Contacts of the strand formed by residues 341 - 346 (chain F) in PDB entry 6FF7
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 341 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334F ALA 3.8 0.2 - - - +
335F PHE* 3.5 4.5 - - - +
336F HIS* 2.9 45.8 + - + +
339F GLU* 2.7 14.6 + - + +
340F PRO* 1.3 73.9 - - - +
342F ILE* 1.3 60.9 + - - +
343F ILE 4.1 0.6 + - - -
353F MET* 5.7 6.7 - - + -
354F GLY 3.2 8.1 - - - +
355F GLU* 4.6 3.8 - - + +
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Residues in contact with ILE 342 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333F VAL* 6.3 2.5 - - + -
334F ALA 3.3 8.1 - - - +
335F PHE* 4.8 1.1 - - - +
340F PRO 4.3 0.4 + - - -
341F ILE* 1.3 74.2 - - - +
343F ILE* 1.3 61.1 + - - +
344F SER* 3.7 3.5 + - - -
352F TYR 3.1 5.0 - - - +
353F MET* 3.4 3.0 - - - -
354F GLY* 2.8 43.1 + - - +
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Residues in contact with ILE 343 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F CYS* 5.3 12.0 - - + +
73F LYS 6.4 1.6 - - - -
332F GLU 3.7 1.7 - - - +
333F VAL* 3.4 4.6 - - - +
334F ALA* 2.8 50.1 + - + +
341F ILE 4.1 1.2 + - - -
342F ILE* 1.3 72.1 - - - +
344F SER* 1.3 61.0 + - - +
345F ALA* 4.0 1.0 + - - +
351F LEU* 6.2 2.7 - - + -
352F TYR 3.4 6.5 - - - +
353F MET* 4.9 1.3 - - + +
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Residues in contact with SER 344 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309F VAL* 5.2 14.4 - - - -
330F ILE* 6.1 4.5 - - - -
332F GLU 3.8 3.4 - - - -
333F VAL* 4.7 5.6 - - - +
342F ILE* 3.7 3.8 + - - -
343F ILE* 1.3 74.1 - - - +
345F ALA* 1.3 59.5 + - - +
346F SER* 5.5 0.8 - - - -
350F ARG 3.9 1.7 - - - +
351F LEU* 3.4 10.7 - - - +
352F TYR* 3.1 37.6 + - - -
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Residues in contact with ALA 345 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69F VAL* 4.5 18.4 - - + +
71F CYS* 4.6 8.1 - - - +
72F CYS* 4.1 24.2 - - + -
330F ILE* 3.7 3.7 - - - +
331F ASN 2.8 21.7 + - - -
332F GLU* 2.9 24.6 + - + +
343F ILE 4.0 0.2 + - - -
344F SER* 1.3 74.1 - - - +
346F SER* 1.3 61.9 + - - +
350F ARG 4.4 2.9 - - - -
351F LEU* 5.1 3.8 - - + +
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Residues in contact with SER 346 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69F VAL* 3.3 28.8 + - - +
326F HIS* 4.5 18.8 - - - -
328F GLY 4.7 0.7 - - - -
329F SER 3.2 16.6 - - - -
330F ILE* 3.8 8.3 - - - -
331F ASN 3.9 3.4 - - - +
344F SER 5.5 0.4 - - - -
345F ALA* 1.3 77.2 - - - +
347F SER* 1.3 62.4 - - - +
348F ASP* 3.1 12.6 + - - -
349F LYS* 3.3 8.4 + - - -
350F ARG 4.0 12.0 + - - -
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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