Contacts of the strand formed by residues 122 - 131 (chain B) in PDB entry 1KY9
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 122 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A ASP* 2.8 48.7 + - - +
97A LYS* 3.8 23.1 + - + +
99A TYR* 4.7 2.3 + - - -
140A GLN* 3.0 22.4 + - - +
141A ILE 5.3 0.4 + - - -
144A PRO* 3.6 21.8 + - + +
114B LYS* 5.3 11.8 - - - +
115B VAL 3.5 4.3 - - - +
116B GLN* 3.9 31.6 - - + +
120B GLY 3.6 4.7 + - - +
121B ARG* 1.3 74.0 - - - +
123B PHE* 1.3 72.5 + - - +
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Residues in contact with PHE 123 (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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97A LYS* 4.1 8.0 - - - +
99A TYR* 5.3 7.4 - - - -
140A GLN* 4.4 9.2 - - - -
114B LYS* 3.8 6.4 - - - +
115B VAL* 2.8 35.0 + - + +
117B LEU* 3.2 33.0 - - + -
121B ARG* 3.6 45.5 - - + -
122B LYS* 1.3 81.8 - - - +
124B ASP* 1.3 69.1 + - - +
141B ILE* 3.4 29.4 - - + -
142B GLN 3.9 4.7 - - - +
143B ASN* 3.4 26.2 - - + -
144B PRO* 4.1 1.6 - - + -
145B LYS* 4.1 13.0 - - + -
147B LEU* 4.6 2.2 - - + -
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Residues in contact with ASP 124 (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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97A LYS* 2.6 38.4 + - - +
112B VAL* 5.6 1.4 - - - +
113B ILE 4.0 3.5 - - - +
114B LYS* 3.8 20.1 - - - +
115B VAL* 5.1 0.8 - - - +
123B PHE* 1.3 77.9 - - - +
125B ALA* 1.3 58.8 + - - +
141B ILE* 3.4 5.4 - - - +
142B GLN* 2.5 50.3 + - + -
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Residues in contact with ALA 125 (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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113B ILE* 2.9 54.3 + - + +
115B VAL* 3.9 8.3 - - + -
124B ASP* 1.3 77.3 - - - +
126B LYS* 1.3 68.0 + - - +
139B ILE* 3.8 15.9 - - + -
140B GLN 3.2 15.0 - - - +
141B ILE* 4.3 1.3 - - - -
142B GLN* 4.2 1.3 - - - +
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Residues in contact with LYS 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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113B ILE* 4.9 3.4 - - - -
125B ALA* 1.3 76.7 - - - +
127B MSE 1.3 68.6 + - - +
139B ILE* 3.4 6.3 - - - -
140B GLN* 3.0 31.3 + - + +
142B GLN* 3.2 45.4 - - + +
363B ASP* 5.6 7.9 - - + +
366B SER* 3.6 32.8 + - - +
367B ILE 5.3 0.6 + - - -
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Residues in contact with MSE 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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107B VAL* 3.5 39.9 - - + +
110B ALA* 5.5 4.7 - - + +
113B ILE* 5.0 10.6 - - + +
126B LYS* 1.3 76.3 - - - +
128B VAL* 1.3 59.8 + - - +
129B GLY* 3.0 48.7 - - - +
130B LYS* 3.9 16.6 - - + +
138B LEU 4.2 4.9 - - - +
139B ILE* 4.4 4.3 - - - -
359B GLN 6.0 1.1 - - - +
363B ASP* 3.5 38.9 - - + +
422B ARG* 4.1 0.7 + - - -
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Residues in contact with VAL 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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99B TYR* 4.6 11.7 - - + +
126B LYS 4.2 0.4 - - - +
127B MSE 1.3 76.5 - - - +
129B GLY* 1.3 59.0 + - - +
138B LEU* 3.1 47.1 + - + +
139B ILE* 3.4 17.3 - - - +
140B GLN* 4.0 10.5 - - + +
254B MSE 4.1 15.8 - - - +
255B VAL* 4.6 5.8 - - - -
258B GLY 3.9 6.1 - - - +
360B ASN* 4.7 0.5 - - - +
363B ASP* 5.1 1.1 - - - -
422B ARG* 3.2 37.6 + - - +
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Residues in contact with GLY 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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127B MSE 3.0 16.6 - - - +
128B VAL* 1.3 81.5 - - - +
130B LYS* 1.3 61.8 + - - +
137B ALA* 3.5 1.2 - - - +
138B LEU 2.8 25.6 + - - -
254B MSE 3.3 25.1 - - - -
258B GLY 4.7 5.8 - - - -
259B GLN* 6.0 0.2 - - - -
360B ASN* 5.5 1.8 - - - -
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Residues in contact with LYS 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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104B ASN* 3.1 20.7 - - - +
107B VAL* 5.1 0.7 - - + -
108B ASP* 2.5 51.2 + - - +
109B ASN 4.3 1.6 - - - +
127B MSE 4.0 17.7 - - + -
129B GLY* 1.3 76.5 - - - +
131B ASP* 1.3 61.8 + - - +
132B PRO* 4.7 12.0 - - + +
136B ILE 3.6 4.0 - - - -
137B ALA* 3.9 10.1 - - + -
254B MSE 3.3 12.1 - - - +
259B GLN* 5.7 2.9 - - - +
260B VAL* 4.9 1.6 + - - +
357B SER 5.2 4.5 - - - -
358B SER* 3.4 18.2 - - - -
359B GLN 4.5 18.2 + - - +
361B GLN* 4.8 17.1 - - - +
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Residues in contact with ASP 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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104B ASN* 4.6 1.5 - - - +
130B LYS* 1.3 78.0 - - - +
132B PRO* 1.3 64.1 - - - +
133B ARG* 4.0 4.0 + - - +
134B SER* 2.9 27.5 + - - +
135B ASP 3.0 21.3 + - - -
136B ILE 3.0 12.0 + - - +
250B LEU* 3.3 5.6 - - + +
254B MSE 3.5 15.9 - - + -
260B VAL* 3.6 20.4 - - + +
262B ARG* 3.3 41.6 + - - -
355B GLN* 5.4 0.7 - - - +
357B SER* 5.9 0.3 - - - -
358B SER* 4.0 4.8 - - - -
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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