Contacts of the helix formed by residues 80 - 90 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53G ALA* 3.9 14.4 + - + +
58G GLN* 5.6 2.1 - - - +
79G VAL* 1.3 85.9 - - - +
81G ALA* 1.3 64.3 + - - +
82G PRO* 3.3 6.0 - - - +
83G GLY* 3.1 6.8 + - - +
84G VAL* 3.0 26.1 + - + +
101G LEU* 4.1 4.4 - - - +
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Residues in contact with ALA 81 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52G ALA* 6.1 1.3 - - + -
53G ALA* 4.7 6.5 - - - +
75G LEU* 4.2 12.9 - - - +
76G TYR 4.7 0.4 - - - -
77G ASP* 4.3 11.7 - - + +
79G VAL 2.8 9.6 + - - -
80G ASN* 1.3 71.5 - - - +
82G PRO* 1.3 67.2 - - + +
84G VAL* 3.2 4.1 + - - +
85G THR* 2.8 34.5 + - - -
99G GLY* 5.1 0.2 - - - -
100G PHE 3.2 31.0 - - - +
101G LEU* 4.2 7.4 - - + -
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Residues in contact with PRO 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B LYS* 4.6 27.8 - - + +
80G ASN* 3.5 4.3 - - - -
81G ALA* 1.3 94.8 - - + +
83G GLY* 1.3 56.7 + - - +
85G THR* 3.3 6.9 + - - -
86G ALA* 2.9 30.5 + - - +
99G GLY* 5.2 7.6 - - - +
101G LEU* 4.0 32.1 - - + +
105G GLN* 6.1 0.2 - - - +
260H ALA* 3.7 13.0 - - + +
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Residues in contact with GLY 83 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80G ASN* 3.1 9.6 + - - +
82G PRO* 1.3 75.3 - - - +
84G VAL* 1.3 65.4 + - - +
86G ALA* 3.3 3.6 + - - +
87G ASP 3.2 16.6 + - - -
257H VAL* 4.5 0.3 - - - +
260H ALA* 3.3 24.8 + - - -
261H LYS* 3.6 32.4 - - - +
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Residues in contact with VAL 84 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52G ALA* 4.0 16.6 - - + +
53G ALA* 3.9 13.2 - - + -
58G GLN* 3.4 40.6 - - + +
61G ALA* 4.9 0.2 - - + -
75G LEU* 4.2 16.6 - - + -
80G ASN* 3.0 17.0 + - + +
81G ALA* 3.7 8.1 - - - +
83G GLY* 1.3 74.4 - - - +
85G THR* 1.3 62.4 + - - +
87G ASP* 3.4 7.8 + - - +
88G ILE* 3.1 23.5 + - + +
261H LYS* 4.8 5.6 - - - +
269H LEU* 4.0 14.4 - - + -
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Residues in contact with THR 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75G LEU* 3.9 22.8 - - - +
81G ALA 2.8 18.6 + - - -
82G PRO* 3.5 6.5 - - + +
84G VAL* 1.3 74.8 - - - +
86G ALA* 1.3 68.9 + - - +
88G ILE* 3.1 2.5 + - - +
89G SER* 2.8 24.8 + - - -
97G VAL* 4.1 16.3 - - + +
98G ARG* 3.9 6.6 - - - -
99G GLY* 3.2 37.9 - - - +
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Residues in contact with ALA 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82G PRO 2.9 8.2 + - - +
83G GLY 3.7 3.4 - - - +
85G THR* 1.3 77.3 - - - +
87G ASP* 1.3 62.0 + - - +
89G SER* 2.6 24.0 + - - -
90G HIS* 3.4 15.1 + - - +
256H GLU* 4.4 3.4 - - + +
257H VAL* 4.2 14.4 - - + -
260H ALA* 3.4 33.7 - - + -
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Residues in contact with ASP 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83G GLY 3.2 9.7 + - - +
84G VAL* 3.4 12.3 - - - +
85G THR 3.1 0.2 - - - -
86G ALA* 1.3 81.7 - - - +
88G ILE* 1.3 61.5 + - - +
90G HIS* 3.4 5.9 + - - +
257H VAL* 4.1 17.0 - - + +
261H LYS* 3.9 7.9 + - - -
267H ALA* 3.5 4.9 - - - -
268H THR* 2.6 33.5 + - - -
269H LEU* 3.0 17.5 + - + +
270H SER* 2.6 56.4 + - - -
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Residues in contact with ILE 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61G ALA* 3.2 36.6 - - + -
62G MET* 3.5 16.4 - - - +
65G LYS* 3.5 36.8 - - + -
73G LEU* 4.6 1.8 - - + -
75G LEU* 3.7 12.3 - - + -
84G VAL* 3.1 13.4 + - + +
85G THR* 3.8 3.1 - - - +
87G ASP* 1.3 74.7 - - - +
89G SER* 1.3 66.5 + - - +
91G MET* 3.1 28.0 + - - +
97G VAL* 4.1 12.8 - - + -
269H LEU* 3.7 26.0 - - + -
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Residues in contact with SER 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65G LYS* 4.5 3.8 - - - +
85G THR* 2.8 20.8 + - - -
86G ALA* 2.6 26.0 + - - -
88G ILE* 1.3 73.4 - - - +
90G HIS* 1.3 70.3 + - - +
91G MET 3.2 4.1 + - - +
97G VAL* 3.6 22.7 - - - -
199H THR* 3.5 16.1 - - - +
200H PHE* 5.3 0.2 - - - -
203H GLU* 4.8 3.7 - - - +
249H ARG* 5.6 1.7 + - - -
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Residues in contact with HIS 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G ALA* 3.4 9.1 + - - +
87G ASP 3.4 8.9 + - - +
88G ILE 3.1 2.0 - - - -
89G SER* 1.3 90.5 + - - +
91G MET* 1.3 60.5 + - - +
192H LEU* 5.2 0.2 - - + -
195H VAL* 3.1 15.2 - - - +
196H ARG* 3.1 30.5 + - + +
199H THR* 2.8 23.5 + - - -
200H PHE* 3.6 24.9 - + - -
249H ARG* 4.5 2.0 + - - -
253H GLY* 3.1 30.5 - - - -
256H GLU* 3.5 20.2 + - + +
257H VAL* 3.6 18.5 - - + +
270H SER* 4.3 9.7 + - - -
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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