Contacts of the strand formed by residues 143 - 147 (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 TYR 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A GLN* 3.0 12.4 + - - +
94A SER* 4.6 2.0 - - - -
95A GLU* 4.3 7.3 - - + +
96A GLU* 3.6 58.7 - - + +
110A VAL* 3.4 16.8 - - + -
111A VAL* 3.2 12.3 - - - +
112A LYS* 3.3 53.4 + - + +
113A LEU* 4.3 0.4 - - - +
141A HIS* 2.9 22.7 - - - -
142A THR* 1.3 89.1 - - + +
144A ARG* 1.3 63.7 + - - +
204A PO4 2.5 29.6 + - - +
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Residues in contact with ARG 144 (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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88A GLN* 4.3 0.7 - - - +
110A VAL* 3.4 5.8 - - - -
111A VAL* 2.8 39.4 + - - +
113A LEU* 3.6 25.6 - - + -
114A ARG* 4.0 10.7 - - - +
141A HIS* 4.5 2.0 - - + -
143A TYR* 1.3 75.1 - - - +
145A ALA* 1.3 84.8 + - - +
146A VAL* 3.4 23.0 - - - +
161A GLU* 3.3 27.6 + - - +
162A ILE 3.6 15.2 + - - -
163A PHE* 3.7 32.5 - - + +
164A PRO* 3.4 14.5 - - - +
176A GLN* 3.9 7.4 - - - +
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Residues in contact with ALA 145 (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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87A MET* 3.7 20.8 - - + +
91A PHE* 3.5 39.0 - - + -
109A ASN 3.7 4.7 - - - -
110A VAL* 4.3 5.1 - - + +
144A ARG* 1.3 104.4 + - - +
146A VAL* 1.3 54.3 + - - +
147A CYS 4.1 0.9 - - - +
164A PRO* 3.1 17.8 + - + +
167A VAL* 4.8 6.5 - - + -
176A GLN* 4.4 0.2 + - - -
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Residues in contact with VAL 146 (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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108A GLY* 3.2 2.6 - - - -
109A ASN 2.8 43.9 + - - +
111A VAL* 4.4 8.3 - - + -
144A ARG* 3.4 35.0 - - - +
145A ALA* 1.3 73.9 - - - +
147A CYS* 1.3 59.7 + - - +
164A PRO* 4.9 1.6 - - - -
7B SER* 3.9 3.6 - - - +
34B LEU* 3.8 42.4 - - + +
36B GLU* 3.7 26.4 - - + +
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Residues in contact with CYS 147 (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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91A PHE* 3.6 24.5 - - + -
107A GLU 3.6 11.2 - - - +
145A ALA* 5.3 0.2 - - - -
146A VAL* 1.3 75.6 - - - +
148A GLU* 1.3 73.7 + - - +
149A GLU 3.8 0.5 + - - -
151A HIS* 4.2 10.5 - - + -
152A VAL* 3.9 19.9 - - - +
164A PRO* 4.5 8.6 - - - +
167A VAL* 3.9 24.5 - - - -
36B GLU* 3.3 26.6 - - - +
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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