Contacts of the strand formed by residues 414 - 417 (chain A) in PDB entry 3RSG
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 THR 414 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A ASN 3.7 6.3 + - - +
208A ARG* 3.3 14.5 - - - -
209A TYR* 3.0 24.8 + - - -
385A TYR* 4.6 2.7 - - + -
389A GLU* 2.6 30.7 + - - +
407A ILE* 3.9 27.4 - - + -
408A VAL 3.4 3.8 - - - +
409A THR* 2.8 19.3 + - - -
412A GLU 4.1 2.2 + - - -
413A LYS* 1.3 72.5 + - - +
415A LEU* 1.3 67.1 + - - +
416A PHE* 4.1 21.5 - - + -
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Residues in contact with LEU 415 (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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209A TYR* 3.2 24.9 - - + +
211A ILE* 3.6 17.9 - - + -
215A MET* 3.6 31.0 - - + -
406A THR 3.7 0.7 - - - +
407A ILE* 3.5 4.0 - - - -
408A VAL* 2.8 44.8 + - + +
413A LYS* 4.2 18.4 - - + +
414A THR* 1.3 79.7 - - - +
416A PHE* 1.3 65.6 + - - +
417A ASN 4.2 0.2 - - - -
448A LEU* 4.1 24.5 - - + -
452A THR* 3.6 27.6 - - + +
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Residues in contact with PHE 416 (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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177A ILE* 4.2 29.8 - - + -
180A ILE* 3.4 43.3 - - + -
181A LEU* 4.0 15.3 - - + -
208A ARG* 4.0 26.9 - - + -
209A TYR 2.8 21.1 + - - +
210A VAL* 3.5 10.1 - - + +
211A ILE* 2.9 26.1 + - - -
385A TYR* 4.3 11.7 - + + -
405A THR* 4.1 3.1 - - + -
406A THR 3.4 1.8 - - - -
407A ILE* 3.9 31.9 - - + -
414A THR* 4.1 16.6 - - + -
415A LEU* 1.3 74.4 - - - +
417A ASN* 1.3 59.5 + - - +
418A ILE* 5.0 0.2 - - - -
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Residues in contact with ASN 417 (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 ILE* 4.0 6.8 - - + +
404A ALA 3.9 1.6 + - - +
405A THR* 3.3 11.3 - - - +
406A THR* 2.8 41.5 + - - +
416A PHE* 1.3 73.4 - - - +
418A ILE* 1.3 62.1 + - - +
419A THR* 3.0 40.1 + - - +
455A VAL* 3.4 35.9 + - + +
456A TYR* 3.1 32.9 + - - +
459A GLY* 5.0 0.4 - - - -
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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