Contacts of the helix formed by residues 85 - 98 (chain B) in PDB entry 1S13
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 ARG 85 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58B TYR* 3.7 31.2 - - + -
62B GLU* 2.9 5.5 + - - -
82B GLU 5.7 0.4 + - - -
83B LEU 3.2 8.8 + - - +
84B HIS* 1.3 99.1 + - - +
86B LYS* 1.3 68.5 + - - +
87B ALA* 3.3 2.9 - - - -
88B ALA* 3.0 21.4 + - - +
89B LEU* 2.9 22.5 + - - +
166B PHE* 2.7 74.1 + - + +
168B THR 3.3 23.6 + - - -
169B PHE* 3.2 37.9 - - - +
170B PRO* 3.7 16.0 - - - +
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Residues in contact with LYS 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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55B TYR* 4.6 1.3 - - + +
58B TYR* 4.7 6.1 - - - +
59B VAL* 3.8 38.1 - - + +
62B GLU* 3.0 23.8 + - + +
63B GLU* 6.1 3.6 - - + +
84B HIS* 3.9 1.0 - - + +
85B ARG* 1.3 75.2 - - - +
87B ALA* 1.3 60.0 + - - +
89B LEU* 3.1 12.2 + - - +
90B GLU* 2.9 51.8 + - + +
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Residues in contact with ALA 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B HIS* 4.2 24.0 - - + +
85B ARG 3.3 0.6 - - - -
86B LYS* 1.3 80.7 - - - +
88B ALA* 1.3 62.3 + - - +
90B GLU* 3.2 17.6 + - - +
91B GLN* 3.0 29.0 + - - +
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Residues in contact with ALA 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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84B HIS 5.3 0.6 + - - +
85B ARG* 3.0 44.6 + - - +
87B ALA* 1.3 77.7 - - - +
89B LEU* 1.3 58.2 + - - +
91B GLN* 3.4 8.2 + - - +
92B ASP* 3.1 33.3 + - - +
165B ALA* 3.9 10.6 - - + +
166B PHE* 4.0 13.0 - - - +
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Residues in contact with LEU 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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51B MET* 3.8 32.8 - - + +
54B LEU* 3.5 37.5 - - + +
55B TYR* 3.7 16.6 - - + -
58B TYR* 3.7 26.5 - - + -
85B ARG 2.9 13.7 + - - +
86B LYS* 3.6 7.9 - - - +
88B ALA* 1.3 76.0 - - - +
90B GLU* 1.3 58.9 + - - +
92B ASP* 4.4 2.7 - - - +
93B LEU* 2.9 36.9 + - + +
166B PHE* 3.7 31.4 - - + -
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Residues in contact with GLU 90 (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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55B TYR* 4.0 11.7 + - + -
86B LYS* 2.9 42.6 + - - +
87B ALA* 3.2 18.0 + - - +
89B LEU* 1.3 72.4 - - - +
91B GLN* 1.3 68.0 + - + +
93B LEU* 3.4 1.6 + - - +
94B ALA* 3.1 24.8 + - - +
101B TRP* 3.7 35.9 - - + -
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Residues in contact with GLN 91 (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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87B ALA* 3.0 20.7 + - + +
88B ALA* 3.4 11.2 - - - +
90B GLU* 1.3 80.1 - - - +
92B ASP* 1.3 65.8 + - - +
94B ALA* 3.3 17.4 + - - +
95B PHE* 3.4 8.0 + - - +
162B GLU* 4.6 13.8 - - + +
163B GLY 5.5 1.1 + - - -
165B ALA* 4.6 7.6 - - + -
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Residues in contact with ASP 92 (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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51B MET* 3.4 17.6 - - + +
88B ALA 3.1 10.9 + - - +
89B LEU* 3.8 4.9 - - - +
91B GLN* 1.3 75.5 - - - +
93B LEU* 1.3 61.2 + - + +
95B PHE* 3.0 4.7 + - - +
96B TRP* 2.9 33.7 + - + -
162B GLU* 5.5 0.3 - - - +
163B GLY* 3.2 32.0 + - - +
164B LEU 3.6 0.2 - - - -
165B ALA* 3.0 25.2 + - - +
166B PHE* 2.8 36.2 + - - +
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Residues in contact with LEU 93 (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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51B MET* 3.5 35.9 - - + +
52B ALA* 4.5 2.7 - - - -
55B TYR* 3.4 38.8 - - + -
89B LEU* 2.9 30.6 + - + +
90B GLU 4.0 0.9 - - - +
92B ASP* 1.3 77.0 - - + +
94B ALA* 1.3 56.9 + - - +
96B TRP* 4.3 5.2 - - + +
97B TYR* 2.7 36.0 + - + +
101B TRP* 3.5 42.2 - - + +
105B ILE* 4.1 16.4 - - + -
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Residues in contact with ALA 94 (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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90B GLU 3.1 12.9 + - - +
91B GLN* 3.3 13.9 - - - +
93B LEU* 1.3 75.8 - - - +
95B PHE* 1.3 57.3 + - - +
98B GLY* 3.0 29.6 + - - +
99B PRO* 4.0 4.0 - - + +
101B TRP* 3.6 23.9 - - + +
162B GLU* 5.5 2.7 - - - +
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Residues in contact with PHE 95 (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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44B ARG* 4.8 8.1 + - - -
91B GLN 3.4 7.4 + - - +
92B ASP 3.0 8.1 + - - +
94B ALA* 1.3 81.3 - - - +
96B TRP* 1.3 97.3 + + - +
98B GLY* 4.1 2.9 + - - -
157B LEU* 5.1 4.5 - - + -
158B PRO* 4.4 16.6 - - + -
160B SER* 3.4 33.7 - - - -
162B GLU* 3.3 40.8 + - + +
163B GLY* 3.7 17.7 - - - -
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Residues in contact with TRP 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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44B ARG* 3.4 55.6 + - + +
47B PHE* 3.5 36.9 - + - -
48B LYS* 3.7 35.3 + - + -
51B MET* 4.3 14.8 - - + +
92B ASP* 2.9 35.8 + - + +
93B LEU* 4.4 1.8 - - - -
95B PHE* 1.3 100.1 - + - +
97B TYR* 1.3 74.9 + - + +
98B GLY 3.7 0.2 - - - -
155B LEU* 4.0 16.8 - - + -
157B LEU* 4.8 12.8 - - + -
163B GLY* 2.9 27.1 + - - -
164B LEU* 4.5 5.6 - - + -
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Residues in contact with TYR 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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48B LYS* 3.4 62.8 + - + +
49B LEU* 4.1 2.6 + - - +
51B MET* 5.8 0.4 - - + -
52B ALA* 4.0 4.1 - - + +
93B LEU* 2.7 21.4 + - + -
96B TRP* 1.3 84.0 - - + +
98B GLY* 1.3 61.9 + - - +
100B ARG* 4.3 1.6 + - - +
101B TRP* 3.5 26.9 + - + -
104B VAL* 3.9 24.8 - - + +
105B ILE* 3.6 20.9 - - + -
106B PRO* 3.3 36.5 - - + +
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Residues in contact with GLY 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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94B ALA 3.0 20.0 + - - +
95B PHE 4.1 3.2 + - - -
96B TRP 3.7 1.4 - - - -
97B TYR* 1.3 76.1 - - - +
99B PRO* 1.3 67.9 - - - +
100B ARG 3.1 2.9 - - - -
101B TRP* 2.8 33.1 + - - +
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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