Contacts of the strand formed by residues 370 - 374 (chain A) in PDB entry 2FQ6
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 370 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ILE* 3.6 25.4 - - + -
160A THR* 4.1 22.9 - - + -
287A ASN* 3.9 11.7 - - - +
312A SER* 3.6 28.3 - - - +
313A PHE 3.5 9.0 - - - +
314A VAL* 4.3 8.3 - - + +
349A ALA* 3.3 4.2 - - - -
350A ASN* 2.8 56.5 + - + +
355A ILE* 5.2 0.9 - - + -
366A PHE* 4.0 24.5 - - + -
368A GLY 3.4 2.0 + - - -
369A THR* 1.3 72.4 - - - +
371A ILE* 1.3 68.5 + - - +
372A ARG* 4.0 3.4 - - + +
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Residues in contact with ILE 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A SER* 3.1 3.6 - - - -
313A PHE* 2.7 73.1 + - + +
315A LEU* 3.9 22.7 - - + -
319A LEU* 5.3 0.4 - - + -
327A TYR* 3.9 21.8 - - + +
328A LEU* 4.9 1.6 - - + -
347A ILE* 3.6 31.4 - - + -
348A LEU 3.5 1.6 - - - +
349A ALA* 3.6 28.9 - - + -
369A THR* 4.0 9.6 - - + -
370A LEU* 1.3 77.0 - - - +
372A ARG* 1.3 59.5 + - - +
373A LEU* 3.8 4.0 - - + -
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Residues in contact with ARG 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A TYR* 6.1 1.6 - - - -
158A SER* 5.9 2.2 - - - +
159A ILE* 4.3 34.0 - - + +
161A MET* 5.2 0.9 - - - -
310A LEU* 3.9 27.7 - - + +
311A PHE 3.3 19.5 - - - +
312A SER* 3.8 8.7 - - - -
337A ALA 4.8 0.6 + - - -
339A SER 3.8 8.7 + - - +
340A TRP* 3.7 25.5 - - - +
346A LEU 3.8 0.3 - - - +
347A ILE* 3.4 5.7 - - - +
348A LEU* 2.8 64.9 + - + +
350A ASN* 5.1 5.4 - - - +
370A LEU* 4.0 8.7 - - + +
371A ILE* 1.3 72.6 - - - +
373A LEU* 1.3 59.4 + - - +
700A P3F 2.9 31.1 + - - -
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Residues in contact with LEU 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A VAL* 4.3 0.2 - - + -
277A LEU* 4.0 6.5 - - + -
309A GLY 3.7 1.6 - - - +
310A LEU* 3.4 7.3 - - - +
311A PHE* 2.8 64.2 + - + +
313A PHE* 3.7 26.5 - - + -
334A PHE* 4.0 14.4 - - + -
346A LEU 3.4 2.0 - - - +
347A ILE* 3.6 33.4 - - + -
371A ILE* 3.8 8.3 + - + -
372A ARG* 1.3 73.5 - - - +
374A HIS* 1.3 60.7 + - - +
375A ILE* 3.9 16.4 - - + -
387A LEU* 4.0 20.9 - - + -
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Residues in contact with HIS 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A TYR* 2.9 31.0 + + - -
266A HIS* 3.8 1.6 - + - -
309A GLY 3.7 7.6 - - - -
310A LEU* 3.8 15.2 - - + +
334A PHE* 4.1 1.6 - - - -
340A TRP* 3.9 12.6 - - + -
341A GLY* 3.3 27.3 + - - -
342A GLY 3.1 29.3 + - - -
344A GLU 3.1 20.4 + - - -
345A SER* 2.9 10.2 - - - -
346A LEU* 2.9 45.1 + - + +
372A ARG 4.3 0.2 - - - -
373A LEU* 1.3 70.8 - - - +
375A ILE* 1.3 77.6 + - - +
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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