Contacts of the strand formed by residues 131 - 136 (chain I) in PDB entry 3LUE
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 131 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102I PRO* 3.3 13.3 - - + +
103I VAL 3.1 20.5 + - - -
124I PHE* 4.0 4.3 - - - -
129I THR* 3.1 9.7 - - - +
130I PRO* 1.4 81.3 - - + +
132I MET* 1.3 68.2 + - - +
353I GLN* 4.9 3.8 - - - +
356I TRP* 3.8 24.7 - - + -
357I ILE 3.2 15.5 - - - +
358I SER* 4.2 5.2 - - - -
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Residues in contact with MET 132 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103I VAL* 3.3 19.3 - - + +
105I LEU* 3.5 35.7 - - + -
119I MET 3.9 5.8 - - - +
120I THR* 4.1 21.1 - - - -
123I MET* 3.8 21.5 - - + -
124I PHE* 3.6 25.8 - - + -
129I THR* 4.8 1.8 - - + -
131I ALA* 1.3 79.6 - - - +
133I TYR* 1.3 62.6 + - - +
134I VAL* 4.0 23.8 - - + -
356I TRP* 3.4 5.5 - - - -
357I ILE* 2.9 44.4 + - + +
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Residues in contact with TYR 133 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103I VAL 3.1 5.6 + - - +
104I LEU* 3.4 10.0 - - + -
105I LEU* 2.8 32.4 + - - +
132I MET* 1.3 77.6 - - - +
134I VAL* 1.3 84.4 + - - +
135I ALA* 3.9 13.2 - - + -
346I LEU* 5.1 2.2 - - + -
352I PHE* 3.5 22.4 - + + -
355I MET* 3.1 44.6 - - + +
356I TRP* 3.4 21.3 - - + -
357I ILE* 5.1 0.2 - - + -
373I LYS 3.7 16.8 + - - -
374I CYS* 3.7 32.2 - - - -
375I PHE* 4.5 13.2 + - - -
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Residues in contact with VAL 134 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105I LEU 3.4 11.7 - - - +
107I GLU* 3.4 41.4 - - + +
116I ARG* 4.4 8.7 - - + +
119I MET* 3.9 24.7 - - + -
132I MET* 4.0 20.2 - - + -
133I TYR* 1.3 84.9 - - - +
135I ALA* 1.3 59.1 + - - +
136I ILE 4.3 0.2 + - - -
370I VAL* 3.8 24.5 - - + -
374I CYS* 3.7 22.2 - - - +
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Residues in contact with ALA 135 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104I LEU* 4.4 15.0 - - + +
105I LEU 3.4 5.3 + - - -
106I THR* 3.2 6.8 - - - -
107I GLU* 2.7 33.3 + - - -
133I TYR* 3.9 19.9 - - + -
134I VAL* 1.3 73.8 - - - +
136I ILE* 1.3 57.4 + - - +
139I VAL* 6.1 2.0 - - + -
140I LEU* 3.4 25.8 - - + -
346I LEU* 5.3 3.4 - - + -
375I PHE* 6.6 0.4 - - - -
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Residues in contact with ILE 136 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107I GLU* 3.3 27.3 + - + +
108I ALA 4.4 6.5 - - - +
109I PRO* 3.8 28.0 - - + -
110I LEU 5.4 0.2 - - - +
135I ALA* 1.3 71.8 - - - +
137I GLN* 1.3 63.4 + - - +
138I ALA* 3.9 10.3 - - + +
139I VAL* 3.5 23.6 + - + +
140I LEU* 2.9 19.8 - - - +
161I HIS* 4.2 24.7 - - + +
163I VAL* 5.4 1.1 - - + -
175I ILE* 5.6 2.2 - - + -
374I CYS 6.1 0.7 - - - +
375I PHE* 4.2 31.3 - - + -
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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