Contacts of the helix formed by residues 79 - 89 (chain B) in PDB entry 1SPS
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 SER 79 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69B PHE* 4.1 7.9 - - - -
77B PHE* 3.6 8.0 - - - +
78B SER* 1.3 87.1 + - - +
80B LEU* 1.3 65.4 + - - +
81B GLN* 3.2 30.4 - - - +
82B GLN* 3.2 14.0 + - - +
83B LEU* 3.2 16.8 + - - +
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Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B TRP* 4.3 11.9 - - + -
6B TYR* 4.5 10.5 - - + -
31B VAL* 4.4 11.2 - - + -
41B TYR* 4.1 38.4 - - + -
61B ILE* 3.9 39.0 - - + -
69B PHE* 3.9 28.7 - - + -
79B SER* 1.3 72.6 - - - +
81B GLN* 1.3 65.1 + - - +
83B LEU* 3.3 10.4 + - + +
84B VAL* 3.1 29.5 + - - +
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Residues in contact with GLN 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B ALA* 3.6 26.4 - - + +
5B TRP* 4.1 25.0 - - + -
79B SER* 3.2 24.1 - - - +
80B LEU* 1.3 85.0 + - - +
82B GLN* 1.3 58.1 + - - +
84B VAL* 3.9 2.3 - - - +
85B ALA* 3.2 25.8 + - - +
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Residues in contact with GLN 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B PHE* 3.8 17.4 - - + -
78B SER* 4.1 12.2 + - - +
79B SER* 3.2 26.1 + - - +
81B GLN* 1.3 77.3 - - - +
83B LEU* 1.3 63.5 + - - +
85B ALA* 3.6 10.9 - - - +
86B TYR* 3.1 24.1 + - - +
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Residues in contact with LEU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B LEU* 4.6 9.6 - - + -
61B ILE* 3.8 46.9 - - + -
69B PHE* 4.3 9.4 - - + +
71B ILE* 4.3 14.4 - - + +
77B PHE* 3.6 41.4 - - + -
79B SER 3.2 9.9 + - - +
80B LEU* 3.3 11.2 + - + +
82B GLN* 1.3 76.1 - - - +
84B VAL* 1.3 70.0 + - + +
86B TYR* 3.2 2.3 + - - +
87B TYR* 3.0 46.7 + - + -
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Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B TRP* 4.1 24.7 - - + +
29B PHE* 3.5 32.8 - - + -
31B VAL* 3.8 29.2 - - + -
43B LEU* 4.8 0.2 - - + -
80B LEU* 3.1 16.1 + - + +
81B GLN 4.2 4.3 - - - +
82B GLN 3.4 0.2 - - - -
83B LEU* 1.3 84.2 - - + +
85B ALA* 1.3 55.7 + - - +
88B SER* 2.6 36.1 + - - +
98B LEU* 3.9 11.2 - - + +
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Residues in contact with ALA 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B GLN 3.2 18.4 + - - +
82B GLN* 3.6 15.9 - - - +
84B VAL* 1.3 78.7 - - - +
86B TYR* 1.3 61.8 + - - +
88B SER* 3.3 9.2 + - - -
89B LYS* 3.1 23.1 + - - +
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Residues in contact with TYR 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B THR* 3.8 22.9 + - + +
77B PHE* 3.6 25.4 - + + -
82B GLN* 3.1 15.9 + - + +
83B LEU 3.6 1.1 - - - +
85B ALA* 1.3 78.8 - - - +
87B TYR* 1.3 84.7 + + - +
89B LYS* 2.9 25.2 + - - +
90B HIS* 3.1 42.3 + + - +
92B ASP* 2.7 31.8 + - - -
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Residues in contact with TYR 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B LEU* 5.1 1.8 - - + -
71B ILE* 4.1 19.0 + - + +
72B THR* 3.9 23.7 - - - +
75B THR* 4.1 10.4 + - - -
77B PHE* 3.9 24.0 - + - -
83B LEU* 3.0 37.9 + - + +
84B VAL 4.1 0.2 - - - -
86B TYR* 1.3 93.7 - + - +
88B SER* 1.4 57.1 + - - +
90B HIS 3.4 14.0 - - - +
91B ALA* 3.3 26.6 - - - -
92B ASP* 4.3 8.6 + - + -
94B LEU* 3.9 17.5 - - + -
97B ARG* 3.4 8.1 - - - -
98B LEU* 3.2 36.9 + - + -
3E ILE* 4.1 8.3 - - + +
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Residues in contact with SER 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B PHE* 5.2 2.1 - - - -
84B VAL* 2.6 27.4 + - - +
85B ALA* 3.4 8.2 + - - -
86B TYR 3.1 1.2 - - - -
87B TYR* 1.4 74.4 - - - +
89B LYS* 1.3 62.1 + - - +
90B HIS 3.3 0.4 - - - -
97B ARG* 2.9 30.8 + - - -
98B LEU* 3.5 25.9 + - - +
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Residues in contact with LYS 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ALA 3.1 10.7 + - - +
86B TYR* 2.9 11.9 + - - +
88B SER* 1.3 81.3 - - - +
90B HIS* 1.3 79.8 + - + +
97B ARG* 4.6 6.0 + - - -
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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