Contacts of the helix formed by residues 80 - 90 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A ALA* 4.0 14.4 + - + +
58A GLN* 6.0 0.7 - - - +
79A VAL* 1.3 86.0 - - - +
81A ALA* 1.3 62.1 + - - +
82A PRO* 3.3 8.1 - - - +
83A GLY* 3.3 5.4 + - - +
84A VAL* 3.2 25.8 + - + +
101A LEU* 4.2 3.6 - - - +
261B LYS 5.6 2.4 - - - +
262B ALA* 6.2 0.3 - - - +
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Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ALA* 6.2 1.8 - - + -
53A ALA* 4.6 6.3 - - - -
75A LEU* 4.5 7.8 - - - +
76A TYR 4.7 0.7 - - - -
77A ASP* 4.2 11.0 - - + +
79A VAL 2.7 11.5 + - - +
80A ASN* 1.3 72.4 - - - +
82A PRO* 1.3 61.4 - - + +
84A VAL* 3.4 3.5 + - - +
85A THR* 2.6 38.0 + - - -
99A GLY* 5.2 0.4 - - - -
100A PHE 3.3 34.3 - - - +
101A LEU* 4.0 9.0 - - + -
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Residues in contact with PRO 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ASN* 3.3 6.3 - - - -
81A ALA* 1.3 97.6 - - + +
83A GLY* 1.3 57.1 + - - +
85A THR* 3.4 6.8 + - - +
86A ALA* 2.9 28.9 + - - +
99A GLY* 5.6 3.6 - - - -
100A PHE 6.1 0.9 - - - +
101A LEU* 4.2 26.5 - - + -
260B ALA* 4.1 13.8 - - + +
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Residues in contact with GLY 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ASN* 3.3 8.1 + - - +
82A PRO* 1.3 77.2 - - - +
84A VAL* 1.3 64.6 + - - +
86A ALA* 3.5 2.3 + - - +
87A ASP* 3.2 16.8 + - - +
257B VAL* 4.4 0.3 - - - +
260B ALA* 3.8 18.0 + - - -
261B LYS* 3.5 40.6 - - - +
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Residues in contact with VAL 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ALA* 3.8 17.9 - - + +
53A ALA* 3.8 17.3 - - + -
58A GLN* 3.7 34.1 - - + +
75A LEU* 4.2 7.0 - - + -
80A ASN* 3.2 17.3 + - + +
81A ALA* 3.8 6.3 - - - +
83A GLY* 1.3 73.7 - - - +
85A THR* 1.3 65.7 + - - +
87A ASP* 3.4 7.1 + - - +
88A ILE* 2.9 43.6 + - + +
261B LYS* 4.7 4.9 - - - +
269B LEU* 4.1 6.3 - - + -
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Residues in contact with THR 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LEU* 4.0 18.3 - - - +
81A ALA 2.6 21.8 + - - -
82A PRO* 3.5 7.0 - - - -
84A VAL* 1.3 74.6 - - - +
86A ALA* 1.3 66.3 + - - +
88A ILE* 3.2 2.1 + - - +
89A SER* 2.7 24.9 + - - -
97A VAL* 4.1 12.5 - - + +
98A ARG* 3.7 11.2 - - - +
99A GLY* 3.2 38.3 - - - +
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Residues in contact with ALA 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A PRO 2.9 18.2 + - - +
83A GLY 3.6 3.8 - - - +
85A THR* 1.3 76.6 - - - +
87A ASP* 1.3 63.8 + - - +
89A SER* 2.5 26.9 + - - -
90A HIS* 3.5 9.9 - - - +
256B GLU* 4.9 5.4 - - + +
257B VAL* 4.3 15.5 - - + -
260B ALA* 3.6 24.7 - - + -
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Residues in contact with ASP 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A GLY 3.2 10.8 + - - +
84A VAL* 3.4 11.0 - - - +
86A ALA* 1.3 79.9 - - - +
88A ILE* 1.3 63.6 + - + +
90A HIS* 3.3 7.8 + - - +
257B VAL* 4.1 17.8 - - + +
261B LYS* 3.4 8.3 + - - -
267B ALA* 3.7 5.4 - - - -
268B THR* 2.8 32.8 + - - -
269B LEU* 3.0 15.6 + - + +
270B SER* 2.6 59.8 + - - -
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Residues in contact with ILE 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ALA* 3.2 41.1 - - + +
62A MET* 3.9 7.4 - - - +
65A LYS* 3.4 41.4 - - + -
73A LEU* 4.7 0.7 - - + -
75A LEU* 3.5 14.6 - - + -
84A VAL* 2.9 25.1 + - + +
85A THR 3.8 2.9 - - - +
87A ASP* 1.3 77.7 - - - +
89A SER* 1.3 63.0 + - - +
90A HIS 3.1 0.9 + - - -
91A MET* 3.1 21.4 + - - +
97A VAL* 4.0 13.9 - - + -
269B LEU* 3.9 19.1 - - + -
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Residues in contact with SER 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LYS* 4.5 3.3 + - - +
85A THR* 2.7 20.5 + - - -
86A ALA* 2.5 24.0 + - - -
88A ILE* 1.3 72.8 - - - +
90A HIS* 1.3 72.2 + - - +
91A MET 3.4 3.7 + - - +
97A VAL* 3.6 20.9 - - - -
199B THR* 3.4 18.2 - - - +
200B PHE* 5.4 0.6 - - - -
203B GLU* 5.0 3.4 - - - +
249B ARG* 5.0 4.2 + - - -
256B GLU* 4.8 2.3 + - - -
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Residues in contact with HIS 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ALA* 3.5 7.8 + - - -
87A ASP 3.3 9.3 + - - +
88A ILE 3.1 1.0 - - - -
89A SER* 1.3 91.3 - - - +
91A MET* 1.3 59.6 + - - +
192B LEU* 5.1 0.9 - - + -
195B VAL* 3.0 17.9 - - - +
196B ARG* 3.0 35.9 + - + +
199B THR* 2.8 22.4 + - - -
200B PHE* 3.7 22.2 - + - -
249B ARG* 4.6 0.4 - - - -
253B GLY 3.5 16.8 - - - -
256B GLU* 2.9 26.5 + - - -
257B VAL* 3.5 27.4 - - + +
270B SER* 4.3 9.9 + - - +
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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