Contacts of the strand formed by residues 291 - 295 (chain B) in PDB entry 4ROE
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 LEU 291 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B LEU* 3.6 38.0 - - + +
273B LEU* 4.0 23.3 - - + -
274B VAL* 3.8 19.5 - - + +
281B SER* 3.6 23.6 - - - +
282B SER 3.5 7.0 - - - +
283B TYR* 3.8 21.1 - - + -
290B GLY* 1.3 71.2 - - - -
292B ILE* 1.3 69.9 + - - +
293B TYR* 3.6 13.2 + - + -
302B LEU 3.3 5.2 - - - +
303B LEU* 3.4 2.0 - - - -
304B ILE* 2.9 39.7 + - + +
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Residues in contact with ILE 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A MET* 3.9 29.8 - - + -
280B PHE 3.5 4.5 - - - +
281B SER* 3.5 0.9 - - - -
282B SER* 2.8 53.2 + - - +
284B GLU 6.4 0.4 - - - +
288B PHE* 5.2 4.9 - - + -
290B GLY 4.2 8.3 - - - +
291B LEU* 1.3 71.4 - - - +
293B TYR* 1.3 59.7 + - - +
294B ARG* 4.0 20.4 + - + +
301B VAL* 3.8 23.3 - - + -
302B LEU 3.6 3.1 - - - -
303B LEU* 3.8 17.0 - - + -
13N T 3.9 20.6 - - + +
14N T 4.0 14.6 - - - +
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Residues in contact with TYR 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B LEU* 4.6 7.4 - - + -
277B HIS* 3.4 37.2 - + + -
280B PHE* 3.2 39.9 - + + -
281B SER* 3.6 14.1 - - - -
291B LEU* 3.6 7.6 + - + -
292B ILE* 1.3 71.9 - - - +
294B ARG* 1.3 62.4 + - - +
295B MET* 3.5 26.1 + - + +
300B ILE 3.6 0.2 - - - +
301B VAL* 3.4 4.1 - - - -
302B LEU* 2.8 47.2 + - + +
304B ILE* 3.7 23.1 - - + -
328B ILE* 3.7 30.1 - - + -
331B ILE* 3.8 9.8 - - + +
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Residues in contact with ARG 294 (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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158A LYS* 3.7 37.4 - - - +
280B PHE* 2.8 37.1 + - - +
282B SER* 6.1 2.2 - - - -
292B ILE* 4.2 17.2 - - + +
293B TYR* 1.3 73.0 - - - +
295B MET* 1.3 64.5 + - - +
296B ILE* 3.6 6.6 + - - +
299B ARG* 6.4 0.2 - - - +
300B ILE 3.9 4.0 - - - -
301B VAL* 3.6 20.0 - - + +
14N T 3.9 30.2 + - - -
15N A 2.8 29.7 + - - -
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Residues in contact with MET 295 (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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280B PHE* 5.0 2.0 - - - -
293B TYR* 3.5 16.0 + - + +
294B ARG* 1.3 73.0 - - - +
296B ILE* 1.3 60.4 + - - +
297B LYS 3.7 11.9 - - - +
298B PRO* 3.0 20.8 - - - +
299B ARG* 3.4 8.1 - - - -
300B ILE 2.9 26.4 + - - +
302B LEU* 3.9 11.0 - - + -
324B ALA* 3.4 45.1 - - - +
327B ASN* 3.8 27.1 - - + +
328B ILE* 3.8 27.1 - - + -
331B ILE* 5.5 2.0 - - + -
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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