Contacts of the strand formed by residues 396 - 400 (chain A) in PDB entry 3FVS
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 TYR 396 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A PRO* 3.7 23.7 - - - +
160A TRP* 3.8 18.2 - + - -
332A ILE* 3.7 23.1 - - + -
341A ILE* 3.8 19.5 - - + -
342A THR 3.3 6.1 - - - +
343A ASP* 3.8 28.1 + - - -
344A ILE* 4.3 0.2 - - - +
363A ASP* 3.2 8.9 + - - +
381A VAL* 3.0 47.0 + - + +
393A PHE* 4.2 22.4 + + + -
394A ASP 3.7 0.8 + - - -
395A HIS* 1.3 116.9 + + - +
397A ILE* 1.3 67.6 + - - +
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Residues in contact with ILE 397 (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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329A LEU* 4.3 2.9 - - + -
340A LEU 4.0 0.2 - - - +
341A ILE* 3.1 3.1 - - - -
342A THR* 2.9 51.2 + - - +
344A ILE* 3.8 25.4 - - + -
363A ASP* 4.1 12.6 - - + +
366A PHE* 3.9 17.3 - - + -
367A VAL* 3.5 23.6 - - + -
370A MET* 4.0 5.6 - - + -
378A ALA* 3.9 11.9 - - + -
379A ILE 3.4 7.6 - - - +
380A PRO* 4.3 1.6 - - + -
381A VAL* 3.7 4.9 - - - -
396A TYR* 1.3 79.5 - - - +
398A ARG* 1.3 58.8 + - - +
399A PHE* 3.5 28.9 + - + -
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Residues in contact with ARG 398 (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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18A TRP* 3.9 15.6 - - - -
33A LEU 4.1 2.4 - - - +
34A GLY 3.0 27.5 + - - -
36A GLY* 4.2 4.8 - - - +
125A PHE* 6.0 0.2 - - - -
185A ASN* 3.0 23.6 + - - +
186A PRO* 3.5 24.7 - - + +
339A PHE* 3.3 54.2 - - + -
340A LEU 3.5 5.8 - - - +
341A ILE* 4.1 1.8 - - + -
378A ALA* 3.3 6.6 - - - +
379A ILE* 2.7 61.0 + - + +
381A VAL* 3.7 12.1 - - + +
384A PHE* 3.7 16.6 - - + -
397A ILE* 1.3 72.4 - - - +
399A PHE* 1.3 64.6 + - - +
400A CYS* 5.4 0.4 - - - +
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Residues in contact with PHE 399 (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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33A LEU* 3.6 32.3 - - + -
320A MET* 3.7 16.2 - - - -
324A LEU* 3.7 30.1 - - + -
329A LEU* 4.0 16.6 - - + -
339A PHE* 3.3 8.9 - - - +
340A LEU* 2.8 38.9 + - + +
342A THR* 3.4 31.4 - - + -
370A MET* 4.1 11.0 - - + -
376A LEU* 5.0 5.6 - - + -
377A VAL 4.2 4.0 - - - -
378A ALA* 3.8 13.7 - - + -
397A ILE* 3.5 26.5 - - + -
398A ARG* 1.3 77.5 - - - +
400A CYS* 1.3 59.8 + - - +
401A PHE 4.1 0.4 + - - -
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Residues in contact with CYS 400 (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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33A LEU* 2.8 19.6 + - - +
34A GLY 5.0 0.7 - - - -
35A GLN 3.4 28.5 - - - +
36A GLY* 4.1 3.8 - - - -
37A PHE 4.3 3.6 - - - -
320A MET* 3.5 13.0 - - - +
338A TYR* 3.5 27.1 - - - -
339A PHE* 3.9 14.1 - - + -
398A ARG* 5.5 0.4 - - - +
399A PHE* 1.3 75.1 - - - +
401A PHE* 1.3 61.6 + - - +
402A VAL* 3.7 14.8 - - - -
403A LYS* 3.5 23.1 - - - +
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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