Contacts of the strand formed by residues 79 - 89 (chain B) in PDB entry 6UPQ
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 ARG 79 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75B GLU* 3.0 39.5 + - - +
77B GLY 4.7 2.7 - - - +
78B VAL* 1.3 76.7 - - - +
80B LEU* 1.3 72.9 + - - +
81B LYS* 3.8 29.3 - - - +
101B THR* 3.6 0.5 - - - -
102B VAL* 2.7 53.5 + - + +
116B PRO* 4.7 3.1 - - - -
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Residues in contact with LEU 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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45B LEU* 4.5 5.4 - - + -
78B VAL* 5.0 0.4 - - + -
79B ARG* 1.3 93.9 + - - +
81B LYS* 1.3 63.4 + - - +
82B ALA* 4.1 1.3 + - - -
99B VAL* 4.1 16.8 - - + -
100B ASP 3.3 14.6 - - - +
101B THR* 3.5 24.9 - - + +
102B VAL* 4.8 0.4 - - - -
116B PRO* 3.5 17.7 - - + +
117B ILE* 3.8 17.3 - - + +
120B TYR* 3.3 42.2 - - + -
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Residues in contact with LYS 81 (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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67B GLU* 5.8 3.8 + - - +
69B ASP* 3.7 34.8 + - - +
79B ARG* 3.8 23.8 - - - +
80B LEU* 1.3 73.4 - - - +
82B ALA* 1.3 59.8 + - - +
83B ARG* 3.6 36.4 - - + +
98B ILE 3.5 2.3 - - - +
99B VAL* 3.2 4.2 - - - -
100B ASP* 2.9 39.6 + - + +
102B VAL* 3.6 27.1 - - + +
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Residues in contact with ALA 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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80B LEU 4.1 1.6 + - - -
81B LYS* 1.3 72.5 - - - +
83B ARG* 1.3 83.9 + - - +
97B THR* 4.5 5.8 - - + -
98B ILE 3.5 4.5 - - - -
99B VAL* 4.1 12.3 - - + +
120B TYR* 3.9 26.9 - - + +
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Residues in contact with ARG 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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67B GLU* 4.7 16.1 - - + +
81B LYS* 3.6 36.6 - - + +
82B ALA* 1.3 100.4 + - - +
84B SER* 1.3 62.1 + - - +
85B TYR* 3.2 35.3 - - + +
97B THR* 3.2 2.7 - - - +
98B ILE* 2.8 35.4 + - + +
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Residues in contact with SER 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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83B ARG* 1.3 72.8 - - - +
85B TYR* 1.3 72.8 + - - +
95B LYS* 4.0 21.7 + - - -
96B LEU 3.2 5.2 - - - -
97B THR* 2.9 25.1 + - - +
143B HIS* 4.9 1.2 + - - -
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Residues in contact with TYR 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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66B PHE* 3.5 51.6 - + + +
67B GLU* 3.2 27.6 + - + +
83B ARG* 3.2 43.7 - - + +
84B SER* 1.3 80.5 - - - +
86B GLU* 1.3 63.8 + - - +
87B LEU* 3.8 12.0 + - + -
94B LEU 3.5 1.2 - - - +
95B LYS* 3.6 3.4 - - - +
96B LEU* 2.7 45.9 + - + +
98B ILE* 4.1 16.6 - - + +
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Residues in contact with GLU 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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85B TYR* 1.3 74.0 - - - +
87B LEU* 1.3 68.1 + - - +
88B GLN* 4.4 4.3 - - - +
94B LEU 3.5 5.6 - - - +
95B LYS* 5.2 15.8 - - + -
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Residues in contact with LEU 87 (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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62B PHE* 3.9 25.6 - - + +
64B THR* 4.8 11.2 - - + +
66B PHE* 3.7 38.6 - - + -
85B TYR* 4.3 13.7 - - + +
86B GLU* 1.3 83.5 - - - +
88B GLN* 1.3 70.1 + - - +
89B GLU* 4.0 2.0 - - + +
93B ARG* 3.7 2.1 - - - -
94B LEU* 2.7 49.8 + - + +
96B LEU* 3.9 10.8 - - + -
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Residues in contact with GLN 88 (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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86B GLU 4.4 3.6 - - - +
87B LEU* 1.3 85.1 + - - +
89B GLU* 1.3 63.6 + - - +
90B SER 3.7 13.4 + - - +
91B ASN 5.1 4.5 - - - +
92B VAL 3.6 11.7 - - - +
93B ARG* 5.0 6.9 - - + +
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Residues in contact with GLU 89 (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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61B LEU 5.3 2.3 - - - +
62B PHE* 3.6 28.9 - - + +
87B LEU* 4.0 2.5 - - + +
88B GLN* 1.3 75.9 - - - +
90B SER* 1.3 68.6 + - - +
91B ASN 3.9 0.7 + - - -
92B VAL* 3.3 22.3 + - + +
94B LEU* 3.7 28.0 - - + -
278B ILE* 3.4 29.6 - - + +
279B ARG* 3.5 24.9 + - - +
282B MET* 5.7 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