Contacts of the strand formed by residues 75 - 83 (chain B) in PDB entry 5NC5
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 LEU 75 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ARG* 4.2 44.5 - - + +
169A THR* 6.1 0.5 - - - -
170A SER* 4.6 9.2 + - - -
69B MET* 5.7 2.7 - - + +
72B ILE* 4.9 10.3 - - + +
73B ASP 3.6 0.4 - - - -
74B ASN* 1.3 77.3 - - - +
76B MET* 1.3 63.0 + - - +
77B TYR* 3.7 26.7 - - - +
78B MET* 4.6 4.9 - - + -
92B LEU* 3.7 33.2 - - + -
93B THR 3.6 17.5 - - - +
94B PHE* 4.0 15.7 - - + -
95B GLU* 5.2 1.6 - - - +
820B ASN* 4.9 1.6 - - - +
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Residues in contact with MET 76 (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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40B PRO* 4.3 14.8 - - + -
74B ASN 3.6 0.4 + - - -
75B LEU* 1.3 75.8 - - - +
77B TYR* 1.3 85.0 + - + +
93B THR* 2.9 29.3 + - + +
94B PHE 3.4 18.2 - - - +
95B GLU* 3.3 49.6 - - - +
96B SER* 4.9 3.6 - - - +
820B ASN* 4.7 1.7 + - - +
864B TYR* 3.5 36.1 + - + +
865B GLN* 5.2 6.1 - - - +
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Residues in contact with TYR 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PRO* 5.8 1.2 - - - +
75B LEU* 3.7 7.8 - - - +
76B MET* 1.3 102.7 - - + +
78B MET* 1.3 64.4 + - - +
79B SER* 5.4 2.9 - - - -
91B THR 5.7 0.2 - - - -
92B LEU* 3.6 1.9 - - - -
93B THR* 2.9 57.7 + - + +
819B TYR* 3.4 28.5 - + + +
820B ASN* 3.5 17.5 - - - +
858B ASP* 6.0 0.2 - - - +
860B THR* 3.6 17.3 - - - -
861B GLY* 3.2 23.7 + - - -
864B TYR* 4.0 33.4 - + - -
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Residues in contact with MET 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ARG* 3.8 30.3 - - - +
66B GLU* 3.8 37.2 - - + +
69B MET* 4.1 27.6 - - - -
75B LEU* 4.6 7.6 - - + -
77B TYR* 1.3 79.3 - - - +
79B SER* 1.3 65.3 + - - +
90B ILE* 4.1 11.0 - - + -
91B THR 3.3 7.2 - - - +
92B LEU* 4.0 19.1 - - + +
819B TYR* 3.5 7.3 - - - -
820B ASN* 2.9 31.9 + - - +
821B GLY* 3.9 20.6 - - - +
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Residues in contact with SER 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B GLU* 4.6 3.1 - - - -
77B TYR* 5.6 3.1 - - - -
78B MET* 1.3 76.2 - - - +
80B SER* 1.3 66.6 + - - +
81B ASN* 5.3 1.7 + - - -
90B ILE* 3.4 4.3 - - - +
91B THR* 2.9 45.7 + - - +
683B GLU* 5.6 2.2 - - - -
818B ARG 3.5 11.4 - - - -
819B TYR* 4.0 15.5 - - - -
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Residues in contact with SER 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B THR* 3.6 21.9 - - - +
66B GLU* 2.9 23.5 + - - -
79B SER* 1.3 79.3 - - - +
81B ASN* 1.3 67.7 + - - +
82B SER* 5.0 0.7 + - - -
89B GLN 3.2 11.9 - - - -
90B ILE* 3.8 6.1 - - - -
816B LEU 5.1 0.3 + - - -
817B GLU* 3.3 6.2 - - - +
818B ARG* 3.0 43.0 + - - +
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Residues in contact with ASN 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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79B SER* 5.3 2.4 + - - -
80B SER* 1.3 78.8 - - - +
82B SER* 1.3 64.2 - - - +
83B ASP* 4.2 1.3 - - + -
87B THR 3.9 0.9 - - - +
88B VAL* 3.4 3.4 - - - +
89B GLN* 3.0 51.1 + - - +
815B ARG* 3.4 45.0 + - + +
816B LEU 3.2 8.3 - - - +
817B GLU* 4.9 3.8 - - - +
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Residues in contact with SER 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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54B ALA* 3.5 18.1 - - - +
57B VAL* 3.7 18.2 - - - -
58B GLN* 3.8 13.3 + - - +
62B THR* 2.7 32.4 + - - +
80B SER* 5.0 0.2 + - - -
81B ASN* 1.3 75.1 + - - +
83B ASP* 1.3 61.2 + - - +
87B THR 3.5 5.2 - - - -
88B VAL* 4.1 0.4 - - - +
815B ARG* 3.3 2.1 - - - -
816B LEU* 2.8 34.4 + - - -
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Residues in contact with ASP 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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53B ASP 4.1 0.5 - - - -
54B ALA* 3.5 14.0 + - - -
57B VAL* 4.4 2.3 - - - +
81B ASN* 4.2 2.0 - - + -
82B SER* 1.3 75.0 - - - +
84B SER* 1.4 57.1 + - - +
85B THR* 2.4 56.5 + - - +
86B GLY* 3.3 11.8 + - - -
87B THR* 2.9 26.6 + - - +
620B ARG* 3.7 24.9 + - - +
814B PRO 3.5 12.8 - - - +
815B ARG* 4.1 19.1 + - + +
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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