Contacts of the helix formed by residues 120 - 133 (chain I) in PDB entry 1S72
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 ASP 120 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118I SER* 3.4 7.8 + - - +
119I TYR* 1.3 92.2 - - - +
121I LEU* 1.3 63.5 + - - +
122I THR* 2.9 19.2 + - - +
123I ASN* 3.3 23.6 + - - +
124I ALA* 3.1 18.9 + - - +
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Residues in contact with LEU 121 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109I ALA* 4.6 3.7 - - + +
110I GLU* 4.8 8.3 - - + -
113I HIS* 3.0 43.5 - - + +
120I ASP* 1.3 73.5 - - - +
122I THR* 1.3 57.5 + - - +
124I ALA* 3.6 8.0 - - - +
125I ALA* 3.0 26.9 + - - +
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Residues in contact with THR 122 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120I ASP* 2.9 14.6 - - - +
121I LEU* 1.3 77.5 - - - +
123I ASN* 1.3 68.3 + - - +
125I ALA* 3.0 20.5 - - - +
126I LYS* 3.0 28.0 + - + +
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Residues in contact with ASN 123 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11850 U 3.6 18.7 + - - +
11860 C 3.3 25.8 + - - -
118I SER* 3.1 22.0 - - - -
119I TYR* 4.3 0.6 - - - +
120I ASP* 3.3 42.4 + - - +
122I THR* 1.3 73.3 - - - +
124I ALA* 1.3 53.7 + - - +
125I ALA 3.0 2.0 - - - -
126I LYS* 2.9 25.4 + - - +
127I GLU* 2.8 37.8 + - - +
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Residues in contact with ALA 124 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109I ALA* 4.0 11.7 - - + -
113I HIS* 4.1 9.9 - - - +
116I LEU* 3.8 17.6 - - + +
118I SER* 2.9 22.4 + - - +
120I ASP 3.1 9.8 + - - +
121I LEU* 3.6 11.0 - - - +
123I ASN* 1.3 74.9 - - - +
125I ALA* 1.3 62.0 + - - +
127I GLU* 3.2 10.3 - - - +
128I VAL* 3.0 28.9 + - - +
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Residues in contact with ALA 125 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105I VAL* 4.5 13.5 - - + +
106I LYS* 5.8 6.1 - - + -
109I ALA* 4.1 11.0 - - + +
121I LEU 3.0 14.4 + - - +
122I THR* 3.0 14.1 - - - +
124I ALA* 1.3 75.1 - - - +
126I LYS* 1.3 57.2 + - + +
127I GLU 3.0 0.5 + - - -
128I VAL* 3.1 2.3 + - - +
129I VAL* 2.7 43.4 + - + +
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Residues in contact with LYS 126 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11840 C 3.5 29.4 - - - +
11850 U 2.8 23.8 + - - +
122I THR* 3.0 28.4 + - + +
123I ASN* 2.9 23.1 + - - +
125I ALA* 1.3 78.5 - - + +
127I GLU* 1.3 62.2 + - - +
129I VAL* 3.6 10.1 + - - +
130I GLY* 3.1 14.4 + - - -
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Residues in contact with GLU 127 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11620 G 3.3 18.9 + - - +
11630 G 4.1 13.3 + - - +
11840 C 4.0 14.5 - - - +
11850 U 3.4 27.1 - - - +
116I LEU* 3.2 33.1 - - + +
117I LEU 4.2 2.3 + - - -
118I SER* 2.7 41.7 + - - -
123I ASN 2.8 15.0 + - - +
124I ALA* 3.2 7.6 - - - +
126I LYS* 1.3 73.5 - - - +
128I VAL* 1.3 58.4 + - - +
130I GLY* 2.7 29.8 + - - -
131I THR* 3.6 4.7 + - - -
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Residues in contact with VAL 128 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11630 G 5.5 3.6 + - - +
75I THR* 4.4 11.2 - - + -
105I VAL* 4.0 14.4 - - + -
108I ILE* 3.1 42.8 - - + -
109I ALA* 3.7 16.8 - - + -
112I LYS* 5.0 5.6 - - + +
116I LEU* 4.5 11.0 - - + -
124I ALA 3.0 14.7 + - - +
125I ALA 3.8 3.6 - - - +
127I GLU* 1.3 70.8 - - + +
129I VAL* 1.3 54.5 + - - +
130I GLY 2.7 15.6 + - - -
131I THR* 2.7 20.5 + - - +
132I CYS* 3.2 24.3 + - - -
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Residues in contact with VAL 129 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11840 C 6.5 0.4 - - - -
105I VAL* 3.4 22.0 - - + -
125I ALA* 2.7 33.2 + - + +
126I LYS* 3.7 9.6 - - - +
128I VAL* 1.3 71.8 - - - +
130I GLY* 1.3 57.0 + - - +
131I THR 3.4 0.8 + - - -
132I CYS* 4.1 6.9 + - - +
133I THR* 3.5 23.6 + - - +
139I ILE* 3.2 32.9 - - + +
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Residues in contact with GLY 130 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11630 G 4.8 1.1 - - - -
11830 C 2.9 44.1 + - - +
11840 C 4.7 7.9 - - - -
11920 A 4.1 1.7 + - - -
126I LYS 3.1 8.2 + - - -
127I GLU 2.7 15.5 + - - -
128I VAL 2.7 0.2 + - - -
129I VAL* 1.3 79.2 - - - +
131I THR* 1.3 58.1 + - - -
132I CYS 3.6 0.7 - - - -
133I THR* 4.9 2.7 - - - -
134I SER* 4.0 6.9 + - - -
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Residues in contact with THR 131 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11630 G 4.0 8.1 + - - -
11640 U 3.1 30.4 + - + +
11660 A 4.3 11.4 - - - +
11920 A 5.0 0.9 - - - +
75I THR* 3.7 33.1 - - + +
76I ALA* 4.7 5.2 - - + +
79I ILE* 3.7 6.5 - - + +
127I GLU 4.0 4.5 + - - -
128I VAL* 2.7 14.0 + - - -
130I GLY* 1.3 73.2 - - - -
132I CYS* 1.3 61.2 + - - +
134I SER* 2.9 20.1 + - - +
135I LEU* 3.4 18.9 - - + +
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Residues in contact with CYS 132 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79I ILE* 3.4 28.3 - - - -
100I LEU* 4.7 8.3 - - - -
105I VAL* 5.1 6.1 - - - -
128I VAL* 3.2 27.3 + - - +
129I VAL* 4.3 8.3 - - - +
130I GLY 3.6 0.2 - - - -
131I THR* 1.3 77.4 - - - +
133I THR* 1.3 57.8 + - - +
134I SER 2.9 5.2 - - - -
135I LEU 2.8 19.2 + - - -
137I VAL* 3.0 51.5 + - + +
139I ILE* 5.4 3.6 - - + -
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Residues in contact with THR 133 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11830 C 5.5 7.0 - - - -
92I PRO* 3.9 8.7 - - - +
93I GLN* 4.1 38.1 + - + +
96I PHE* 5.0 11.0 - - + -
129I VAL* 3.5 17.8 + - - +
130I GLY 4.9 0.6 - - - -
131I THR 4.6 0.4 - - - +
132I CYS* 1.3 75.3 - - - +
134I SER* 1.3 55.6 + - - +
135I LEU 3.3 2.2 - - - -
136I GLY* 4.2 2.4 - - - -
137I VAL 3.9 14.3 + - - +
138I THR* 5.5 2.5 - - - -
139I ILE* 4.9 7.8 - - - +
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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