Contacts of the strand formed by residues 143 - 148 (chain D) in PDB entry 2J3T
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 143 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D MET* 3.3 37.8 - - + +
137D LEU 3.5 3.4 - - - +
138D GLU* 3.3 37.5 + - - -
142D PHE* 1.3 78.0 - - - +
144D LEU* 1.3 59.9 + - - +
145D HIS* 3.5 29.6 - - + +
157D VAL 3.6 1.6 - - - +
158D LEU* 3.4 2.4 - - - -
159D ALA 2.7 38.2 + - - +
160D ASP 4.5 1.1 - - - +
161D PRO* 3.4 34.0 + - + +
163D GLN 5.8 0.9 - - - +
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Residues in contact with LEU 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C PHE* 3.6 35.2 - - + -
115D PHE* 3.9 28.5 - - + -
134D ILE* 5.2 2.2 - - + -
135D GLU 5.2 0.4 - - - +
136D MET* 3.2 6.6 - - - +
137D LEU* 2.7 53.4 + - + +
142D PHE* 3.9 6.5 - - + -
143D LYS* 1.3 72.0 - - - +
145D HIS* 1.3 68.4 - - - +
146D CYS* 4.2 2.9 - - + -
156D VAL* 3.6 25.6 - - + -
157D VAL 3.5 2.7 - - - -
158D LEU* 3.3 27.4 - - + -
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Residues in contact with HIS 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D GLU 3.4 5.1 + - - +
136D MET* 3.8 13.7 - - + +
143D LYS* 3.5 45.5 - - + +
144D LEU* 1.3 74.9 - - - +
146D CYS* 1.3 60.3 + - - +
155D PHE 3.6 1.6 - - - +
156D VAL* 3.4 3.8 - - - +
157D VAL* 2.8 49.9 + - + +
159D ALA* 4.9 5.9 - - + +
160D ASP 5.4 0.6 + - - -
163D GLN 4.9 6.1 + - - -
166D ILE* 3.3 51.9 - - + +
170D LEU* 4.1 11.9 - - + +
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Residues in contact with CYS 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D PHE* 3.7 22.4 - - + -
119D PHE* 3.9 11.8 - - - -
134D ILE 3.5 15.3 - - - +
135D GLU* 2.8 32.4 + - - +
144D LEU* 4.2 3.8 - - + -
145D HIS* 1.3 76.7 - - - +
147D TYR* 1.3 65.4 + - - +
148D GLN 4.4 0.5 + - - -
154D LYS* 3.3 42.2 - - - -
155D PHE 3.5 2.9 - - - +
156D VAL* 4.1 4.9 - - + -
170D LEU* 4.3 6.6 - - - +
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Residues in contact with TYR 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D CYS* 1.3 79.5 - - - +
148D GLN* 1.3 78.7 + - - +
149D THR* 4.2 8.0 - - - -
153D ILE 3.5 2.9 - - - +
154D LYS* 3.5 1.4 - - - -
155D PHE* 3.1 49.3 + + + +
170D LEU* 4.0 31.4 - - + -
171D ARG* 5.8 3.8 - - + -
174D TYR* 3.9 37.3 - + + -
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Residues in contact with GLN 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D PHE* 3.6 41.2 - - + -
132D SER* 6.0 1.2 - - - -
133D GLY 5.5 0.2 + - - -
146D CYS* 4.3 1.0 + - - -
147D TYR* 1.3 86.0 - - - +
149D THR* 1.3 75.5 + - - +
150D LEU 4.0 0.2 + - - -
152D GLY* 4.0 19.1 + - - -
153D ILE 3.4 7.4 - - - +
154D LYS* 3.6 20.5 - - + +
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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