Contacts of the helix formed by residues 105 - 111 (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 GLN 105 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211B ASP 4.2 8.5 + - - -
233B LYS* 4.7 5.5 - - - +
234B PRO* 3.3 46.0 - - + +
235B PRO* 4.2 2.1 - - - +
76G TYR* 4.4 0.2 - - - -
82G PRO* 6.1 0.2 - - - +
99G GLY 4.4 0.7 - - - +
100G PHE* 3.1 38.4 - - + +
101G LEU* 3.0 46.5 + - - +
102G GLY 3.3 5.5 + - - -
104G GLN* 1.3 99.9 - - + +
106G LEU* 1.3 58.8 + - - +
107G GLU 3.7 0.7 - - - -
108G ALA* 4.3 7.9 - - - -
109G ALA 3.7 0.2 + - - -
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Residues in contact with LEU 106 (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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50G LEU* 4.3 5.4 - - + -
76G TYR* 3.8 41.1 - - + +
102G GLY 3.6 0.4 + - - -
103G GLN* 3.2 39.4 + - - +
104G GLN 3.1 2.6 - - - -
105G GLN* 1.3 76.1 - - - +
107G GLU* 1.3 69.5 + - + +
108G ALA 3.1 1.8 - - - -
109G ALA* 3.1 3.4 + - + +
110G LEU* 3.0 49.9 + - + +
143G THR 4.3 10.8 - - - +
144G LEU* 4.3 19.3 - - + -
147G GLY* 4.6 6.7 - - - -
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Residues in contact with GLU 107 (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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103G GLN* 5.6 1.6 - - - +
104G GLN 4.2 6.8 + - - +
106G LEU* 1.3 80.1 - - + +
108G ALA* 1.3 62.8 + - - +
110G LEU* 3.1 2.2 + - + +
111G THR* 2.8 34.1 + - - +
147G GLY* 5.8 2.5 - - - -
150G LYS* 2.8 44.3 + - - +
151G CYS* 3.5 23.3 - - - -
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Residues in contact with ALA 108 (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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234B PRO* 5.8 4.3 - - + -
235B PRO* 5.4 4.9 - - + +
74G HIS* 3.7 11.4 - - - -
100G PHE* 3.2 29.2 - - + -
104G GLN 5.1 1.0 + - - +
105G GLN* 4.0 11.1 - - + +
106G LEU 3.1 0.2 - - - -
107G GLU* 1.3 81.0 - - - +
109G ALA* 1.3 60.0 + - - +
111G THR* 4.1 10.4 + - - +
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Residues in contact with ALA 109 (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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48G ALA* 3.9 5.0 - - + +
50G LEU* 5.5 0.4 - - + -
74G HIS* 2.9 31.1 + - + +
76G TYR* 4.2 17.3 - - + -
100G PHE* 3.3 34.8 - - + -
105G GLN 3.9 1.1 - - - +
106G LEU* 3.1 12.6 + - + +
108G ALA* 1.3 79.8 - - - +
110G LEU* 1.3 63.2 + - + +
113G MET* 3.4 9.7 - - - +
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Residues in contact with LEU 110 (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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48G ALA* 5.1 1.8 - - + -
50G LEU* 3.8 29.6 - - + -
106G LEU* 3.0 30.2 + - + +
107G GLU* 3.1 0.8 + - - +
109G ALA* 1.3 78.0 - - - +
111G THR* 1.3 66.4 + - - +
112G GLY 3.3 0.2 + - - -
113G MET* 3.0 23.7 + - - +
116G ILE* 3.9 23.6 - - + -
144G LEU 4.6 0.9 - - - +
147G GLY* 3.2 42.0 - - - +
148G ILE* 3.4 7.9 - - + +
151G CYS* 3.5 17.7 - - + -
152G CYS* 3.4 13.9 - - - +
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Residues in contact with THR 111 (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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74G HIS* 4.4 5.7 - - - -
107G GLU* 2.8 19.5 + - - +
108G ALA* 4.3 11.8 - - - +
109G ALA 3.7 0.6 - - - -
110G LEU* 1.3 77.5 - - - +
112G GLY* 1.3 64.7 + - - +
113G MET* 3.4 7.3 + - - +
151G CYS* 3.8 23.0 + - - +
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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