Contacts of the strand formed by residues 128 - 133 (chain I) in PDB entry 6O81
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 LEU 128 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121I PHE* 4.3 2.5 - - - -
126I ALA* 3.4 3.9 - - - +
127I SER* 1.3 86.0 - - - +
129I ALA* 1.3 70.8 + - - +
130I MET* 4.0 25.1 - - + -
205I TYR* 5.1 7.9 - - + -
206I CYS 3.3 11.4 - - - +
207I LEU* 4.0 24.2 - - + -
211I ILE* 5.5 3.6 - - + -
228I LEU* 3.7 29.2 - - + +
229I ILE* 5.1 3.4 - - + +
232I LEU* 5.0 6.1 - - + -
262I ASP 3.4 2.9 + - - +
263I ILE* 3.4 29.1 - - + -
264I TYR 2.9 24.1 + - - -
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Residues in contact with ALA 129 (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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117I VAL* 3.9 19.5 - - + +
120I LEU* 4.8 1.1 - - + -
121I PHE* 3.8 34.8 - - + +
128I LEU* 1.3 79.6 - - - +
130I MET* 1.3 60.9 + - - +
204I LEU 3.6 1.4 - - - +
205I TYR* 3.4 5.0 - - - -
206I CYS* 3.1 33.7 + - - -
264I TYR* 3.2 13.9 - - + +
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Residues in contact with MET 130 (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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117I VAL* 3.8 8.3 - - - +
128I LEU* 4.0 15.7 - - + -
129I ALA* 1.3 75.8 - - - +
131I LEU* 1.3 60.3 + - - +
132I MET* 3.8 24.5 - - + -
167I LEU* 3.7 20.4 - - - -
170I MET* 4.5 16.8 - - + +
201I ASP* 3.8 13.9 - - - +
204I LEU 3.4 6.1 - - - -
205I TYR* 3.6 35.0 - - + -
229I ILE* 5.3 7.0 - - + -
263I ILE* 5.1 0.2 - - - -
264I TYR 2.9 10.7 + - - +
265I SER* 3.0 20.1 - - - -
266I PHE 2.9 23.2 + - - -
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Residues in contact with LEU 131 (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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110I THR* 4.4 18.4 - - + -
112I VAL* 5.0 8.7 - - + -
114I LEU* 5.9 1.6 - - + -
116I GLU* 3.8 11.0 - - - +
117I VAL* 4.7 7.9 - - + -
130I MET* 1.3 76.7 - - - +
132I MET* 1.3 72.9 + - - +
133I ARG* 5.9 0.4 - - + -
201I ASP* 4.0 3.8 - - - +
202I ALA* 3.4 38.7 + - + +
203I HIS 4.6 0.3 + - - -
204I LEU* 3.6 38.4 + - + +
266I PHE* 3.4 38.4 - - + +
268I LYS* 3.9 10.8 - - + -
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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
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130I MET* 3.8 35.7 - - + -
131I LEU* 1.3 84.0 - - - +
133I ARG* 1.3 63.6 + - - +
156I ASP* 5.3 2.5 - - - +
158I ILE* 3.8 37.7 - - + -
167I LEU* 5.0 1.1 - - + -
170I MET* 4.4 9.6 - - + -
199I LEU* 3.7 29.2 - - + -
200I VAL 3.3 16.6 - - - +
201I ASP* 4.6 9.0 - - - +
202I ALA* 4.7 1.1 - - - +
265I SER* 4.9 7.2 - - - -
266I PHE 2.9 7.6 + - - +
267I ILE* 3.5 18.8 - - + -
268I LYS 2.9 24.0 + - - -
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Residues in contact with ARG 133 (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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131I LEU* 5.9 0.9 - - + -
132I MET* 1.3 77.6 - - - +
134I LYS* 1.3 62.1 + - - +
199I LEU* 3.4 9.2 - - - -
200I VAL* 2.8 38.7 + - + +
202I ALA* 5.5 5.6 - - + +
268I LYS* 4.0 16.4 - - + +
271I ASN 3.5 24.2 - - - +
272I THR* 4.3 10.8 - - - -
273I LEU 5.3 0.4 - - - +
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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