Contacts of the helix formed by residues 99 - 112 (chain A) in PDB entry 1SKM
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 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A THR* 6.1 0.7 - - - +
93A PHE* 3.2 27.1 - - + +
95A ASP 3.8 6.7 - - - +
96A SER* 3.7 13.4 + - - -
97A ARG 3.5 0.8 - - - -
98A GLY* 1.3 77.9 - - - +
100A LEU* 1.3 68.1 + - - +
101A PHE 3.1 3.4 - - - -
102A PHE* 3.0 38.1 + - + +
103A ASP* 3.7 8.1 + - - +
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Residues in contact with LEU 100 (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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18A PHE* 3.6 36.7 - - + -
61A ILE* 3.9 5.2 - - + -
62A THR* 4.1 6.5 - - + -
79A PHE* 4.4 4.3 - - + -
80A PRO* 4.1 19.5 - - + -
96A SER 4.0 6.3 - - - +
97A ARG* 3.4 35.4 - - - +
98A GLY 3.6 1.4 - - - -
99A THR* 1.3 79.0 - - - +
101A PHE* 1.3 63.9 + - - +
103A ASP* 2.9 29.9 + - - +
104A ILE* 3.1 15.5 + - - +
328A SAH 3.8 24.9 - - - +
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Residues in contact with PHE 101 (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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79A PHE* 4.1 22.7 - + + -
93A PHE* 4.8 15.3 - + + -
98A GLY 4.9 1.9 + - - +
99A THR 3.0 1.8 + - - -
100A LEU* 1.3 78.3 - - - +
102A PHE* 1.3 80.5 + + - +
104A ILE* 2.9 19.0 + - + +
105A ALA* 2.9 26.0 + - + -
118A MET* 4.0 28.0 - - + -
124A PHE* 5.6 0.2 - - + -
135A VAL* 4.7 0.9 - - + -
136A VAL* 3.7 46.7 - - + -
139A THR* 3.7 40.8 - - + -
140A MET* 4.1 10.8 - - - -
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Residues in contact with PHE 102 (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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93A PHE* 3.6 49.8 - + + -
99A THR* 3.0 31.7 + - + +
101A PHE* 1.3 93.5 - + - +
103A ASP* 1.3 61.0 + - - +
105A ALA* 3.3 8.5 + - + +
106A ARG* 2.9 27.5 + - - +
109A ARG* 5.5 0.3 + - - -
135A VAL* 4.3 14.1 - - + -
139A THR* 4.9 5.2 - - + -
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Residues in contact with ASP 103 (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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18A PHE* 5.2 1.6 - - + -
61A ILE* 4.5 16.4 - - + -
62A THR* 3.5 27.4 - - - +
99A THR* 3.7 6.8 + - - +
100A LEU* 2.9 37.7 + - - +
102A PHE* 1.3 77.3 - - - +
104A ILE* 1.3 61.8 + - - +
106A ARG* 2.5 37.4 + - - +
107A ILE* 3.0 29.0 + - - +
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Residues in contact with ILE 104 (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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17A LEU* 4.7 4.7 - - + -
18A PHE* 3.9 18.6 - - + -
75A LEU* 4.2 15.7 - - + -
77A ALA* 3.6 27.6 - - + -
79A PHE* 3.7 26.0 - - + -
100A LEU 3.1 9.3 + - - +
101A PHE* 2.9 18.3 + - + +
103A ASP* 1.3 74.8 - - - +
105A ALA* 1.3 67.4 + - - +
107A ILE* 3.1 11.0 + - - +
108A VAL* 2.9 39.7 + - + +
116A VAL* 4.6 2.2 - - + -
118A MET* 4.1 20.4 - - - -
140A MET* 5.8 0.9 - - - -
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Residues in contact with ALA 105 (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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101A PHE* 2.9 17.2 + - + +
102A PHE* 3.5 15.0 - - + +
103A ASP 3.3 0.2 - - - -
104A ILE* 1.3 77.0 - - - +
106A ARG* 1.3 58.5 + - - +
108A VAL* 3.2 4.7 + - - +
109A ARG* 2.9 46.8 + - - +
139A THR* 3.9 28.0 - - + -
140A MET* 5.7 0.9 - - - -
143A LEU* 4.2 9.2 - - + +
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Residues in contact with ARG 106 (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 ILE* 3.2 19.8 + - - +
62A THR 4.4 9.1 + - - -
64A VAL* 3.0 26.2 + - - +
66A GLU* 2.9 39.2 + - - +
102A PHE 2.9 13.7 + - - +
103A ASP* 2.5 47.8 + - - +
105A ALA* 1.3 78.3 - - - +
107A ILE* 1.3 74.3 + - - +
109A ARG* 3.6 20.2 + - - +
110A GLU* 3.5 17.7 + - - +
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Residues in contact with ILE 107 (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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15A ILE* 4.4 5.8 - - + -
17A LEU* 3.7 25.4 - - + -
61A ILE* 3.7 22.2 - - + -
66A GLU* 4.1 12.1 - - + -
69A ILE* 3.6 35.0 - - + -
75A LEU* 3.9 18.2 - - + -
103A ASP 3.0 16.8 + - - +
104A ILE* 3.1 5.8 + - - +
106A ARG* 1.3 78.9 - - - +
108A VAL* 1.3 68.1 + - - +
110A GLU* 3.1 3.1 + - - +
111A LYS* 2.9 35.4 + - + +
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Residues in contact with VAL 108 (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* 3.9 15.3 - - + -
104A ILE* 2.9 31.0 + - + +
105A ALA* 3.6 5.8 - - - +
107A ILE* 1.3 75.9 - - - +
109A ARG* 1.3 59.2 + - - +
112A LYS* 2.7 30.5 + - - +
113A PRO* 4.2 9.6 - - + -
116A VAL* 3.9 22.9 - - + -
140A MET* 4.6 4.5 - - + -
143A LEU* 4.1 15.0 - - + -
145A TYR* 3.6 38.6 - - + +
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Residues in contact with ARG 109 (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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102A PHE 5.5 0.4 + - - -
105A ALA* 2.9 34.2 + - - +
106A ARG* 3.7 27.2 - - - +
107A ILE 3.3 0.2 - - - -
108A VAL* 1.3 76.6 - - - +
110A GLU* 1.3 61.1 + - + +
112A LYS* 4.6 4.5 + - - +
139A THR* 4.8 5.5 - - - +
143A LEU* 3.6 31.9 - - + +
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Residues in contact with GLU 110 (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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66A GLU* 3.5 36.6 - - + +
67A LYS* 3.3 41.5 + - + +
106A ARG 3.5 3.5 + - - +
107A ILE 3.1 7.5 + - - +
108A VAL 3.0 0.6 - - - -
109A ARG* 1.3 82.7 - - + +
111A LYS* 1.3 71.1 + - + +
112A LYS* 3.7 2.3 + - - +
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Residues in contact with LYS 111 (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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66A GLU 3.9 15.3 - - - +
67A LYS* 4.6 6.1 + - - +
69A ILE* 2.9 29.4 + - + +
70A PRO 3.7 13.0 - - - -
71A ASP* 2.7 35.1 + - - +
72A HIS* 3.4 31.5 + - + +
107A ILE* 2.9 26.0 + - + +
110A GLU* 1.3 82.6 - - + +
112A LYS* 1.3 76.9 + - - +
113A PRO* 3.2 2.6 - - + +
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Residues in contact with LYS 112 (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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72A HIS 4.8 0.7 - - - +
108A VAL* 2.7 20.3 + - - +
109A ARG 5.0 3.6 - - - +
110A GLU 4.7 4.0 - - - +
111A LYS* 1.3 78.0 - - - +
113A PRO* 1.3 70.1 - - - +
145A TYR* 3.3 12.6 - - + +
172A ARG* 3.3 22.9 + - - +
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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