Contacts of the strand formed by residues 125 - 134 (chain E) in PDB entry 1K9A
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 LYS 125 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121E SER* 3.4 4.4 + - - -
122E CYS* 2.5 50.4 + - + +
123E GLU* 3.1 4.8 - - + +
124E GLY* 1.3 75.3 - - - +
126E VAL* 1.3 71.4 + - - +
127E GLU* 3.1 28.0 - - - +
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Residues in contact with VAL 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93E GLU* 3.2 62.2 + - + +
96E LEU* 4.2 27.1 - - + +
97E TYR* 5.8 0.4 - - - -
119E CYS* 4.9 0.2 - - + -
120E VAL 3.5 7.4 - - - +
121E SER* 5.0 4.0 - - - +
124E GLY 5.0 3.4 - - - +
125E LYS* 1.3 91.7 + - - +
127E GLU* 1.3 64.4 + - - +
128E HIS* 3.6 23.9 + - + +
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Residues in contact with GLU 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D ARG* 4.1 14.2 + - - +
118E LEU 3.4 1.6 - - - +
119E CYS* 3.1 7.3 - - - +
120E VAL 2.6 40.8 + - - +
122E CYS* 3.8 11.9 - - + -
125E LYS* 3.1 38.1 - - - +
126E VAL* 1.3 71.8 - - - +
128E HIS* 1.3 61.6 + - - +
129E TYR* 3.0 39.2 + - + -
164E CYS* 3.2 27.9 - - - -
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Residues in contact with HIS 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89E ARG* 3.1 50.0 + - + +
92E ALA* 4.4 1.6 - - + -
93E GLU* 3.4 38.5 + - + +
107E ARG* 3.1 24.1 + - - -
117E THR* 4.0 5.4 - - + -
118E LEU 3.5 1.6 - - - -
119E CYS* 3.3 21.4 - - + -
126E VAL* 3.6 21.4 + - + +
127E GLU* 1.3 73.4 + - - +
129E TYR* 1.3 67.9 + - - +
130E ARG 4.1 1.3 + - - -
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Residues in contact with TYR 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D VAL* 3.5 40.6 - - + -
55D GLY 6.2 0.2 - - - -
56D ARG* 3.9 6.5 - - + -
117E THR* 3.2 5.5 - - - +
118E LEU* 2.7 49.9 + - + +
120E VAL* 4.1 18.8 - - + -
127E GLU* 3.0 35.7 + - + -
128E HIS* 1.3 77.6 - - - +
130E ARG* 1.3 64.6 + - - +
131E ILE* 3.4 2.4 + - - +
140E ILE* 4.2 21.8 - - + -
163E LEU* 3.8 24.0 - - + -
164E CYS* 3.0 37.0 + - - +
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Residues in contact with ARG 130 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109E SER* 5.3 0.7 - - - +
112E TYR* 3.1 62.8 + - + +
115E ASP* 3.1 26.3 + - + +
116E TYR 3.7 7.4 - - - +
117E THR* 4.5 6.4 - - - +
128E HIS 4.1 2.4 + - - -
129E TYR* 1.3 70.5 - - - +
131E ILE* 1.3 64.4 + - - +
132E MET* 3.0 47.7 - - + +
140E ILE* 3.7 16.0 - - - +
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Residues in contact with ILE 131 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E VAL* 4.3 4.9 - - + -
115E ASP* 3.1 8.3 - - - +
116E TYR* 2.7 45.1 + - + +
117E THR 4.2 1.1 - - - -
118E LEU* 3.9 23.6 - - + +
129E TYR 3.7 13.0 - - - +
130E ARG* 1.3 72.0 - - - +
132E MET* 1.3 61.4 + - - +
138E LEU* 3.8 29.6 - - + -
139E SER 3.6 8.3 - - - +
140E ILE* 3.9 10.3 - - + -
149E LEU* 4.0 15.9 - - + -
152E LEU* 3.6 35.0 - - + -
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Residues in contact with MET 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E ASP* 3.6 5.6 - - - +
130E ARG* 3.0 74.9 - - + +
131E ILE* 1.3 71.8 - - - +
133E TYR* 1.3 62.5 + - - +
134E HIS* 4.0 4.3 - - + -
137E LYS 3.4 1.6 - - - +
138E LEU* 3.0 6.6 - - - -
139E SER* 2.7 46.2 + - - +
140E ILE 4.0 10.8 - - - +
142E GLU* 4.7 23.3 - - + +
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Residues in contact with TYR 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114E GLY 3.5 27.3 - - - +
115E ASP* 3.2 16.2 + - - +
116E TYR* 3.8 14.4 - + - -
131E ILE 3.6 0.2 + - - -
132E MET* 1.3 72.4 - - - +
134E HIS* 1.3 64.2 + - - +
136E SER* 3.6 26.7 - - - -
137E LYS 3.5 10.1 - - - -
138E LEU* 3.5 24.9 - - + -
147E GLU 4.6 2.1 + - - -
226E ASN* 3.1 28.2 - - + -
227E ASP 3.3 0.5 + - - -
228E ALA* 3.0 39.4 + - + -
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Residues in contact with HIS 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E MET* 4.0 5.1 - - + -
133E TYR* 1.3 77.4 - - - +
135E ALA* 1.3 93.3 + - + +
136E SER 3.1 2.0 - - - +
137E LYS* 2.8 30.2 + - - +
145E TYR* 5.6 2.9 - - + -
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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