Contacts of the helix formed by residues 431 - 442 (chain B) in PDB entry 5DSG
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 PRO 431 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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428B SER 4.7 4.0 - - - +
429B CYS 3.5 11.0 - - - +
430B ILE* 1.3 89.5 - - - +
432B ASP* 1.3 65.2 + - - +
433B THR* 3.2 8.3 - - - +
434B VAL* 3.2 38.1 + - + +
435B TRP* 3.2 11.2 + - - -
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Residues in contact with ASP 432 (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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430B ILE 5.3 0.3 - - - +
431B PRO* 1.3 72.8 - - - +
433B THR* 1.3 57.7 - - - +
435B TRP* 3.4 11.9 + - - +
436B SER* 2.9 35.7 + - - +
1205B P6G 4.6 15.7 - - - +
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Residues in contact with THR 433 (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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431B PRO* 3.2 7.8 - - - +
432B ASP* 1.3 79.1 - - - +
434B VAL* 1.3 61.4 + - + +
436B SER* 3.3 5.8 + - - -
437B ILE* 2.9 52.0 + - + +
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Residues in contact with VAL 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B MET* 3.5 29.8 - - + +
430B ILE* 3.8 12.8 - - + -
431B PRO* 3.2 32.1 + - + +
433B THR* 1.3 75.7 - - + +
435B TRP* 1.3 66.7 + - - +
437B ILE* 3.3 10.4 + - + +
438B GLY 2.9 19.6 + - - -
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Residues in contact with TRP 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B TYR* 3.7 36.3 - + - -
419B MET* 3.4 37.2 - - + -
420B VAL* 3.8 7.4 - - + -
423B ASN* 3.5 30.4 + - + -
427B GLN 4.8 2.0 + - - -
430B ILE* 3.2 43.0 + - + +
431B PRO 3.2 23.1 + - - -
432B ASP* 3.5 13.2 - - - +
434B VAL* 1.3 78.6 - - - +
436B SER* 1.3 56.8 + - - +
438B GLY* 3.3 1.4 + - - -
439B TYR* 2.9 31.5 + - - +
1205B P6G 3.7 60.3 - - - -
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Residues in contact with SER 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B TYR* 3.2 24.3 + - - -
93B ILE* 4.8 15.3 - - - +
432B ASP* 2.9 20.2 + - - +
433B THR* 3.6 6.5 - - - -
435B TRP* 1.3 76.0 - - - +
437B ILE* 1.3 60.1 + - - +
440B TRP* 2.9 32.5 + - - +
1205B P6G 4.5 6.8 - - - -
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Residues in contact with ILE 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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419B MET* 6.0 1.1 - - + -
433B THR* 2.9 39.6 + - + +
434B VAL* 3.3 9.8 + - + +
436B SER* 1.3 76.6 - - - +
438B GLY* 1.3 58.1 + - - +
440B TRP* 3.5 5.9 + - - +
441B LEU* 2.9 33.2 + - + +
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Residues in contact with GLY 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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412B THR 4.6 0.3 - - - +
415B PRO* 5.1 0.4 - - - -
416B TYR* 4.1 14.0 - - - +
419B MET* 3.8 22.2 - - - +
434B VAL 2.9 10.7 + - - -
435B TRP 3.8 2.5 - - - -
437B ILE* 1.3 76.0 - - - +
439B TYR* 1.3 65.1 + - - +
441B LEU* 2.9 21.4 + - - +
442B CYS* 3.0 17.0 + - - -
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Residues in contact with TYR 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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89B TYR* 3.6 39.0 - + - +
108B TRP* 4.5 3.1 - + - -
109B LEU* 4.9 1.4 - - - +
112B ASP* 3.0 17.9 + - - -
113B TYR* 3.6 13.3 - - - -
416B TYR* 3.7 29.3 - + + -
435B TRP 2.9 17.3 + - - +
438B GLY* 1.3 76.2 - - - +
440B TRP* 1.3 62.0 + - - +
442B CYS* 3.4 17.2 + - - +
443B TYR* 3.3 25.1 + - - -
1201B 0HK 3.4 40.1 - - + -
1205B P6G 3.6 41.3 - - - -
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Residues in contact with TRP 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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38B VAL* 5.8 0.6 - - - +
39B THR* 3.4 49.9 - - + +
42B LEU* 3.7 27.3 - - + +
86B MET* 3.4 57.2 - - + -
89B TYR* 3.7 20.6 - + + -
90B THR* 3.6 10.1 - - + -
93B ILE* 5.1 5.6 - - + -
436B SER 2.9 18.5 + - - +
437B ILE* 3.9 5.6 - - - +
439B TYR* 1.3 74.9 - - - +
441B LEU* 1.3 63.6 + - - +
443B TYR* 2.9 43.7 + + + +
444B VAL* 3.6 10.8 - - + +
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Residues in contact with LEU 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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411B LEU 4.5 1.6 - - - +
412B THR* 3.4 39.9 - - + +
415B PRO* 3.8 27.6 - - + -
437B ILE* 2.9 25.9 + - + +
438B GLY* 2.9 10.3 + - - +
440B TRP* 1.3 78.2 - - + +
442B CYS* 1.3 60.6 + - - +
444B VAL* 3.2 31.4 + - + +
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Residues in contact with CYS 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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81B ILE* 6.0 1.2 - - - +
412B THR 3.9 1.1 - - - -
413B TRP* 2.8 54.8 + - - +
416B TYR* 3.7 23.6 - - - -
438B GLY 3.0 16.8 + - - -
439B TYR 3.4 10.8 - - - +
440B TRP 3.1 0.2 - - - -
441B LEU* 1.3 78.6 - - - +
443B TYR* 1.3 61.4 + - - +
444B VAL 3.5 0.3 + - - -
445B ASN* 3.8 5.4 - - - +
446B SER* 5.2 1.0 + - - -
1201B 0HK 3.6 39.0 - - + -
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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