Contacts of the strand formed by residues 125 - 130 (chain B) in PDB entry 3RCY
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 ILE 125 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B ASN* 4.2 16.8 - - + +
124B ARG* 1.3 75.4 - - - +
126B ARG* 1.3 75.8 + - - +
127B ALA 3.4 0.3 + - - -
322B VAL* 3.4 43.1 - - + +
325B ALA* 4.0 10.3 - - + -
326B ALA* 3.7 13.5 - - - +
331B ILE* 4.4 13.5 - - + -
334B CYS* 3.7 26.9 - - + -
356B TYR* 3.3 4.1 - - - -
357B ILE* 2.7 48.2 + - + +
359B PRO* 4.0 12.1 - - + -
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Residues in contact with ARG 126 (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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124B ARG 4.1 1.4 + - - -
125B ILE* 1.3 75.7 - - - +
127B ALA* 1.3 57.8 + - - +
162B THR* 2.8 45.6 + - - +
163B ALA* 4.1 0.8 - - - +
204B ASP* 2.7 30.5 + - - -
231B LEU* 4.4 2.8 - - - +
331B ILE* 6.0 0.4 - - - +
332B LEU* 3.8 31.9 + - - +
333B MET* 3.2 31.4 - - + +
334B CYS 2.7 31.4 + - - -
356B TYR* 3.6 30.1 + - + -
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Residues in contact with ALA 127 (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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125B ILE 3.4 0.8 + - - -
126B ARG* 1.3 82.3 - - - +
128B TYR* 1.3 63.0 + - - +
161B TYR* 3.7 14.0 - - + -
162B THR* 4.4 8.0 + - - -
163B ALA* 4.7 1.4 + - - +
333B MET* 4.8 0.7 - - - -
334B CYS 3.3 4.9 - - - +
336B SER* 3.6 19.3 - - - +
352B VAL* 4.1 17.9 - - + -
355B GLY 3.0 20.3 + - - +
357B ILE* 3.8 16.4 - - + -
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Residues in contact with TYR 128 (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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127B ALA* 1.3 75.4 - - - +
129B THR* 1.3 72.4 + - - +
130B TYR 5.0 0.2 - - - -
161B TYR* 3.7 7.0 - - - -
163B ALA* 3.4 29.6 - - + +
165B LYS* 3.0 38.8 + - + -
206B LEU* 3.4 18.2 - - + -
232B TRP* 3.5 25.2 - + - -
281B GLN* 4.4 3.3 + - - -
308B ALA* 5.2 3.8 + - + -
309B PRO 5.1 1.1 + - - -
310B HIS* 5.5 0.2 - - - -
333B MET* 3.4 26.0 - - + -
334B CYS 3.0 7.0 + - - -
335B GLU* 3.1 51.0 + - + +
336B SER* 2.8 30.0 + - - +
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Residues in contact with THR 129 (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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128B TYR* 1.3 82.6 - - - +
130B TYR* 1.3 80.1 + - - +
132B TYR* 3.5 16.1 - - - -
156B CYS* 3.7 25.4 - - + -
159B ARG* 5.0 2.2 - - - +
161B TYR* 3.8 32.1 - - + -
163B ALA 3.9 3.0 + - - +
164B VAL* 3.5 5.6 - - + -
165B LYS 3.0 20.8 + - - -
335B GLU* 5.7 0.2 - - - -
336B SER 3.7 13.5 + - - -
337B ILE* 5.0 1.8 - - - -
338B GLU 5.2 1.8 + - - -
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Residues in contact with TYR 130 (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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128B TYR* 4.6 1.6 - - - -
129B THR* 1.3 95.8 + - - +
131B LEU* 1.3 66.8 + - - +
132B TYR* 3.4 41.3 + + + -
143B TRP* 6.2 3.1 - + + -
156B CYS* 4.6 1.6 - - - -
165B LYS* 3.3 47.9 + - + +
166B PHE* 4.1 12.3 - - - -
167B ASP* 4.7 1.6 - - + -
208B GLY 4.1 2.6 + - - -
210B HIS* 3.2 34.5 + + - -
234B GLU* 5.4 0.9 + - - -
311B LEU 5.8 0.2 - - - -
312B TYR* 4.3 21.1 - + + -
335B GLU* 3.8 22.1 + - + +
336B SER 4.6 1.4 + - - -
337B ILE* 6.1 0.7 - - + -
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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