Contacts of the helix formed by residues 95 - 107 (chain B) in PDB entry 1SL1
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 95 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41B ILE* 4.5 3.4 - - - -
93B ALA 3.8 0.6 + - - -
94B LEU* 1.3 75.2 - - - +
96B LYS* 1.3 64.4 + - - +
97B GLY* 3.0 5.9 + - - -
98B GLN* 2.8 47.3 + - - +
99B LEU* 3.0 21.8 + - - +
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Residues in contact with LYS 96 (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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41B ILE* 3.7 29.4 - - + +
44B GLU* 3.4 34.3 - - - +
45B ILE* 3.3 25.9 - - + +
48B GLU* 2.6 41.5 + - - -
95B SER* 1.3 73.0 - - - +
97B GLY* 1.3 56.8 + - - +
99B LEU* 3.6 1.6 + - - +
100B LYS* 2.9 32.2 + - + +
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Residues in contact with GLY 97 (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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95B SER* 3.0 6.7 + - - -
96B LYS* 1.3 77.3 - - - +
98B GLN* 1.3 58.7 + - - +
100B LYS* 3.4 6.7 + - - +
101B GLU* 3.0 29.3 + - - +
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Residues in contact with GLN 98 (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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297A ILE* 3.5 17.0 - - + +
321A VAL* 2.8 35.4 - - + +
322A ALA 4.2 7.2 + - - +
323A GLY 5.9 0.6 - - - -
324A ALA* 4.6 5.5 - - - +
93B ALA 4.8 1.4 + - - -
94B LEU* 3.8 19.4 - - + +
95B SER* 2.8 41.9 + - - +
97B GLY* 1.3 75.5 - - - +
99B LEU* 1.3 56.8 + - - +
101B GLU* 3.4 4.4 + - - -
102B PHE* 2.9 27.3 + - - +
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Residues in contact with LEU 99 (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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24B LEU* 4.3 7.9 - - + -
38B ILE* 4.2 17.7 - - + -
41B ILE* 4.1 22.4 - - + -
42B LEU* 4.4 15.3 - - + -
45B ILE* 4.4 13.7 - - + -
78B LEU* 4.2 18.8 - - + -
94B LEU* 4.3 11.4 - - + +
95B SER 3.0 14.8 + - - +
96B LYS* 3.9 4.0 - - - +
98B GLN* 1.3 74.8 - - - +
100B LYS* 1.3 58.2 + - - +
101B GLU 3.0 1.3 - - - -
102B PHE* 2.8 21.6 + - + +
103B LEU* 2.7 58.2 + - + +
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Residues in contact with LYS 100 (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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45B ILE* 5.2 3.7 - - + +
48B GLU* 6.1 0.9 - - - +
49B TYR* 3.4 23.2 + - + +
96B LYS* 2.9 22.6 + - + +
97B GLY* 3.6 6.7 - - - +
99B LEU* 1.3 76.3 - - - +
101B GLU* 1.3 55.3 + - - +
103B LEU* 4.7 2.0 - - - +
104B ASP* 2.7 42.9 + - - +
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Residues in contact with GLU 101 (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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297A ILE* 3.9 17.1 - - + +
97B GLY 3.0 17.3 + - - +
98B GLN* 3.5 7.4 - - - +
100B LYS* 1.3 76.0 - - - +
102B PHE* 1.3 65.8 + - - +
104B ASP* 4.3 4.6 - - - +
105B ALA* 3.0 28.1 + - - +
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Residues in contact with PHE 102 (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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297A ILE* 3.7 17.0 - - + +
24B LEU* 4.6 14.6 - - + -
78B LEU* 4.9 4.5 - - + -
80B LEU* 4.7 5.4 - - + -
88B ALA* 3.5 28.5 - - + -
89B THR 3.9 11.7 - - - -
90B LYS* 3.6 47.3 - - + -
94B LEU* 4.9 4.5 - - + -
98B GLN 2.9 15.4 + - - +
99B LEU* 2.8 27.3 + - + +
101B GLU* 1.3 76.9 - - - +
103B LEU* 1.3 71.2 + - + +
105B ALA* 3.7 0.5 - - - +
106B ASN* 2.5 57.6 + - - -
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Residues in contact with LEU 103 (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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24B LEU* 4.3 15.0 - - + -
45B ILE* 3.7 26.5 - - + -
49B TYR* 4.0 23.1 - - + -
53B LEU* 3.6 32.3 - - + -
80B LEU* 4.6 5.8 - - + -
99B LEU* 2.7 35.2 + - + +
100B LYS 4.0 1.6 - - - +
102B PHE* 1.3 85.2 - - + +
104B ASP* 1.3 68.2 + - - +
105B ALA 3.0 1.3 - - - -
106B ASN* 2.8 3.1 + - - -
107B LEU* 2.7 41.7 + - + +
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Residues in contact with ASP 104 (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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49B TYR* 3.0 26.9 + - - -
52B LYS* 5.3 1.2 + - - -
100B LYS* 2.7 28.5 + - - +
101B GLU* 4.3 4.2 - - - +
103B LEU* 1.3 78.6 - - - +
105B ALA* 1.3 62.2 + - - +
106B ASN 3.4 0.2 + - - -
107B LEU* 3.5 18.1 + - - +
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Residues in contact with ALA 105 (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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297A ILE* 4.6 10.3 - - + -
101B GLU 3.0 20.6 + - - +
102B PHE 3.7 4.3 - - - +
103B LEU 3.0 0.4 - - - -
104B ASP* 1.3 79.1 - - - +
106B ASN* 1.3 64.0 + - - +
107B LEU 5.2 0.3 - - - -
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Residues in contact with ASN 106 (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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297A ILE* 5.7 0.4 - - - +
80B LEU* 3.6 22.3 - - + +
87B ALA* 5.1 2.2 - - + +
88B ALA* 3.6 19.8 - - + +
102B PHE* 2.5 54.3 + - - +
103B LEU 2.8 5.4 + - - +
105B ALA* 1.3 78.1 - - - +
107B LEU* 1.3 69.3 + - - +
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Residues in contact with LEU 107 (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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22B ALA* 4.9 10.1 - - + -
49B TYR* 3.8 34.8 - - + -
52B LYS* 4.7 16.4 - - + +
53B LEU* 4.6 14.4 - - + -
80B LEU* 3.9 22.4 - - + -
103B LEU* 2.7 43.1 + - + +
104B ASP* 3.5 13.8 + - - +
105B ALA 5.2 0.7 - - - -
106B ASN* 1.3 79.2 - - - +
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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