Contacts of the strand formed by residues 125 - 134 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99B PRO* 4.8 0.4 - - - +
121B SER* 4.5 2.4 + - - -
122B CYS* 2.8 35.2 + - - +
123B GLU* 4.4 4.0 - - + +
124B GLY* 1.3 81.7 - - - +
126B VAL* 1.3 73.5 + - - +
127B GLU* 3.0 30.7 + - - +
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Residues in contact with VAL 126 (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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92B ALA 5.3 0.7 - - - +
93B GLU* 3.5 33.0 + - - +
96B LEU* 3.8 50.0 - - + +
119B CYS* 4.2 3.4 - - + -
120B VAL 3.5 5.2 - - - +
121B SER* 4.6 5.6 - - - +
125B LYS* 1.3 89.3 + - - +
127B GLU* 1.3 70.6 + - - +
128B HIS* 3.6 34.2 + - + +
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Residues in contact with GLU 127 (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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118B LEU 3.3 2.6 - - - +
119B CYS* 3.3 3.8 - - - -
120B VAL* 2.7 41.7 + - + +
122B CYS* 4.3 8.5 - - + +
125B LYS* 3.0 38.1 + - - +
126B VAL* 1.3 72.3 - - - +
128B HIS* 1.3 61.6 + - - +
129B TYR* 3.4 38.2 + - + +
164B CYS* 4.0 20.3 - - + -
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Residues in contact with HIS 128 (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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89B ARG* 3.3 69.2 + - + +
92B ALA* 4.2 3.6 - - + -
93B GLU* 2.8 28.4 + - - -
107B ARG* 3.4 15.7 + - - -
117B THR* 4.0 8.3 - - + -
118B LEU 3.5 3.6 - - - -
119B CYS* 3.5 14.5 - - - -
126B VAL* 3.6 27.1 - - + +
127B GLU* 1.3 71.9 + - - +
129B TYR* 1.3 65.5 + - - +
130B ARG 3.9 1.7 + - - -
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Residues in contact with TYR 129 (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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117B THR* 3.2 4.7 - - - +
118B LEU* 2.6 54.2 + - + +
120B VAL* 4.2 19.5 - - + -
127B GLU* 3.4 35.2 + - + +
128B HIS* 1.3 73.1 - - - +
130B ARG* 1.3 64.5 + - - +
131B ILE* 3.5 1.7 + - - +
140B ILE* 4.1 26.7 - - + -
162B GLY 5.4 1.6 - - - -
163B LEU* 4.0 30.5 - - + -
164B CYS* 2.9 38.0 + - + +
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Residues in contact with ARG 130 (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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109B SER* 5.1 2.5 - - - +
112B TYR* 3.0 63.5 + - + +
115B ASP* 3.0 28.8 + - + +
116B TYR 3.7 6.3 - - - +
117B THR* 4.4 5.6 - - - +
128B HIS 3.9 3.0 + - - -
129B TYR* 1.3 73.3 - - - +
131B ILE* 1.3 62.5 - - - +
132B MET* 3.3 41.4 - - + +
140B ILE* 3.6 18.9 - - - +
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Residues in contact with ILE 131 (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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106B VAL* 4.5 5.6 - - + -
115B ASP* 3.4 3.5 - - - +
116B TYR* 2.6 44.0 + - + +
117B THR 4.3 1.1 - - - -
118B LEU* 4.0 22.7 - - + +
129B TYR 3.8 7.2 - - - +
130B ARG* 1.3 74.6 - - - +
132B MET* 1.3 63.0 + - - +
133B TYR* 3.3 2.1 + - - -
138B LEU* 3.6 31.0 - - + +
139B SER 3.6 8.7 - - - +
140B ILE* 3.6 15.5 - - + -
149B LEU* 4.2 14.4 - - + -
152B LEU* 3.6 34.8 - - + -
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Residues in contact with MET 132 (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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115B ASP* 3.4 5.8 - - - +
130B ARG* 3.3 67.5 - - + +
131B ILE* 1.3 70.8 - - - +
133B TYR* 1.3 61.1 + - - +
134B HIS* 3.8 7.2 - - + +
137B LYS 3.2 1.2 - - - +
138B LEU* 3.1 26.0 - - - -
139B SER* 2.9 23.3 + - - +
140B ILE 4.6 11.7 - - - +
142B GLU* 4.6 24.0 - - + +
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Residues in contact with TYR 133 (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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114B GLY 3.3 24.5 - - - +
115B ASP* 2.5 23.8 + - - +
116B TYR* 3.5 13.2 - + + -
132B MET* 1.3 71.8 - - - +
134B HIS* 1.3 64.8 + - - +
136B SER* 4.2 7.2 - - - -
137B LYS* 2.9 29.2 - - - -
138B LEU* 3.4 22.9 - - + -
147B GLU 4.7 3.7 + - - -
226B ASN* 3.0 41.1 - - + -
227B ASP 3.5 0.3 + - - -
228B ALA* 3.1 26.8 + - + -
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Residues in contact with HIS 134 (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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132B MET* 3.8 7.9 - - + -
133B TYR* 1.3 78.6 + - - +
135B ALA* 1.3 89.2 + - + +
136B SER 3.2 2.5 - - - +
137B LYS* 3.0 21.0 + - - +
145B TYR* 5.9 0.5 - - - -
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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