Contacts of the strand formed by residues 129 - 133 (chain C) in PDB entry 6BW4
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 ARG 129 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B ARG* 4.4 14.6 - - - +
45C LEU 5.4 2.8 + - - -
46C THR* 3.7 7.6 - - - +
127C VAL* 3.3 4.7 - - - +
128C ASN* 1.3 81.4 + - - +
130C ALA* 1.3 61.9 + - - +
131C ARG* 3.6 45.3 - - + +
142C THR* 3.1 7.4 - - - -
143C LYS* 2.9 31.4 + - + +
181C TYR* 3.2 48.2 + - - +
183C LEU* 4.0 15.5 + - + +
231C GLU 4.8 1.2 + - - -
232C ASP* 3.4 29.1 + - - -
277C ASN 5.7 0.8 + - - -
321C PHE 5.1 4.9 + - - -
322C GLN* 4.3 16.3 - - - +
378C SER 5.0 7.9 + - - -
379C ASP* 4.6 4.8 + - - -
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Residues in contact with ALA 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C THR* 3.1 14.5 + - + -
48C GLN* 3.9 6.6 - - - +
67C VAL* 3.7 26.9 - - + +
79C LEU* 3.8 18.6 - - + -
127C VAL* 3.9 11.0 - - + -
129C ARG* 1.3 74.9 - - - +
131C ARG* 1.3 82.0 + - - +
140C ILE* 4.1 1.6 - - + -
141C ALA 3.2 9.6 - - - +
142C THR* 4.1 1.1 - - + -
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Residues in contact with ARG 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C THR* 3.2 17.2 + - - -
47C ALA 3.5 14.1 + - - -
48C GLN* 3.2 29.8 - - - +
67C VAL* 5.9 0.2 - - - -
129C ARG* 3.6 32.2 - - + +
130C ALA* 1.3 97.3 + - - +
132C TYR* 1.3 60.8 + - - +
140C ILE* 4.1 4.2 - - - +
141C ALA 2.9 23.9 + - - -
183C LEU* 3.9 31.3 + - + +
184C SER* 5.6 0.4 - - - -
185C TRP* 2.9 30.6 + - + +
322C GLN* 3.8 9.1 - - - +
324C GLN* 5.6 2.6 - - - +
379C ASP* 3.0 28.7 + - - -
380C PHE 5.6 0.4 + - - -
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Residues in contact with TYR 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C GLN* 2.9 45.6 + - + +
49C TRP 3.4 22.3 + - - -
50C LEU* 3.9 27.8 - - + -
51C PRO* 3.8 31.3 - - + +
67C VAL* 4.8 2.6 - - + +
131C ARG* 1.3 73.9 - - - +
133C MET* 1.3 70.7 + - - +
134C PRO* 3.4 28.9 - - + +
137C PRO* 3.6 19.1 - - + +
139C ILE 3.3 9.4 - - - +
140C ILE* 4.1 8.0 - - + +
185C TRP* 3.1 11.8 - - - -
384C PRO* 6.1 0.3 - - - +
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Residues in contact with MET 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C TYR* 1.3 72.0 - - - +
134C PRO* 1.4 67.6 - - + +
135C GLN* 3.6 21.3 - - - +
136C ASN* 3.0 42.9 - - - +
137C PRO* 3.1 5.4 - - - +
139C ILE* 2.8 28.0 + - + +
185C TRP* 3.2 50.4 - - + +
190C SER* 4.7 2.0 - - - -
191C GLY* 3.8 18.6 - - - +
207C ILE* 3.3 23.1 - - + -
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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
------------------------------------------------------------
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