Contacts of the strand formed by residues 121 - 131 (chain I) in PDB entry 1S9C
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 GLY 121 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117I ASP* 3.7 3.3 - - - +
118I LYS 2.8 33.1 + - - -
119I GLY 3.7 2.4 - - - +
120I SER* 1.3 84.2 + - - +
122I VAL* 1.3 56.9 - - - -
145I PHE* 3.7 17.3 - - - -
146I LEU 3.1 17.7 - - - -
148I GLY 3.7 7.6 - - - -
150I GLY* 4.1 3.3 - - - -
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Residues in contact with VAL 122 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I PHE* 4.3 11.9 - - + -
115I VAL* 3.4 25.1 - - + -
116I LEU 2.9 21.3 - - - +
117I ASP* 4.1 0.4 - - - +
118I LYS 4.3 0.2 - - - +
121I GLY* 1.3 75.2 - - - +
123I VAL* 1.3 66.8 + - - +
124I ILE* 4.0 7.9 + - + +
144I LEU 3.9 0.2 - - - +
145I PHE* 3.6 2.7 - - - -
146I LEU* 3.0 36.2 + - + +
149I SER* 3.2 34.3 - - - +
150I GLY* 3.3 14.1 - - - +
152I PHE* 4.2 7.0 - - + -
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Residues in contact with VAL 123 (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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115I VAL* 3.1 4.3 - - - -
116I LEU* 2.8 47.2 + - + +
118I LYS* 3.2 41.3 - - + -
122I VAL* 1.3 75.5 - - - +
124I ILE* 1.3 65.9 + - - +
125I ILE* 4.1 14.5 + - + -
143I SER* 3.7 20.6 - - - +
144I LEU 3.3 12.6 - - - +
145I PHE* 4.0 13.9 - - + -
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Residues in contact with ILE 124 (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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7I PHE* 5.5 5.2 - - + -
74I LEU* 3.9 38.6 - - + -
77I ILE* 4.7 8.3 - - + -
80I LEU* 5.7 7.9 - - + -
112I VAL* 5.0 6.7 - - + -
114I ASP 3.9 4.0 - - - +
115I VAL* 4.3 14.1 - - + +
122I VAL* 4.3 12.8 - - + -
123I VAL* 1.3 77.3 - - - +
125I ILE* 1.3 61.4 + - - +
126I MET* 4.9 8.5 - - + +
142I PHE 3.7 1.6 - - - +
143I SER* 3.9 0.5 - - - -
144I LEU* 2.9 41.6 + - + -
146I LEU* 3.8 28.7 - - + -
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Residues in contact with ILE 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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112I VAL* 3.4 5.1 - - - -
113I ALA* 2.9 34.7 + - + +
114I ASP* 3.4 22.5 + - + +
116I LEU* 3.9 22.0 - - + -
123I VAL* 4.1 14.6 + - + -
124I ILE* 1.3 74.8 - - - +
126I MET* 1.3 60.2 + - - +
141I GLN* 3.6 34.5 - - + +
142I PHE 3.7 4.5 - - - +
143I SER* 4.7 8.5 - - - +
158I SER* 4.8 1.1 - - - +
160I LYS* 5.2 0.7 - - + +
161I VAL* 3.4 37.2 - - + +
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Residues in contact with MET 126 (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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15I LEU* 3.8 18.4 - - + -
68I SER* 2.8 43.7 - - - +
69I MET* 3.9 7.9 - - + -
74I LEU* 3.1 33.2 - - + -
110I ALA* 4.4 3.1 - - + -
111I VAL 2.8 23.1 - - - +
112I VAL* 4.2 11.4 - - - +
124I ILE* 3.9 8.7 + - + -
125I ILE* 1.3 73.6 - - - +
127I ASP* 1.3 67.1 + - - +
128I VAL* 4.0 4.2 + - + -
140I ASN 3.7 0.7 - - - +
141I GLN* 3.5 2.0 - - - -
142I PHE* 3.0 44.4 + - + +
144I LEU* 5.2 2.5 - - + -
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Residues in contact with ASP 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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109I GLU 4.0 0.2 - - - +
110I ALA* 3.5 0.5 - - - -
111I VAL* 3.0 37.5 + - + +
113I ALA* 3.4 24.7 - - + +
125I ILE 4.0 2.0 + - - -
126I MET* 1.3 73.9 - - - +
128I VAL* 1.3 60.7 + - - +
129I TYR* 3.8 22.3 + - + -
139I HIS* 2.6 29.9 + - - +
140I ASN 3.4 2.0 - - - -
141I GLN* 2.8 34.1 + - - +
160I LYS* 4.2 4.0 - - - +
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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
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18I PHE* 4.4 1.1 - - + -
65I GLY* 3.6 29.2 - - - +
68I SER* 4.4 9.4 - - - +
108I CYS* 4.4 9.6 - - + -
109I GLU 3.2 14.6 - - - +
110I ALA* 4.0 7.2 - - + -
126I MET* 4.3 4.3 - - + +
127I ASP* 1.3 78.9 - - - +
129I TYR* 1.3 69.3 + - - +
130I SER* 4.1 1.3 + - - +
138I CYS 4.1 0.3 - - - +
139I HIS* 3.7 1.3 - - - -
140I ASN* 2.8 43.4 + - + +
142I PHE* 3.5 31.2 - - + -
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Residues in contact with TYR 129 (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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97I TYR* 5.0 3.6 - - - -
108I CYS* 3.3 2.4 - - - -
109I GLU* 2.9 41.4 + - + +
111I VAL* 4.9 10.8 - - + -
127I ASP* 3.8 28.1 + - + +
128I VAL* 1.3 75.0 - - - +
130I SER* 1.3 61.4 + - - +
131I TYR* 3.5 32.1 - - + +
136I LEU* 3.8 20.4 - - + -
138I CYS 3.7 2.7 - - - -
139I HIS* 3.7 43.8 + + + -
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Residues in contact with SER 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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64I ILE* 3.6 15.6 - - - +
65I GLY* 4.2 8.7 - - - -
106I LEU* 4.7 7.2 - - - -
107I LYS 3.4 4.7 - - - -
108I CYS* 3.4 25.9 - - - +
128I VAL* 4.5 2.6 + - - +
129I TYR* 1.3 75.8 - - - +
131I TYR* 1.3 62.4 + - - +
136I LEU* 3.5 1.4 - - - +
137I ILE* 2.8 25.5 + - - +
138I CYS* 3.0 34.6 + - - -
140I ASN* 4.8 0.2 + - - -
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Residues in contact with TYR 131 (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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106I LEU* 3.3 9.8 - - - +
107I LYS* 2.8 51.7 + - + +
109I GLU* 3.7 31.8 + - - -
129I TYR* 3.5 40.4 - - + +
130I SER* 1.3 73.3 - - - +
132I SER* 1.3 60.9 + - - +
133I GLU* 4.7 3.4 - - - +
134I LYS 5.4 1.6 - - - +
135I GLU 3.3 12.8 - - - +
136I LEU* 3.4 38.8 - - + +
137I ILE* 4.7 0.2 - - - -
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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