Contacts of the helix formed by residues 108 - 115 (chain A) in PDB entry 1SK1
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 PRO 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A THR* 4.6 0.4 - - + -
106A CYS 3.1 10.7 - - - -
107A ARG* 1.3 83.9 + - + +
109A SER* 1.3 67.6 + - - +
110A GLU* 3.4 28.9 - - + +
111A VAL* 3.0 25.4 + - + +
126A LYS* 4.6 2.2 - - - +
203A SO4 3.3 15.5 - - - +
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Residues in contact with SER 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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14A THR* 3.6 9.6 - - - +
17A ASN* 3.5 2.5 - - - +
18A THR* 3.1 23.5 + - - -
21A MET* 3.4 18.8 - - - +
106A CYS* 3.4 12.3 + - - +
108A PRO* 1.3 72.4 - - - +
110A GLU* 1.3 58.8 + - - +
111A VAL 3.0 5.4 + - - -
112A VAL* 3.0 26.7 + - - +
126A LYS* 3.5 11.1 - - - -
203A SO4 2.7 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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21A MET* 3.8 11.9 - - + -
108A PRO* 3.4 27.9 - - + +
109A SER* 1.3 74.3 + - - +
111A VAL* 1.4 66.0 + - + +
112A VAL 3.0 2.0 - - - -
113A LEU* 2.9 23.5 + - + +
114A ASP* 4.3 1.7 + - - +
126A LYS* 2.7 32.3 + - - -
130A GLU* 4.6 4.5 - - - +
132A VAL* 3.9 26.0 - - + -
139A ARG* 3.8 35.0 + - - +
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Residues in contact with VAL 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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104A ARG* 3.8 44.0 - - + +
105A LEU 3.9 9.9 - - - +
106A CYS* 4.0 5.2 - - - -
107A ARG 4.0 6.1 - - - +
108A PRO* 3.0 37.2 + - + +
109A SER 3.0 0.2 + - - -
110A GLU* 1.4 78.3 - - + +
112A VAL* 1.4 61.7 + - - +
114A ASP* 2.9 27.3 + - - +
115A ILE 4.2 0.3 + - - -
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Residues in contact with VAL 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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18A THR* 3.9 18.8 - - + +
21A MET* 3.8 31.9 - - + -
22A ILE* 4.0 16.8 - - + -
97A VAL* 4.1 13.0 - - + -
106A CYS* 3.6 23.8 - - - -
109A SER 3.0 17.4 + - - +
110A GLU 3.0 0.8 - - - -
111A VAL* 1.4 78.6 - - - +
113A LEU* 1.3 64.7 + - + +
115A ILE* 3.1 18.5 + - + +
116A LEU* 3.2 24.0 + - + +
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Residues in contact with LEU 113 (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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21A MET* 4.1 14.4 - - - -
110A GLU* 2.9 18.2 + - + +
112A VAL* 1.3 78.0 - - - +
114A ASP* 1.3 65.1 + - - +
115A ILE 3.4 0.3 + - - -
116A LEU* 3.7 15.6 + - + +
120A GLN* 3.7 37.5 - - + +
132A VAL* 4.0 11.4 - - + -
133A VAL* 4.0 13.2 - - + -
139A ARG* 3.7 35.4 - - + +
401A CS 3.2 18.0 - - - -
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Residues in contact with ASP 114 (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 LEU* 4.4 5.0 - - - +
104A ARG* 2.5 44.4 + - - +
110A GLU 5.0 1.2 - - - +
111A VAL* 2.9 20.2 + - - +
113A LEU* 1.3 82.1 - - - +
115A ILE* 1.3 61.3 + - + +
139A ARG* 5.9 0.9 + - - -
401A CS 3.2 17.5 - - - -
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Residues in contact with ILE 115 (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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97A VAL* 3.5 33.7 - - + +
99A THR* 2.6 44.3 + - + +
101A LEU* 3.6 16.3 - - + +
102A GLY* 3.6 29.4 - - - +
104A ARG* 3.8 43.3 - - + +
112A VAL* 3.1 19.0 + - + +
114A ASP* 1.3 81.5 - - + +
116A LEU* 1.3 64.0 + - - +
117A GLN* 3.4 2.9 + - - +
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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