Contacts of the strand formed by residues 130 - 135 (chain D) in PDB entry 5JLH
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 ALA 130 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D PRO* 3.3 13.4 - - + +
102D VAL 3.0 20.6 + - - -
123D PHE* 4.4 4.3 - - - -
128D THR* 3.3 11.3 + - - -
129D PRO* 1.3 84.3 - - + +
131D MET* 1.3 63.5 + - - +
355D TRP* 3.8 23.8 - - + -
356D ILE 3.2 15.5 - - - +
357D SER* 4.1 5.2 - - - +
358D LYS 4.4 1.1 - - - +
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Residues in contact with MET 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D VAL* 3.0 23.3 - - + +
104D LEU* 3.9 21.3 - - + -
119D THR* 3.4 38.4 - - + -
122D MET* 3.7 15.9 - - + -
123D PHE* 3.6 23.3 - - + -
128D THR* 5.0 0.4 - - + -
130D ALA* 1.3 78.1 - - - +
132D TYR* 1.3 66.2 + - - +
133D VAL* 3.4 33.4 - - + -
355D TRP* 3.4 6.6 - - - -
356D ILE* 2.8 37.4 + - + +
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Residues in contact with TYR 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D VAL 3.1 5.1 + - - +
103D LEU* 3.5 16.3 - - + +
104D LEU* 2.8 25.8 + - - +
131D MET* 1.3 82.5 - - - +
133D VAL* 1.3 89.1 + - - +
134D ALA* 3.6 14.6 - - + -
345D LEU* 5.2 3.8 - - + -
351D PHE* 3.7 26.2 - + + -
354D MET* 4.0 36.0 - - + +
355D TRP* 3.7 18.8 - - + -
356D ILE* 4.5 9.9 - - + -
372D LYS* 5.8 1.8 - - + -
373D CYS* 3.2 37.6 - - + +
374D PHE* 4.1 7.1 + - - +
42E VAL* 5.3 5.7 - - - +
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Residues in contact with VAL 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D LEU* 3.3 16.4 - - + +
106D GLU* 5.1 5.4 - - + -
115D ARG* 4.1 19.2 + - + +
118D MET* 4.2 17.3 - - + -
119D THR* 4.5 6.3 - - + -
131D MET* 3.4 28.2 - - + +
132D TYR* 1.3 85.5 - - - +
134D ALA* 1.3 60.9 + - - +
356D ILE* 4.9 1.9 - - + +
369D VAL* 3.4 33.0 - - + -
373D CYS* 3.6 17.0 - - - -
374D PHE* 4.2 4.9 - - - +
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Residues in contact with ALA 134 (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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103D LEU* 3.8 12.8 - - + -
104D LEU 2.8 6.9 + - - +
105D THR* 3.4 3.2 - - - -
106D GLU* 2.8 29.5 + - - +
115D ARG* 6.1 1.1 - - - -
132D TYR* 3.6 24.0 - - + -
133D VAL* 1.3 75.8 - - - +
135D ILE* 1.3 63.8 + - - +
139D LEU* 3.7 25.4 - - + -
345D LEU* 5.1 3.1 - - + -
374D PHE* 5.4 1.8 - - - -
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Residues in contact with ILE 135 (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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105D THR* 4.2 0.2 - - - -
106D GLU* 3.4 1.3 - - - +
107D ALA 3.9 1.6 - - - -
108D PRO* 3.4 50.9 - - + -
115D ARG* 3.6 23.1 - - - +
134D ALA* 1.3 73.4 - - - +
136D GLN* 1.3 64.9 + - - +
137D ALA* 4.1 2.7 - - + +
138D VAL* 3.2 40.4 - - + +
139D LEU* 3.2 19.6 + - - +
162D VAL* 5.3 4.7 - - + -
174D ILE* 6.2 0.2 - - + -
374D PHE* 4.3 36.4 + - + +
42E VAL* 5.6 1.6 - - + -
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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