Contacts of the strand formed by residues 413 - 419 (chain A) in PDB entry 3IND
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 ARG 413 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A TYR* 3.4 47.1 + - + -
253A THR 3.4 15.3 - - - +
254A PRO* 4.3 2.0 - - + -
255A ILE* 3.6 5.3 - - - +
352A GLU* 2.8 36.9 + - + +
408A ASP* 2.9 57.3 + - + +
411A ARG* 3.2 55.7 - - - +
412A LYS* 1.3 78.6 - - - +
414A ILE* 1.3 67.7 + - - +
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Residues in contact with ILE 414 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A TRP 3.5 1.9 - - - +
252A TYR* 3.3 4.6 - - - -
253A THR* 2.8 45.5 + - + +
255A ILE* 3.7 18.2 - - + -
261A TYR* 3.8 31.0 - - + -
263A VAL* 4.0 8.5 - - + -
289A VAL* 3.8 17.9 - - + -
405A VAL* 3.7 17.9 - - + -
406A VAL 3.1 10.8 - - - +
407A PHE* 4.2 11.7 - - + -
413A ARG* 1.3 80.3 - - - +
415A GLY* 1.3 62.3 + - - +
416A PHE* 3.5 26.4 - - + -
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Residues in contact with GLY 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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250A LEU* 3.8 11.0 - - - -
251A TRP 3.0 8.5 - - - -
252A TYR* 3.3 23.0 - - - -
404A TYR 3.4 0.2 - - - +
405A VAL* 3.3 7.3 - - - +
406A VAL* 2.8 38.8 + - - -
414A ILE* 1.3 74.0 - - - +
416A PHE* 1.3 64.6 + - - -
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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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250A LEU* 3.4 3.4 - - - +
251A TRP 2.7 34.6 + - - +
253A THR* 4.4 4.5 - - + -
263A VAL* 5.8 0.4 - - + -
289A VAL* 4.5 12.6 - - + -
349A LEU* 3.7 22.7 - - + -
358A PHE* 4.1 7.4 - + + -
360A ILE* 4.0 31.0 - - + -
395A MET* 3.6 29.6 - - + -
399A ILE* 5.6 1.3 - - + -
400A MET* 5.4 3.4 - - + -
403A PHE* 4.3 13.7 - + + -
404A TYR 3.5 2.5 - - - -
405A VAL* 3.8 29.2 - - + -
414A ILE* 3.5 32.3 - - + -
415A GLY* 1.3 75.7 - - - -
417A ALA* 1.3 61.8 + - - +
432A VAL* 3.4 12.1 - - + +
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Residues in contact with ALA 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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246A TYR* 3.4 31.2 - - + -
247A THR 4.3 0.9 - - - +
249A SER 3.6 13.5 - - - +
250A LEU* 3.3 19.3 - - + -
403A PHE* 3.1 4.2 - - - +
404A TYR 2.6 38.5 + - - +
416A PHE* 1.3 75.6 - - - +
418A VAL* 1.3 59.7 + - - +
432A VAL* 3.7 9.6 - - - -
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Residues in contact with VAL 418 (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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246A TYR* 3.2 6.2 - - - +
247A THR* 3.0 52.9 + - - +
248A GLY* 6.2 0.4 - - - -
249A SER 5.0 0.2 + - - -
402A GLY 4.2 4.3 - - - +
403A PHE* 4.3 2.7 - - + -
417A ALA* 1.3 71.2 - - - +
419A SER* 1.3 71.2 + - - +
422A HIS* 3.8 21.3 - - + +
430A ALA 3.7 18.4 - - - +
431A ALA* 3.8 2.9 - - - -
432A VAL* 3.6 29.2 - - + +
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Residues in contact with SER 419 (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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215A GLN* 2.9 30.8 + - - +
245A LEU 3.7 4.9 - - - -
247A THR* 4.9 1.3 + - - +
401A GLU 4.4 2.0 - - - -
402A GLY 3.1 25.4 + - - -
403A PHE 3.4 18.2 - - - -
404A TYR 3.8 3.4 - - - +
417A ALA 3.2 1.4 + - - -
418A VAL* 1.3 77.9 - - - +
420A ALA* 1.3 61.2 + - - +
421A CYS* 3.0 13.4 + - - -
422A HIS* 3.4 24.5 - - - -
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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