Contacts of the strand formed by residues 125 - 131 (chain K) 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 ILE 125 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112K VAL* 3.8 1.4 - - - +
113K ALA* 3.0 29.2 + - + -
114K ASP* 2.7 30.6 + - + +
116K LEU* 4.8 13.5 - - + -
123K VAL* 3.4 28.3 - - + +
124K ILE* 1.3 72.5 - - - +
126K MET* 1.3 61.1 + - - +
141K GLN* 3.8 33.9 - - + +
142K PHE 3.7 6.1 - - - +
143K SER* 4.6 10.5 - - - +
158K SER* 4.9 0.7 - - - -
160K LYS 4.8 1.3 - - - +
161K VAL* 3.1 40.6 - - + -
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Residues in contact with MET 126 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15K LEU* 4.0 21.3 - - + -
65K GLY 4.9 0.9 - - - +
66K GLN* 5.7 1.1 - - - +
68K SER 3.6 26.2 - - - +
110K ALA* 4.7 4.3 - - + -
111K VAL 3.5 20.6 - - - +
112K VAL* 4.6 3.4 - - + +
113K ALA 4.2 0.2 - - - +
124K ILE* 3.7 18.1 + - + +
125K ILE* 1.3 73.2 - - - +
127K ASP* 1.3 66.7 + - - +
128K VAL* 3.9 7.8 + - + -
140K ASN 3.8 0.9 - - - +
141K GLN* 3.6 1.6 - - - -
142K PHE* 3.0 68.4 + - + +
144K LEU* 5.1 13.5 - - + -
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Residues in contact with ASP 127 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110K ALA* 3.3 1.6 - - - -
111K VAL* 2.9 40.1 + - + +
113K ALA* 3.0 26.1 - - + +
126K MET* 1.3 73.9 - - - +
128K VAL* 1.3 62.0 + - - +
129K TYR* 3.8 26.1 + - + +
139K HIS* 2.9 20.0 + - - +
140K ASN 3.5 1.6 - - - -
141K GLN* 2.8 39.1 + - - +
160K LYS* 4.2 4.9 - - - +
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Residues in contact with VAL 128 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18K PHE* 4.5 3.4 - - + -
65K GLY* 3.8 28.0 - - - +
108K CYS* 4.4 9.6 - - + -
109K GLU 3.1 16.4 - - - +
110K ALA* 4.0 8.7 - - + -
126K MET* 4.2 7.4 - - + +
127K ASP* 1.3 78.6 - - - +
129K TYR* 1.3 68.0 + - - +
130K SER* 4.1 1.2 + - - +
138K CYS 4.2 0.2 - - - +
139K HIS* 3.7 1.7 - - - -
140K ASN* 2.9 38.5 + - + +
142K PHE* 3.4 37.0 - - + -
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Residues in contact with TYR 129 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97K TYR* 5.1 3.8 - - - -
108K CYS* 3.5 1.0 - - - -
109K GLU* 2.9 36.8 + - + +
111K VAL* 5.1 11.9 - - + -
127K ASP* 3.8 29.2 + - + -
128K VAL* 1.3 77.0 - - - +
130K SER* 1.3 61.5 + - - +
131K TYR* 3.5 35.5 - - + +
136K LEU* 3.9 16.8 - - + -
138K CYS 3.7 3.1 - - - -
139K HIS* 3.6 43.5 + + + -
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Residues in contact with SER 130 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64K ILE* 3.7 11.5 - - - +
65K GLY* 4.4 7.8 - - - -
106K LEU* 4.9 7.4 - - - -
107K LYS 3.4 5.2 - - - -
108K CYS* 3.6 24.8 - - - +
128K VAL* 4.5 3.1 + - - +
129K TYR* 1.3 75.8 - - - +
131K TYR* 1.3 62.6 + - - +
136K LEU* 3.5 1.6 - - - +
137K ILE* 2.8 24.6 + - - +
138K CYS* 2.9 39.3 + - - -
140K ASN* 4.6 0.9 + - - -
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Residues in contact with TYR 131 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106K LEU* 3.6 12.7 - - - +
107K LYS* 3.0 41.4 + - + +
109K GLU* 3.6 33.2 + - - -
129K TYR* 3.5 41.5 - - + +
130K SER* 1.3 75.6 - - - +
132K SER* 1.3 62.5 + - - +
135K GLU 3.2 15.9 - - - +
136K LEU* 3.4 39.2 - - + +
137K ILE* 4.6 0.9 - - - -
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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