Contacts of the strand formed by residues 3338 - 3345 (chain R) in PDB entry 2FDB
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 GLY3338 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3292R LYS* 3.0 9.6 - - - -
3293R HIS 5.4 1.6 - - - -
3336R ASP 3.5 0.6 + - - -
3337R ALA* 1.3 75.4 - - - +
3339R GLU* 1.3 59.6 + - - -
3340R TYR* 3.5 5.8 - - - -
3356R TRP* 3.5 15.8 - - - -
3357R LEU 2.8 33.6 + - - -
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Residues in contact with GLU3339 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3292R LYS* 3.7 7.4 - - - +
3293R HIS* 3.1 74.2 + - + +
3338R GLY* 1.3 70.9 - - - -
3340R TYR* 1.3 63.9 + - - +
3354R SER* 3.4 24.8 + - - -
3355R ALA 3.3 10.5 - - - +
3356R TRP* 3.5 46.5 - - + +
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Residues in contact with TYR3340 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3263R PRO* 4.4 3.2 - - - +
3276R PHE* 3.6 33.7 - + + -
3290R TRP* 5.2 6.7 - - + -
3291R ILE 3.4 5.2 - - - +
3292R LYS* 3.6 22.5 + - + +
3312R LEU* 3.7 29.4 - - + -
3327R LEU* 4.0 8.5 - - + -
3329R ILE* 3.3 28.4 - - + +
3336R ASP* 2.5 41.5 + - - +
3338R GLY 3.5 7.2 - - - -
3339R GLU* 1.3 77.9 - - - +
3341R THR* 1.3 62.2 + - - +
3353R HIS 4.1 0.2 - - - +
3354R SER* 3.2 2.3 - - - -
3355R ALA* 2.7 42.3 + - - +
3357R LEU* 3.6 17.4 - - + +
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Residues in contact with THR3341 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1032N PHE* 3.6 27.9 - - + -
3289R GLN 3.4 1.6 - - - +
3290R TRP* 3.3 10.6 - - - -
3291R ILE* 2.7 44.9 + - + +
3293R HIS* 2.7 28.2 + - - -
3340R TYR* 1.3 74.3 - - - +
3342R CYS* 1.3 72.5 + - - +
3343R LEU* 4.0 4.7 - - + +
3352R PHE* 3.8 8.1 - - + -
3353R HIS 3.4 9.4 - - - +
3354R SER* 2.6 21.0 + - - +
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Residues in contact with CYS3342 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3258R LEU* 3.7 5.2 - - + +
3263R PRO* 4.2 5.8 - - + +
3278R CYS* 2.6 50.0 - - + -
3280R VAL* 4.6 2.7 - - - -
3288R ILE* 3.6 27.6 - - - -
3289R GLN 3.5 3.4 - - - -
3290R TRP* 3.9 17.9 - - + -
3341R THR* 1.3 72.7 - - - +
3343R LEU* 1.3 57.9 + - - +
3352R PHE* 3.1 24.1 - - - -
3353R HIS 2.9 14.1 + - - +
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Residues in contact with LEU3343 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1032N PHE* 4.1 22.7 - - + -
1035N HIS* 3.6 27.4 - - + -
1036N VAL* 3.7 19.5 - - + -
1093N PHE* 3.6 25.9 - - + -
3287R HIS 3.7 0.9 - - - +
3288R ILE* 3.3 4.2 - - - -
3289R GLN* 2.8 43.2 + - + +
3291R ILE* 3.9 14.8 - - + -
3341R THR* 4.5 2.2 - - + -
3342R CYS* 1.3 71.8 - - - +
3344R ALA* 1.3 71.2 + - - +
3350R ILE* 4.3 9.0 - - + -
3351R SER 3.8 9.4 - - - +
3352R PHE* 3.9 11.4 - - + -
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Residues in contact with ALA3344 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093N PHE* 4.4 0.2 - - - -
3256R PRO* 4.0 8.7 - - + +
3258R LEU* 3.9 12.6 - - + -
3280R VAL* 3.9 34.3 - - + -
3286R PRO* 5.2 0.9 - - + -
3287R HIS 3.3 7.4 - - - +
3288R ILE* 4.2 5.4 - - + -
3342R CYS* 4.0 1.0 + - - -
3343R LEU* 1.3 78.2 - - - +
3345R GLY* 1.3 59.7 + - - +
3350R ILE* 3.2 4.3 - - - +
3351R SER 2.8 38.7 + - - +
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Residues in contact with GLY3345 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1093N PHE* 3.9 13.4 - - - -
1094N GLY 4.4 4.4 + - - -
1095N SER 4.5 0.3 + - - -
3256R PRO* 3.9 4.9 - - - +
3285R GLN 4.2 0.2 - - - +
3286R PRO* 3.2 3.1 - - - +
3287R HIS* 2.9 35.4 + - - +
3344R ALA* 1.3 76.4 - - - +
3346R ASN* 1.3 61.7 + - - -
3349R GLY 3.3 10.3 - - - -
3350R ILE* 4.0 10.3 - - - -
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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