Contacts of the helix formed by residues 262 - 268 (chain B) in PDB entry 3A4Y
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 PRO 262 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258B LEU 3.3 9.0 - - - +
259B SER* 3.2 20.0 - - - +
260B LEU 3.2 0.4 - - - -
261B TYR* 1.3 93.2 - - + +
263B ARG* 1.3 58.0 + - + +
264B LEU 3.2 0.4 - - - -
265B VAL* 3.3 21.6 - - - +
276B PHE* 4.0 19.2 - - + -
281B ASN* 3.6 26.0 - - - +
284B ARG* 6.1 0.2 - - - +
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Residues in contact with ARG 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ARG* 5.8 1.0 - - - -
88B LEU* 3.7 20.8 - - - +
259B SER 5.3 2.7 - - - +
260B LEU* 3.0 30.8 + - + +
262B PRO* 1.3 79.3 - - + +
264B LEU* 1.3 71.7 + - + +
265B VAL* 3.7 2.7 - - - -
266B ARG* 5.5 3.5 + - - +
267B TYR* 5.3 1.4 - - - -
433B SO4 2.8 51.1 + - - +
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Residues in contact with LEU 264 (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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84B ARG* 5.5 1.3 - - - -
85B ALA* 3.7 38.1 - - + +
88B LEU* 3.7 27.8 - - + -
89B LEU* 4.6 4.9 - - + -
143B PRO* 4.3 14.1 - - + -
260B LEU* 4.2 28.3 - - + +
261B TYR* 2.9 21.3 + - + +
263B ARG* 1.3 92.3 - - - +
265B VAL* 1.3 58.5 + - - +
266B ARG* 3.2 4.5 - - - -
267B TYR* 2.8 38.0 + - + +
268B PHE* 3.6 11.2 - - + -
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Residues in contact with VAL 265 (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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261B TYR 3.6 2.4 + - - -
262B PRO 3.3 21.8 - - - +
263B ARG 4.7 1.6 - - - -
264B LEU* 1.3 72.2 - - - +
266B ARG* 1.3 61.0 + - + +
267B TYR 3.0 4.7 + - - -
268B PHE* 3.2 18.6 + - - +
273B GLN* 3.2 37.4 - - + +
276B PHE* 4.1 35.0 - - + -
277C LEU* 6.3 2.5 - - + -
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Residues in contact with ARG 266 (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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84B ARG* 3.5 35.2 - - - +
122B GLU* 4.0 18.6 + - - +
263B ARG 5.5 3.0 + - - +
264B LEU* 4.6 2.5 - - - -
265B VAL* 1.3 78.5 - - + +
267B TYR* 1.3 92.5 + - + +
268B PHE 3.5 0.7 - - - +
273B GLN* 3.8 20.6 + - - +
433B SO4 5.1 2.2 + - - -
266C ARG* 6.4 1.8 - - + -
270C GLU* 4.2 19.4 + - - -
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Residues in contact with TYR 267 (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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83B THR* 4.2 2.5 - - - -
84B ARG* 3.3 6.7 + - + +
85B ALA* 3.3 36.4 + - + -
122B GLU* 2.7 38.8 + - - -
123B TYR* 4.0 17.9 - + - -
138B GLN* 5.0 4.0 + - - +
143B PRO* 4.4 13.7 - - + +
144B GLY* 3.6 31.5 + - - +
171B LEU* 4.5 4.5 - - - +
172B PRO* 3.3 21.7 - - - +
263B ARG 5.4 0.7 - - - -
264B LEU* 2.8 27.0 + - + +
266B ARG* 1.3 113.6 - - + +
268B PHE* 1.3 63.7 + - - +
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Residues in contact with PHE 268 (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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143B PRO* 3.8 22.0 - - + -
170B VAL* 3.5 26.7 - - + -
171B LEU* 3.9 5.6 - - + -
172B PRO* 3.9 8.4 - - - +
261B TYR* 3.3 66.6 - + - -
264B LEU* 3.6 16.4 - - + -
265B VAL* 3.2 16.5 + - - +
266B ARG 4.3 1.0 - - - +
267B TYR* 1.3 81.9 - - - +
269B SER* 1.3 68.4 + - - +
272B VAL* 3.5 28.3 - - + -
273B GLN* 3.2 14.9 + - - -
276B PHE* 4.6 1.8 - + - -
283B PHE* 3.7 13.5 - + - -
443B SO4 4.5 1.2 + - - -
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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