Contacts of the strand formed by residues 135 - 140 (chain C) in PDB entry 4B2B
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 GLN 135 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C GLY 3.3 7.5 + - - +
134C THR* 1.3 76.5 - - - +
136C CYS* 1.3 64.7 + - - +
159C LYS* 4.5 6.6 - - + +
160C ALA* 3.4 27.3 + - - +
161C PRO* 3.5 23.3 - - - +
184C TYR* 4.6 2.4 - - - +
201C CYS* 3.7 13.2 - - - +
202C SER* 4.4 4.5 + - - -
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Residues in contact with CYS 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C THR* 3.6 13.0 - - - -
135C GLN* 1.3 76.8 - - - +
137C LEU* 1.3 61.0 + - - +
138C ILE* 4.2 2.5 - - + -
159C LYS* 3.3 9.5 - - - +
160C ALA 2.8 37.0 + - - +
162C ILE* 3.8 16.8 - - - -
183C ALA* 6.2 0.7 - - + -
199C VAL* 3.6 17.5 - - + -
200C VAL 3.2 5.6 - - - +
201C CYS* 2.0 46.2 - - - -
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Residues in contact with LEU 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C TYR* 3.6 23.6 - - - +
26C THR 5.9 0.2 - - - +
27C VAL* 4.4 15.9 - - + -
29C TYR* 3.9 22.3 + - - +
136C CYS* 1.3 74.9 - - - +
138C ILE* 1.3 64.5 + - - +
139C SER* 4.4 2.3 + - - +
157C CYS* 4.0 14.8 - - + -
158C LEU 3.5 15.7 - - - +
159C LYS* 4.3 12.3 - - + +
198C PRO* 3.6 2.6 - - - +
199C VAL* 3.5 1.6 - - - -
200C VAL* 2.7 38.0 + - + +
1250C GOL 4.1 19.7 - - - +
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Residues in contact with ILE 138 (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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16C ILE* 4.1 14.8 - - + +
136C CYS* 5.1 0.9 - - + -
137C LEU* 1.3 77.0 - - - +
139C SER* 1.3 65.2 + - - +
157C CYS* 3.3 3.3 - - - +
158C LEU* 2.8 51.3 + - + +
160C ALA* 3.8 26.5 - - + -
183C ALA* 4.7 4.3 - - + +
190C ALA* 4.4 2.5 - - + +
198C PRO 3.4 11.7 - - - +
199C VAL* 4.0 20.4 - - + -
213C VAL* 3.9 22.4 - - + -
228C TYR* 3.5 33.4 - - + +
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Residues in contact with SER 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ILE* 3.9 8.6 - - - +
22C CYS* 4.5 0.2 - - - -
27C VAL* 3.6 16.7 - - - +
29C TYR* 4.9 0.7 + - - -
30C GLN* 2.7 28.8 + - - +
137C LEU* 5.1 3.4 + - - +
138C ILE* 1.3 81.1 - - - +
140C GLY* 1.3 59.9 + - - +
155C LEU* 4.4 4.9 - - - -
156C LYS 3.1 13.9 - - - -
157C CYS* 4.2 13.9 - - - -
194C ASP* 4.4 5.7 - - - +
197C GLY* 4.6 4.0 - - - -
198C PRO* 3.4 26.0 + - - +
213C VAL* 4.8 0.5 - - - +
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Residues in contact with GLY 140 (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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16C ILE* 3.8 3.8 - - - +
30C GLN* 4.1 8.7 - - - -
139C SER* 1.3 76.6 - - - +
141C TRP* 1.4 58.9 + - - -
142C GLY 3.4 1.1 + - - -
155C LEU* 3.5 15.8 - - - +
156C LYS* 2.9 36.7 + - - +
194C ASP* 3.2 18.8 - - - +
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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