Contacts of the helix formed by residues 429 - 442 (chain B) in PDB entry 4EG8
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 429 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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637A GLU* 5.8 0.7 - - - +
681A ASP* 5.3 3.1 - - - +
427B ILE 4.0 0.2 - - - +
428B VAL* 1.3 97.6 - - + +
430B GLU* 1.3 65.8 + - - +
431B PHE* 3.3 28.7 - - + -
432B ARG* 3.0 28.7 + - - +
433B ARG 3.3 4.5 + - - -
544B ALA 3.2 20.6 - - - +
587B PHE* 4.2 7.2 - - + +
588B SER* 3.9 28.9 - - - +
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Residues in contact with GLU 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637A GLU* 4.8 5.7 + - - +
681A ASP* 3.5 37.3 + - - +
682A MET* 3.6 34.8 - - + +
687A LEU* 5.1 6.4 - - - +
694A ARG* 4.9 3.7 + - - +
424B PRO 3.9 6.2 - - - +
427B ILE 4.7 2.6 - - - +
428B VAL* 4.3 1.0 - - - +
429B PRO* 1.3 75.0 - - - +
431B PHE* 1.3 62.3 + - - +
433B ARG* 2.8 55.8 + - - +
434B ARG* 3.1 27.2 + - - +
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Residues in contact with PHE 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A ASP* 4.9 3.2 + - - +
429B PRO* 3.7 17.0 - - + -
430B GLU* 1.3 79.0 - - - +
432B ARG* 1.3 101.4 + - + +
434B ARG* 3.5 33.5 + - - +
435B GLU* 3.2 45.9 + - - +
438B ARG* 4.8 1.2 + - - -
588B SER* 3.7 35.2 - - - -
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Residues in contact with ARG 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B ILE* 4.1 6.7 - - + -
428B VAL 4.7 0.4 - - - +
429B PRO* 3.0 23.3 + - + +
431B PHE* 1.3 108.9 - - + +
433B ARG* 1.3 62.9 + - - +
435B GLU* 3.3 17.1 + - - +
436B VAL* 3.2 26.0 + - - +
517B LYS* 3.1 44.3 - - - +
520B LEU* 3.5 24.6 - - + +
544B ALA* 3.4 27.1 + - + -
545B HIS 4.0 6.1 - - - -
546B GLY* 4.3 0.8 - - - +
587B PHE 2.8 29.1 + - - -
588B SER* 4.0 6.3 + - - +
590B ASP* 4.9 2.8 + - - -
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Residues in contact with ARG 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A LEU* 5.9 2.0 - - - +
691A ASP* 4.1 16.2 + - - -
694A ARG* 4.8 7.7 - - - +
420B TYR* 3.4 25.1 + - + +
421B HIS* 4.6 1.4 - - - +
423B ASN 4.5 0.8 + - - -
424B PRO* 3.2 46.5 + - - +
426B CYS* 4.8 2.7 - - - +
427B ILE* 3.7 49.9 - - + +
429B PRO 3.3 2.4 + - - -
430B GLU* 2.8 45.7 + - - +
432B ARG* 1.3 79.8 - - - +
434B ARG* 1.3 65.0 + - - +
436B VAL* 3.2 4.5 + - - +
437B ILE* 3.0 47.9 + - + +
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Residues in contact with ARG 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A ASP 3.0 27.1 + - - -
682A MET 4.3 6.7 + - - -
683A ALA* 4.2 19.3 - - - +
686A LYS* 4.2 17.3 - - - +
687A LEU* 5.2 9.2 - - + -
814A GOL 3.7 47.7 - - - -
430B GLU* 3.1 33.9 + - - +
431B PHE* 3.6 30.9 - - - +
433B ARG* 1.3 80.3 - - - +
435B GLU* 1.3 61.0 + - - +
437B ILE* 3.4 7.0 + - + +
438B ARG* 3.0 29.5 + - - +
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Residues in contact with GLU 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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431B PHE* 3.2 39.8 + - + +
432B ARG* 3.5 22.8 + - - +
433B ARG 3.2 0.4 - - - -
434B ARG* 1.3 73.9 - - - +
436B VAL* 1.3 65.6 + - + +
438B ARG* 3.4 31.8 + - - +
439B ALA* 3.1 22.3 + - - +
520B LEU* 5.0 3.6 - - + +
521B LYS* 5.0 8.1 - - - -
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Residues in contact with VAL 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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420B TYR* 3.5 34.5 - - + +
427B ILE* 4.0 8.1 - - + -
432B ARG 3.2 13.9 + - - +
433B ARG 3.2 6.0 + - - +
435B GLU* 1.3 76.7 - - + +
437B ILE* 1.3 64.7 + - - +
439B ALA* 3.1 7.5 + - - +
440B VAL* 3.0 20.8 + - - +
520B LEU* 3.8 27.6 - - + -
521B LYS* 4.9 11.7 - - + +
524B ALA* 3.9 21.1 - - + -
525B ILE* 3.9 10.8 - - + -
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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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690A THR* 5.3 2.2 - - + -
814A GOL 4.0 10.8 - - - +
417B LEU* 4.0 6.6 - - + +
420B TYR* 3.9 35.9 - - + -
421B HIS* 4.2 22.4 - - + +
433B ARG* 3.0 53.5 + - + +
434B ARG* 3.7 10.5 - - + +
436B VAL* 1.3 77.0 - - + +
438B ARG* 1.3 57.1 - - - +
440B VAL* 3.3 2.8 + - - +
441B GLU* 2.8 51.4 + - - +
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Residues in contact with ARG 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
686A LYS* 4.9 5.1 - - - +
814A GOL 2.9 53.0 + - - +
431B PHE 4.8 1.0 + - - -
434B ARG* 3.0 14.2 + - - +
435B GLU* 3.7 40.9 + - - +
437B ILE* 1.3 77.1 - - - +
439B ALA* 1.3 65.2 + - - +
441B GLU* 3.3 12.3 + - - +
442B LYS* 3.2 34.3 + - - +
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Residues in contact with ALA 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 GLU 3.1 14.0 + - - +
436B VAL* 3.3 10.8 - - - +
438B ARG* 1.3 78.4 - - - +
440B VAL* 1.3 62.5 + - - +
442B LYS* 3.1 21.6 + - - +
443B GLY 3.8 8.0 + - - +
444B LEU* 4.9 3.1 - - + +
521B LYS* 4.0 27.1 - - + +
525B ILE* 4.3 12.3 - - + -
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Residues in contact with VAL 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B ARG* 3.2 30.6 + - + +
416B LEU* 4.3 3.1 - - + -
417B LEU* 3.7 27.1 - - + -
420B TYR* 3.5 28.5 - - + +
436B VAL 3.0 13.7 + - - +
437B ILE 3.9 3.1 - - - +
439B ALA* 1.3 75.2 - - - +
441B GLU* 1.3 60.6 + - - +
443B GLY* 3.2 10.4 + - - -
444B LEU* 4.1 23.1 - - + -
525B ILE* 3.8 23.3 - - + -
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Residues in contact with GLU 441 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A THR* 4.7 9.1 - - - +
814A GOL 4.2 11.4 + - - -
413B ARG* 3.1 26.5 + - - +
417B LEU* 4.2 17.9 - - + +
421B HIS* 4.3 10.0 + - - -
437B ILE* 2.8 36.0 + - - +
438B ARG* 3.7 11.8 - - - +
439B ALA 3.3 0.2 - - - -
440B VAL* 1.3 76.5 - - - +
442B LYS* 1.3 62.7 + - + +
443B GLY 3.1 1.3 + - - -
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Residues in contact with LYS 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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438B ARG* 3.2 21.9 + - - +
439B ALA* 3.1 13.9 + - - +
441B GLU* 1.3 76.4 - - + +
443B GLY* 1.3 59.6 + - - +
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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