Contacts of the helix formed by residues 434 - 442 (chain B) in PDB entry 3L9X
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 HIS 434 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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407B PHE* 3.3 33.2 + - + +
408B GLY* 3.7 12.8 - - - -
412B GLN* 3.7 12.1 + - - +
429B ASP* 3.0 35.9 + - - +
431B ASP* 3.1 32.0 + - + +
433B ASP* 1.3 83.9 - - + +
435B ILE* 1.3 64.5 + - - +
436B GLU 3.4 2.9 - - - -
437B THR* 3.3 9.0 + - - -
438B LEU* 3.0 32.7 + - + +
1180B SO4 5.4 2.0 - - - -
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Residues in contact with ILE 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429B ASP* 6.0 0.2 - - - +
431B ASP 3.8 1.3 + - - +
432B PRO* 3.4 36.4 + - + +
433B ASP 3.5 0.2 - - - -
434B HIS* 1.3 76.7 - - - +
436B GLU* 1.3 73.9 + - + +
438B LEU* 3.3 8.9 + - - +
439B ARG* 2.9 30.9 + - + +
445B VAL* 6.4 0.2 - - - -
447B TYR* 4.0 27.4 - - + +
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Residues in contact with GLU 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432B PRO 4.9 0.4 + - - -
433B ASP 4.8 3.8 + - - +
434B HIS 3.4 0.6 - - - -
435B ILE* 1.3 89.5 - - + +
437B THR* 1.3 60.3 + - - +
439B ARG* 2.8 43.7 + - - +
440B LYS* 2.9 46.4 + - - +
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Residues in contact with THR 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407B PHE* 3.8 14.4 - - + -
412B GLN* 3.7 29.2 + - - +
433B ASP 4.8 3.7 + - - -
434B HIS* 3.3 14.0 + - - -
436B GLU* 1.3 77.4 - - - +
438B LEU* 1.3 63.1 + - - +
440B LYS* 3.3 9.2 + - - +
441B PHE* 3.2 44.9 + - + -
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Residues in contact with LEU 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407B PHE* 3.6 32.1 - - + -
427B VAL* 3.8 23.1 - - + -
429B ASP* 4.1 25.6 - - + +
434B HIS* 3.0 23.9 + - + +
435B ILE* 3.6 7.0 - - - +
437B THR* 1.3 79.7 - - - +
439B ARG* 1.3 62.2 + - - +
441B PHE* 3.3 3.7 + - - -
442B GLY 3.3 3.3 + - - -
443B MET* 3.1 37.1 + - + +
445B VAL* 3.6 40.6 - - + -
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Residues in contact with ARG 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435B ILE* 2.9 22.1 + - + +
436B GLU* 2.8 38.3 + - - +
438B LEU* 1.3 71.7 - - - +
440B LYS* 1.3 77.6 + - - +
442B GLY* 2.9 20.7 + - - +
443B MET 5.0 3.4 - - - +
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Residues in contact with LYS 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436B GLU* 2.9 34.8 + - - +
437B THR* 3.3 9.4 + - - +
439B ARG* 1.3 92.4 - - - +
441B PHE* 1.3 67.3 + - + +
442B GLY* 3.4 1.2 + - - -
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Residues in contact with PHE 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407B PHE* 4.6 15.5 - + - -
412B GLN* 5.7 2.9 - - + -
416B ARG* 4.0 32.8 - - + -
419B LEU* 3.7 25.7 - - + +
437B THR* 3.2 43.9 + - + +
438B LEU 3.3 1.7 + - - +
439B ARG 3.3 0.4 - - - -
440B LYS* 1.3 79.8 - - + +
442B GLY* 1.3 61.3 + - - +
443B MET* 3.2 23.9 + - - +
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Residues in contact with GLY 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439B ARG* 2.9 17.8 + - - -
440B LYS 3.2 1.2 + - - -
441B PHE* 1.3 78.0 - - - +
443B MET* 1.3 61.1 + - - +
444B LYS 3.7 1.9 + - - -
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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