TRP* 3.5 35.6 - + + +
69B GLN 4.9 0.4 - - - -
70B ALA* 2.9 40.3 + - - +
72B VAL* 4.2 23.1 - - + +
80B THR* 3.5 26.3 - - + +
81B VAL* 1.3 70.6 - - - +
83B VAL* 1.3 60.0 + - - +
84B LEU 4.1 0.2 + - - -
91B GLN* 4.2 1.6 - - - +
92B PRO* 3.8 5.2 - - - +
106B LYS* 3.4 27.5 - - + +
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Residues in contact with VAL 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B TRP* 2.8 14.5 + - - -
81B VAL* 3.7 21.1 - - + +
82B TYR* 1.3 74.5 - - - +
84B LEU* 1.3 69.0 + - - +
90B TYR* 4.4 7.6 - - + -
91B GLN 3.4 13.2 - - - +
92B PRO* 4.5 0.2 - - - -
95B ILE* 3.9 26.5 - - + -
105B PHE* 3.9 15.9 - - + -
106B LYS 3.0 4.9 + - - -
107B ILE* 3.1 21.0 - - + +
108B THR 3.1 15.1 + - - -
116B PHE* 3.7 23.1 - - + -
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Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B VAL* 3.6 29.2 - - + -
59B ARG* 3.7 32.8 - - + +
64B TRP* 3.7 12.9 - - + +
82B TYR 4.1 0.2 + - - -
83B VAL* 1.3 77.0 - - - +
85B ALA* 1.3 60.1 + - - +
86B PHE* 3.9 15.0 - - + -
90B TYR* 3.4 5.5 - - - -
91B GLN* 2.9 61.9 + - + +
108B THR* 3.5 20.9 - - + +
110B PRO* 3.7 19.3 - - + -
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Residues in contact with ALA 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B VAL 4.1 0.2 - - - -
84B LEU* 1.3 71.0 - - - +
86B PHE* 1.3 59.4 + - - +
89B GLY 3.9 4.7 - - - -
90B TYR* 3.7 24.9 - - + -
107B ILE* 4.3 4.0 - - + +
108B THR 2.8 14.0 + - - +
109B SER* 3.3 28.2 + - - -
110B PRO* 3.3 1.0 - - - +
114B HIS* 3.4 24.1 - - + -
127B VAL* 4.1 16.2 - - + -
160B MET* 4.0 0.2 - - + -
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Residues in contact with PHE 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ARG* 3.5 36.6 - - - +
84B LEU* 3.9 20.2 - - + -
85B ALA* 1.3 74.4 - - - +
87B ALA* 1.3 65.2 - - - +
88B PHE* 2.2 24.8 + - - -
89B GLY* 3.1 37.1 + - - +
90B TYR 3.6 6.7 - - - -
91B GLN* 3.5 33.0 - - + -
110B PRO* 3.8 13.0 - - + -
111B ASP* 3.7 4.0 - - - -
114B HIS* 3.3 6.7 - - - -
160B MET* 3.4 7.8 - - - +
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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