Contacts of the strand formed by residues 130 - 135 (chain B) in PDB entry 6CXI
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B PRO* 3.2 24.2 - - + +
123B PHE* 4.6 0.9 - - - -
128B THR* 3.0 20.0 + - - -
129B PRO* 1.3 85.2 - - + +
131B MET* 1.3 63.4 + - - +
355B TRP* 3.7 22.4 - - + -
356B ILE 3.2 13.5 - - - +
357B SER* 3.8 10.3 - - - +
358B LYS 4.2 0.9 - - - +
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Residues in contact with MET 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B VAL* 3.4 21.8 - - + +
104B LEU* 4.3 13.2 - - + -
118B MET* 4.2 1.6 - - + +
119B THR* 3.6 29.4 - - + +
122B MET* 3.3 41.1 - - + -
123B PHE* 3.4 37.0 - - + -
128B THR* 4.7 2.2 - - + -
130B ALA* 1.3 76.6 - - - +
132B TYR* 1.3 61.5 + - - +
133B VAL* 4.6 9.4 - - + -
355B TRP* 3.3 9.9 - - - -
356B ILE* 2.6 44.4 + - + +
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Residues in contact with TYR 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B VAL 3.5 1.2 + - - +
103B LEU* 3.3 17.9 - - + +
104B LEU* 3.6 12.3 + - - +
131B MET* 1.3 79.9 - - - +
133B VAL* 1.3 97.9 + - - +
134B ALA* 3.9 9.6 - - + -
345B LEU* 4.8 0.7 - - + -
351B PHE* 3.4 33.4 - + + -
354B MET* 3.4 54.2 - - + +
355B TRP* 3.1 27.7 - - + -
356B ILE* 4.6 9.9 - - + -
372B LYS* 5.8 1.3 - - + -
373B CYS* 3.8 26.8 - - + +
374B PHE* 5.2 0.9 + - - +
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Residues in contact with VAL 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LEU* 4.0 6.3 - - + +
106B GLU* 3.1 38.6 - - + +
115B ARG* 4.7 11.7 - - + +
118B MET* 5.5 10.8 - - - -
119B THR* 3.8 29.6 - - + -
131B MET* 4.6 5.8 - - + -
132B TYR* 1.3 97.9 + - - +
134B ALA* 1.3 61.9 + - - +
356B ILE* 5.0 6.0 - - + +
369B VAL* 5.2 8.1 - - + -
373B CYS* 4.3 15.7 - - - -
374B PHE* 5.7 0.3 - - - +
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Residues in contact with ALA 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU* 3.9 12.6 - - + -
104B LEU 3.3 9.9 + - - +
105B THR* 4.8 2.0 - - - -
106B GLU* 2.9 31.9 + - - +
132B TYR* 3.9 6.2 + - + -
133B VAL* 1.3 75.5 - - - +
135B ILE* 1.3 61.3 + - - +
139B LEU* 3.5 28.0 - - + -
345B LEU* 3.6 18.4 - - + -
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Residues in contact with ILE 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B THR* 4.8 0.7 - - - -
106B GLU* 3.1 17.0 - - + +
107B ALA 3.4 3.8 - - - +
108B PRO* 3.2 43.7 - - + -
115B ARG* 4.7 13.0 - - - +
134B ALA* 1.3 75.1 - - - +
136B GLN* 1.3 64.4 + - - +
137B ALA* 4.5 5.4 - - + +
138B VAL* 3.4 34.8 - - + +
139B LEU* 2.8 28.8 + - + +
162B VAL* 5.5 2.7 - - + -
374B PHE* 6.5 0.9 - - + -
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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