Contacts of the strand formed by residues 152 - 158 (chain A) in PDB entry 1KXJ
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 VAL 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129A LYS* 2.9 38.0 + - - +
147A CYS* 3.9 15.5 - - - +
148A GLU 3.5 17.7 - - - +
149A GLU* 3.1 20.3 + - + +
150A GLU 5.2 0.7 - - - -
151A HIS* 1.3 77.4 - - - +
153A LEU* 1.3 58.0 + - - +
154A GLY 3.5 24.7 - - - +
155A THR* 4.6 9.6 - - + -
164A PRO* 4.0 20.9 - - + -
166A ALA 3.8 2.2 - - - -
167A VAL* 4.5 1.6 - - - +
168A ARG* 5.4 2.0 + - - -
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Residues in contact with LEU 153 (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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128A PHE* 3.4 9.0 - - + -
129A LYS* 2.8 40.4 + - + +
130A ASP* 4.6 7.2 - - - +
132A PHE* 3.5 36.8 - - + -
151A HIS 3.4 2.4 + - - -
152A VAL* 1.3 72.8 - - - +
154A GLY* 1.3 56.6 - - - +
166A ALA* 2.7 35.2 + - + +
167A VAL 3.7 15.7 - - - +
168A ARG* 3.7 39.7 - - + +
173A LEU* 4.3 6.1 - - + -
175A PHE* 4.1 9.0 - - + -
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Residues in contact with GLY 154 (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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126A VAL* 4.4 1.1 - - - -
127A ILE 3.4 11.0 - - - -
128A PHE* 4.0 8.3 - - - -
152A VAL* 3.5 5.7 - - - +
153A LEU* 1.3 79.3 - - - +
155A THR* 1.3 61.1 + - - -
164A PRO* 3.5 5.0 - - - +
165A SER* 3.1 25.0 + - - -
166A ALA* 2.9 23.4 + - - +
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Residues in contact with THR 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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125A GLU 3.9 0.5 - - - +
126A VAL* 3.5 0.3 - - - -
127A ILE* 2.9 51.2 + - + +
129A LYS* 6.1 6.3 - - + -
152A VAL* 4.6 11.2 - - + -
154A GLY* 1.3 75.2 - - - -
156A THR* 1.3 61.4 + - - +
162A ILE* 3.3 26.2 - - - +
163A PHE 3.6 7.6 - - - -
165A SER* 3.4 6.0 + - - -
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Residues in contact with THR 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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120A HIS* 5.1 0.4 - - + -
124A ASN* 3.7 24.2 - - + -
125A GLU 3.1 24.6 + - - +
126A VAL* 3.5 2.4 - - - +
139A PHE* 3.3 12.1 - - + -
155A THR* 1.3 74.0 + - - +
157A GLU* 1.3 76.3 + - - +
162A ILE* 3.4 5.1 - - - +
163A PHE* 2.9 47.9 + - + +
165A SER* 2.7 33.1 + - - -
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Residues in contact with GLU 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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124A ASN* 3.3 19.8 - - - +
125A GLU 4.5 0.8 + - - -
156A THR* 1.3 79.7 - - - +
158A TYR* 1.3 64.4 + - - +
159A ASP 4.3 0.2 - - - -
160A GLY* 3.4 29.5 - - - +
161A GLU 3.4 14.8 - - - +
162A ILE* 3.9 22.8 - - + +
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Residues in contact with TYR 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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113A LEU* 4.2 17.0 - - + -
115A SER* 3.7 25.9 - - - -
117A ARG* 2.7 58.2 + - - +
118A LEU* 4.5 0.7 - - + -
119A PRO 4.4 0.5 + - - -
120A HIS* 3.4 57.7 - + + -
121A MET 5.0 0.5 + - - -
124A ASN* 4.7 4.3 - - - -
157A GLU* 1.3 76.2 - - - +
159A ASP* 1.3 74.2 + - + +
160A GLY 3.3 1.1 - - - -
161A GLU* 2.8 28.5 + - - +
163A PHE* 3.8 19.5 - - + -
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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