Contacts of the helix formed by residues 429 - 439 (chain B) in PDB entry 5YGP
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 GLY 429 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75B GLY 3.9 7.4 - - - -
269B ALA* 3.7 23.8 + - - +
418B MET* 3.3 15.5 - - - +
428B ALA* 1.3 72.0 - - - +
430B LEU* 1.3 63.1 + - - -
431B GLY 3.2 3.1 - - - -
432B ALA* 3.1 6.2 + - - +
433B VAL* 3.1 21.5 + - - +
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Residues in contact with LEU 430 (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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422B TRP* 3.5 40.6 - - + +
428B ALA 3.6 7.1 + - - +
429B GLY* 1.3 69.6 - - - -
431B GLY* 1.3 60.1 + - - +
432B ALA 3.3 0.2 - - - -
433B VAL* 3.6 8.3 - - + -
434B TYR* 2.9 71.7 + - + +
455B ARG* 3.4 43.1 - - - +
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Residues in contact with GLY 431 (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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74B SER 4.5 1.1 - - - -
75B GLY* 4.3 11.8 - - - -
429B GLY 3.2 1.2 - - - -
430B LEU* 1.3 79.4 - - - +
432B ALA* 1.3 60.2 + - - +
434B TYR* 3.5 5.4 + - - +
435B ALA* 3.1 24.9 + - - +
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Residues in contact with ALA 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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74B SER 3.2 23.3 - - - +
75B GLY* 3.5 19.7 - - - +
76B LEU* 4.4 4.5 - - + -
415B GLN* 3.4 29.6 - - + +
418B MET* 3.9 18.6 - - + -
429B GLY 3.1 7.0 + - - +
431B GLY* 1.3 75.5 - - - +
433B VAL* 1.3 62.6 + - - +
435B ALA 3.5 0.2 + - - -
436B ALA 3.2 17.2 + - - -
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Residues in contact with VAL 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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415B GLN 4.5 4.9 - - - -
418B MET* 3.3 33.2 - - + +
419B LEU* 3.6 22.1 - - + +
422B TRP* 3.8 30.1 - - + -
428B ALA* 4.0 3.8 - - + -
429B GLY 3.1 15.3 + - - +
430B LEU* 3.7 13.7 - - + +
431B GLY 3.2 0.2 - - - -
432B ALA* 1.3 77.3 - - - +
434B TYR* 1.3 70.7 + - + +
436B ALA* 3.4 4.0 + - - +
437B LEU* 3.2 30.2 + - + +
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Residues in contact with TYR 434 (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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422B TRP* 5.6 0.2 - - - -
430B LEU* 2.9 55.8 + - + +
431B GLY* 4.1 4.7 - - - +
433B VAL* 1.3 80.8 - - + +
435B ALA* 1.3 63.5 + - - +
437B LEU* 4.6 3.6 - - + +
438B GLU* 3.1 32.4 + - - +
448B ASP* 3.5 20.0 - - - +
451B SER* 4.0 22.9 + - - -
452B ARG* 3.6 61.5 + - + +
455B ARG* 3.9 20.6 + - - +
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Residues in contact with ALA 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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380B ASP* 4.0 22.3 - - - +
415B GLN* 3.4 31.6 - - - +
431B GLY 3.1 13.5 + - - +
432B ALA 3.9 0.4 - - - +
434B TYR* 1.3 79.4 - - - +
436B ALA* 1.3 62.3 + - - +
438B GLU* 3.7 11.2 + - - +
439B ARG* 3.3 23.0 + - - +
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Residues in contact with ALA 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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415B GLN* 3.7 23.6 - - + +
416B TYR* 3.6 27.0 - - + -
419B LEU* 4.4 4.7 - - + -
432B ALA 3.2 7.9 + - - +
433B VAL 3.8 3.8 - - - +
434B TYR 3.3 0.2 - - - -
435B ALA* 1.3 79.9 - - - +
437B LEU* 1.3 62.9 + - - +
439B ARG* 3.4 22.5 - - - +
440B MET* 3.2 25.4 - - + +
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Residues in contact with LEU 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B LEU* 3.7 25.8 - - + -
422B TRP* 5.2 0.7 - - + -
423B ARG* 3.8 9.6 - - - +
433B VAL* 3.2 23.4 + - + +
434B TYR* 4.1 4.5 - - + +
436B ALA* 1.3 78.4 - - - +
438B GLU* 1.3 59.0 + - - +
440B MET* 3.0 24.3 + - - -
444B GLY* 3.2 36.0 - - - +
445B CYS 3.7 0.2 + - - -
447B GLU* 3.4 39.0 - - + +
448B ASP* 3.7 31.0 - - + +
451B SER* 4.2 6.1 - - - +
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Residues in contact with GLU 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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377A ASP 3.6 10.0 - - - +
378A VAL* 3.2 20.1 - - + +
381A ALA* 3.6 28.9 - - + +
380B ASP 5.3 2.9 - - - +
434B TYR* 3.1 23.0 + - - +
435B ALA* 3.7 7.5 + - - +
436B ALA 3.3 0.4 - - - -
437B LEU* 1.3 75.3 - - - +
439B ARG* 1.3 56.5 + - - +
440B MET 3.5 0.8 + - - -
441B GLY 4.9 1.2 + - - -
445B CYS* 3.6 20.9 - - - -
448B ASP* 3.0 17.6 - - + +
452B ARG* 2.7 32.2 + - - -
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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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379B MET 4.4 2.9 + - - -
380B ASP* 3.6 24.3 + - - +
381B ALA 4.5 4.5 - - - +
382B VAL 3.5 23.3 - - - +
383B PRO* 3.6 8.0 - - + +
384B ALA 2.9 22.5 + - - -
412B ARG* 3.0 51.8 + - - +
415B GLN* 2.5 36.8 + - - +
416B TYR* 2.4 44.7 + - - +
435B ALA* 3.3 13.5 + - - +
436B ALA* 3.4 15.2 - - - +
437B LEU 3.1 0.2 - - - -
438B GLU* 1.3 76.5 - - - +
440B MET* 1.3 55.9 + - - +
441B GLY 3.4 5.7 + - - -
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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