Contacts of the helix formed by residues 77 - 88 (chain A) in PDB entry 1SK0
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 THR 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A PHE* 1.3 76.4 - - - +
78A ASP* 1.3 65.8 + - - +
79A ASP* 3.5 7.8 + - - +
80A GLN* 2.9 42.6 + - - +
81A LEU* 3.0 21.8 + - - +
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Residues in contact with ASP 78 (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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54A SER* 5.7 2.3 - - - -
55A VAL* 3.7 36.2 + - + +
56A ARG* 4.7 3.3 + - - +
76A PHE 3.9 0.9 + - - +
77A THR* 1.3 73.9 - - - +
79A ASP* 1.3 61.2 + - - +
81A LEU* 3.1 11.4 + - - +
82A ILE* 2.8 33.5 + - + +
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Residues in contact with ASP 79 (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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41A ARG* 2.8 33.3 + - - +
45A VAL* 5.5 0.3 - - - +
77A THR* 3.3 6.9 + - - +
78A ASP* 1.3 75.8 - - - +
80A GLN* 1.3 65.9 + - + +
82A ILE* 3.4 12.1 + - - +
83A ASP* 2.9 31.2 + - - +
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Residues in contact with GLN 80 (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 LYS 3.9 5.6 + - - +
76A PHE* 3.3 19.4 - - + +
77A THR* 2.9 45.8 + - - +
79A ASP* 1.3 77.2 - - + +
81A LEU* 1.3 57.6 + - - +
83A ASP* 3.2 7.1 + - - +
84A PHE* 3.0 42.2 + - + -
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Residues in contact with LEU 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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55A VAL* 3.7 10.3 - - + -
56A ARG* 4.1 37.0 - - + +
59A LEU* 4.1 30.3 - - + +
71A LEU* 4.3 15.3 - - + -
76A PHE* 3.4 34.8 - - + +
77A THR 3.0 18.1 + - - +
78A ASP* 3.1 13.0 + - - +
80A GLN* 1.3 73.8 - - - +
82A ILE* 1.3 64.9 + - - +
84A PHE* 3.2 8.1 + - + +
85A MET* 3.0 31.5 + - + +
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Residues in contact with ILE 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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41A ARG* 3.7 26.0 - - + +
44A LEU* 4.1 14.3 - - + +
45A VAL* 4.1 23.6 - - + -
48A ILE* 4.0 15.9 - - + -
55A VAL* 3.8 25.1 - - + +
78A ASP* 2.8 22.2 + - + +
79A ASP* 3.7 25.4 - - - +
81A LEU* 1.3 72.6 - - - +
83A ASP* 1.3 63.3 + - - +
85A MET* 3.2 11.7 + - - +
86A LEU* 3.0 26.6 + - + +
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Residues in contact with ASP 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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41A ARG* 2.9 34.6 + - - -
79A ASP* 2.9 23.8 + - - +
80A GLN* 3.2 6.7 + - - +
82A ILE* 1.3 75.7 - - - +
84A PHE* 1.3 63.2 + - + +
86A LEU* 3.3 12.1 + - - +
87A GLN* 3.0 31.1 + - + +
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Residues in contact with PHE 84 (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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59A LEU* 5.9 0.2 - - + -
69A LEU* 3.8 37.5 - - + -
71A LEU* 3.9 17.5 - - + -
76A PHE* 3.9 31.4 - + - -
80A GLN* 3.0 32.8 + - + -
81A LEU* 3.2 10.7 + - + +
83A ASP* 1.3 76.3 - - + +
85A MET* 1.3 58.4 + - - +
87A GLN* 3.1 3.5 + - + -
88A HIS* 2.8 44.6 + + - +
91A LEU* 3.7 16.4 - - + -
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Residues in contact with MET 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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38A PRO* 5.5 0.2 - - - +
44A LEU* 4.0 11.2 - - + -
48A ILE* 4.8 2.2 - - + -
55A VAL* 3.3 47.6 - - + +
58A LEU* 4.0 29.4 - - + -
59A LEU* 3.8 27.1 - - + -
81A LEU 3.0 17.9 + - - +
82A ILE* 3.2 11.4 + - - +
84A PHE* 1.3 76.8 - - - +
86A LEU* 1.3 61.9 + - - +
88A HIS 3.2 6.4 - - - -
89A PRO* 3.2 26.7 - - - +
91A LEU* 4.0 11.7 - - + +
92A ILE* 3.8 23.6 - - + +
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Residues in contact with LEU 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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38A PRO* 4.7 11.3 - - + +
39A PRO* 3.5 24.7 - - + +
40A SER 3.9 0.7 - - - -
41A ARG* 3.5 48.2 - - + +
44A LEU* 3.5 21.8 - - + -
82A ILE* 3.0 18.0 + - + +
83A ASP* 3.6 22.2 - - - +
84A PHE 3.3 0.4 - - - -
85A MET* 1.3 77.7 - - - +
87A GLN* 1.3 70.4 + - - +
88A HIS 3.6 0.2 + - - -
89A PRO* 4.0 10.8 - - - +
92A ILE* 5.6 0.4 - - + -
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Residues in contact with GLN 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 ASP* 3.0 22.6 + - + +
84A PHE* 3.1 2.7 + - + -
86A LEU* 1.3 86.5 - - - +
88A HIS* 1.3 86.5 + - + +
89A PRO* 3.6 4.7 - - - +
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Residues in contact with HIS 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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65A PRO* 3.8 30.0 - - + +
69A LEU* 4.1 26.1 - - + +
84A PHE* 2.8 24.7 + + - +
85A MET 3.2 5.7 - - - +
87A GLN* 1.3 97.5 + - + +
89A PRO* 1.3 59.5 - - - +
90A ILE* 3.0 6.7 - - + -
91A LEU* 2.9 28.2 + - + +
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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