Contacts of the strand formed by residues 311 - 315 (chain B) in PDB entry 3CUQ
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 MET 311 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A ALA 4.5 7.4 - - - +
154A LEU 3.7 28.7 + - - +
155A GLY* 4.1 4.0 - - - -
156A THR 5.5 0.2 + - - -
265B SER* 3.5 4.5 - - - -
266B LEU* 2.9 40.5 + - + +
267B THR* 5.9 0.3 - - - +
288B VAL* 4.7 8.3 - - + -
292B LYS* 4.6 12.8 - - - +
303B LEU* 3.5 25.6 - - + -
304B ARG 3.4 4.5 - - - -
305B VAL* 3.3 32.5 - - + -
309B GLY 3.5 9.6 + - - +
310B VAL* 1.3 76.8 - - - +
312B VAL* 1.3 65.2 + - - +
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Residues in contact with VAL 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B ILE* 3.7 31.0 - - + -
264B MET 3.0 21.5 - - - +
265B SER* 3.4 14.6 - - - +
266B LEU 4.0 1.8 - - - +
303B LEU* 3.3 3.9 - - - +
304B ARG* 2.8 45.4 + - + +
306B PHE* 3.8 28.5 - - + -
310B VAL* 4.8 1.6 - - + -
311B MET* 1.3 76.5 - - - +
313B ILE* 1.3 74.3 + - - +
314B GLU* 4.4 2.5 - - + +
352B LEU* 4.1 9.9 - - + -
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Residues in contact with ILE 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B LEU* 4.6 10.1 - - + -
257B LEU* 3.8 15.5 - - + +
263B ILE* 3.3 4.9 - - - +
264B MET 2.7 34.7 + - - +
266B LEU* 3.2 20.2 - - + -
269B VAL* 4.6 11.0 - - + -
291B CYS* 3.1 40.8 - - + -
294B LEU* 4.1 10.1 - - + -
301B LEU* 4.1 25.6 - - + -
302B ARG 3.4 7.2 - - - +
303B LEU* 4.3 5.2 - - + -
312B VAL* 1.3 80.2 - - - +
314B GLU* 1.3 64.1 - - - +
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Residues in contact with GLU 314 (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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257B LEU* 4.7 3.8 - - - -
262B GLY 3.3 15.5 - - - +
263B ILE* 3.2 16.2 - - + +
301B LEU* 3.3 3.7 - - - -
302B ARG* 2.9 49.8 + - + +
304B ARG* 2.7 49.9 + - + +
312B VAL* 4.4 5.6 - - + -
313B ILE* 1.3 78.0 - - - +
315B LEU* 1.3 67.6 + - - +
318B HIS* 3.0 30.9 - - + +
319B LYS* 4.5 1.4 - - - +
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Residues in contact with LEU 315 (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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254B GLN* 3.5 35.4 - - - +
257B LEU* 3.8 27.8 - - + -
258B GLU* 4.2 20.0 - - + +
262B GLY* 3.3 26.1 + - - +
300B PRO* 3.8 4.0 - - + +
301B LEU* 3.9 13.0 - - + +
302B ARG* 5.5 2.5 - - - +
314B GLU* 1.3 79.8 - - - +
316B GLN* 1.3 67.1 + - - +
317B SER* 4.0 15.5 - - - +
318B HIS* 2.9 22.9 + - + +
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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