Contacts of the strand formed by residues 154 - 160 (chain A) in PDB entry 5JKC
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 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A GLU* 2.7 42.4 + - - +
145A THR* 3.5 28.6 - - + +
146A LEU 3.4 7.9 - - - +
147A ILE* 3.9 16.4 - - + +
152A CYS 3.5 5.1 + - - +
153A LYS* 1.3 80.9 + - - +
155A GLU* 1.3 67.2 + - - +
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Residues in contact with GLU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A THR* 3.4 3.7 - - - -
146A LEU 2.9 30.3 + - - +
148A TRP* 3.6 17.4 - - + -
153A LYS* 3.1 42.4 + - - +
154A LYS* 1.3 78.6 - - - +
156A VAL* 1.3 67.8 + - - +
83B MET* 3.2 12.9 - - + +
84B PRO* 3.4 23.1 - - + +
85B GLY* 4.1 9.9 + - - -
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Residues in contact with VAL 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A LEU* 3.8 36.3 - - + -
144A GLN 3.7 8.1 - - - +
145A THR* 3.8 18.4 - - + +
155A GLU* 1.3 76.9 - - - +
157A HIS* 1.3 62.0 + - - +
158A ALA 4.2 0.7 + - - -
191A GLU* 4.0 8.7 - - + +
84B PRO* 3.4 19.6 - - - +
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Residues in contact with HIS 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A TYR* 3.5 19.0 + + - -
135A CYS* 3.7 8.2 - - - -
143A LEU* 3.4 3.4 - - - -
144A GLN* 2.8 40.5 + - + +
146A LEU* 3.7 19.1 - - + -
148A TRP* 4.2 10.5 - - + -
155A GLU 3.7 1.6 + - - -
156A VAL* 1.3 74.2 - - - +
158A ALA* 1.3 75.2 + - - +
159A CYS* 3.6 18.6 + - - -
67B ASP* 4.3 6.8 + - - -
81B LEU* 4.1 29.4 - - + +
82B LEU 5.5 1.6 + - - -
84B PRO* 4.6 7.0 - - - +
87B ARG* 3.5 30.9 + - - -
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Residues in contact with ALA 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A VAL* 4.4 3.6 - - + -
143A LEU* 3.7 24.7 - - + +
156A VAL 4.2 0.8 + - - -
157A HIS* 1.3 80.1 + - - +
159A CYS* 1.3 59.3 + - - +
160A ARG* 3.5 39.2 + - - +
239A ASN* 5.5 1.3 - - - +
67B ASP* 5.5 0.2 - - - +
84B PRO* 6.1 0.2 - - - +
87B ARG* 2.7 29.2 + - - +
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Residues in contact with CYS 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A CYS* 2.0 56.3 - - + -
137A ASN* 3.1 27.3 + - - +
141A VAL* 3.2 3.4 - - - -
142A MET* 2.8 33.4 + - + +
144A GLN* 3.3 19.1 - - - -
157A HIS* 3.6 11.9 - - - -
158A ALA* 1.3 68.0 - - - +
160A ARG* 1.3 60.3 + - - +
161A LYS* 5.3 1.1 - - - -
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Residues in contact with ARG 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A GLY 3.9 2.9 - - - -
141A VAL* 4.0 14.0 - - + +
158A ALA* 3.5 31.9 + - - +
159A CYS* 1.3 72.6 - - - +
161A LYS* 1.3 66.7 + - - +
239A ASN* 5.5 1.6 + - - -
44B TYR* 3.1 31.1 + - - -
45B GLU* 4.1 12.9 + - - +
62B TRP* 3.7 16.4 - - + -
65B HIS* 3.2 45.8 + - - +
66B LEU* 4.0 16.8 - - + +
67B ASP* 5.7 4.2 + - - +
87B ARG* 4.0 11.2 - - - +
91B ILE* 4.0 21.0 - - - +
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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