Contacts of the helix formed by residues 80 - 90 (chain B) in PDB entry 1SMK
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 ASN 80 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261A LYS* 6.2 1.5 - - + -
53B ALA* 4.0 14.4 + - + +
58B GLN* 5.9 1.5 - - - +
79B VAL* 1.3 86.1 - - - +
81B ALA* 1.3 65.2 + - - +
82B PRO* 3.2 7.6 - - - +
83B GLY* 3.2 13.2 + - - +
84B VAL* 3.3 17.9 + - + +
101B LEU* 3.9 5.1 - - - +
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Residues in contact with ALA 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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52B ALA* 6.3 1.3 - - - -
53B ALA* 4.8 3.1 - - - -
75B LEU* 3.9 13.9 - - - +
76B TYR 4.5 0.4 - - - -
77B ASP* 4.1 14.6 - - + +
79B VAL 2.9 5.9 + - - -
80B ASN* 1.3 75.9 - - - +
82B PRO* 1.3 68.2 - - + +
84B VAL* 3.5 4.5 + - - +
85B THR* 2.7 33.6 + - - -
99B GLY* 5.1 0.7 - - - -
100B PHE 3.2 32.3 - - - +
101B LEU* 4.2 4.7 - - + -
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Residues in contact with PRO 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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260A ALA* 3.7 16.1 - - + +
80B ASN* 3.3 5.4 - - - -
81B ALA* 1.3 95.0 - - + +
83B GLY* 1.3 56.2 + - - +
85B THR* 3.5 5.9 - - - -
86B ALA* 2.9 30.5 + - - +
99B GLY* 5.4 4.3 - - - -
100B PHE 5.9 1.1 - - - +
101B LEU* 4.1 31.6 - - + +
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Residues in contact with GLY 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A VAL* 4.1 1.4 - - - +
260A ALA* 3.5 15.7 + - - -
261A LYS* 3.5 35.6 - - - -
80B ASN* 3.2 9.3 + - - +
82B PRO* 1.3 79.5 - - - +
84B VAL* 1.3 62.1 + - - +
86B ALA* 3.2 4.0 + - - +
87B ASP* 3.0 22.3 + - - +
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Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LYS* 4.2 6.5 - - - +
269A LEU* 4.0 21.3 - - + -
52B ALA* 4.0 16.4 - - + +
53B ALA* 4.0 12.3 - - + -
58B GLN* 3.6 32.3 - - + +
61B ALA* 4.7 1.6 - - + -
75B LEU* 4.0 16.6 - - + -
80B ASN* 3.3 16.1 + - + +
81B ALA* 3.9 7.2 - - - +
83B GLY* 1.3 73.2 - - - +
85B THR* 1.3 53.6 + - - +
87B ASP* 3.1 9.5 - - - +
88B ILE* 2.8 36.8 + - + +
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Residues in contact with THR 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 3.6 22.7 - - - +
81B ALA 2.7 21.9 + - - -
82B PRO* 3.5 6.1 - - - -
84B VAL* 1.3 73.7 - - - +
86B ALA* 1.3 55.2 + - - +
88B ILE* 3.5 1.1 - - - +
89B SER* 2.6 40.7 + - - -
97B VAL* 4.1 13.4 - - + +
98B ARG* 3.7 10.5 - - - -
99B GLY* 3.3 38.4 - - - +
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Residues in contact with ALA 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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256A GLU* 4.3 5.8 - - + +
257A VAL* 3.8 14.3 - - + +
260A ALA* 3.5 31.6 - - + -
82B PRO 2.9 8.1 + - - +
83B GLY 3.6 3.1 - - - +
85B THR* 1.3 73.4 - - - +
87B ASP* 1.3 67.8 + - - +
89B SER* 2.8 22.1 + - - -
90B HIS* 3.4 16.7 + - - +
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Residues in contact with ASP 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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257A VAL* 3.8 16.7 - - + +
261A LYS* 4.0 6.8 + - - -
267A ALA* 3.6 6.0 - - - -
268A THR* 2.9 30.9 + - - -
269A LEU* 3.0 19.6 + - + +
270A SER* 2.7 55.1 + - - -
58B GLN* 5.3 0.2 - - - +
83B GLY 3.0 12.6 + - - +
84B VAL* 3.1 13.0 - - - +
86B ALA* 1.3 81.1 - - - +
88B ILE* 1.3 62.5 + - - +
90B HIS* 3.4 6.9 + - - +
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Residues in contact with ILE 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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269A LEU* 3.9 20.6 - - + -
61B ALA* 3.2 47.8 - - + +
62B MET* 3.5 2.7 - - - +
65B LYS* 3.4 32.4 - - + -
73B LEU* 4.6 1.3 - - + -
75B LEU* 3.7 13.0 - - + -
84B VAL* 2.8 19.6 + - + +
85B THR 3.8 2.2 - - - +
87B ASP* 1.3 71.2 - - - +
89B SER* 1.3 63.2 + - - +
90B HIS 2.9 6.9 + - - -
91B MET* 2.9 33.1 + - - +
97B VAL* 3.8 15.9 - - + -
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Residues in contact with SER 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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199A THR* 3.5 17.0 - - - +
200A PHE* 5.2 0.2 - - - -
203A GLU* 4.4 5.9 - - - +
249A ARG* 5.4 2.5 + - - -
256A GLU* 5.3 0.5 + - - -
65B LYS* 4.4 2.9 - - - +
85B THR* 2.6 23.3 + - - -
86B ALA* 2.8 25.5 + - - -
88B ILE* 1.3 71.1 - - - +
90B HIS* 1.3 70.0 + - - +
91B MET 3.2 3.7 + - - +
97B VAL* 3.4 25.1 - - - -
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Residues in contact with HIS 90 (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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192A LEU* 5.2 0.7 - - + -
195A VAL* 3.0 17.6 - - - +
196A ARG* 3.2 28.4 + - + +
199A THR* 2.9 22.5 + - - -
200A PHE* 3.5 26.9 - + - -
249A ARG* 4.5 1.6 - - - -
253A GLY 3.2 27.6 - - - -
256A GLU* 2.7 27.7 + - + +
257A VAL* 3.8 17.4 - - + +
270A SER* 4.4 8.7 + - - -
86B ALA* 3.4 13.7 + - - -
87B ASP 3.4 9.8 + - - +
88B ILE 2.9 1.8 + - - -
89B SER* 1.3 84.4 + - - +
91B MET* 1.3 58.2 + - - +
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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