Contacts of the helix formed by residues 433 - 448 (chain B) in PDB entry 4PKO
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 ASN 433 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B ASP* 3.1 24.2 + - - -
432B GLN* 1.3 77.5 + - + +
434B GLU* 1.3 65.6 + - - +
435B ASP* 3.9 19.6 + - - +
436B GLN* 3.0 42.5 + - - +
437B ASN* 3.2 17.9 + - - +
34C LYS* 5.0 6.5 - - - +
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Residues in contact with GLU 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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433B ASN* 1.3 75.8 - - - +
435B ASP* 1.3 65.9 + - - +
437B ASN* 3.1 38.2 + - - +
438B VAL* 3.3 22.0 + - + +
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Residues in contact with ASP 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B MET* 3.2 28.4 - - + +
112B ASN* 3.3 34.5 + - - +
115B ASP* 3.8 20.4 - - + +
116B LEU* 3.3 25.7 - - + +
433B ASN* 3.3 12.7 + - - +
434B GLU* 1.3 80.2 - - - +
436B GLN* 1.3 62.4 + - - +
438B VAL* 3.3 12.5 + - - +
34C LYS* 5.8 0.9 + - - -
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Residues in contact with GLN 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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115B ASP* 3.2 42.7 + - - +
118B ARG* 3.9 21.1 - - - +
119B GLY* 3.4 11.1 + - - +
122B LYS* 5.6 2.6 - - - +
431B GLY* 3.7 6.2 - - - -
432B GLN* 2.7 54.9 + - - +
433B ASN* 3.0 26.8 + - - +
435B ASP* 1.3 75.4 - - - +
437B ASN* 1.3 66.2 + - - +
439B GLY 3.2 1.6 + - - -
440B ILE* 3.1 26.3 + - - +
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Residues in contact with ASN 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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429B LEU 5.8 0.2 - - - -
430B ARG* 3.2 31.2 - - - +
431B GLY 2.8 32.4 + - - +
433B ASN 3.2 10.4 + - - -
434B GLU* 3.1 35.5 + - - +
436B GLN* 1.3 77.3 - - - +
438B VAL* 1.3 61.1 + - - +
440B ILE* 3.1 10.4 + - - +
441B LYS* 3.0 26.9 + - + +
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Residues in contact with VAL 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ALA* 4.2 10.3 - - + -
111B MET* 4.0 35.7 - - + -
116B LEU* 4.2 3.4 - - + -
434B GLU* 3.3 27.3 + - + +
435B ASP* 3.6 7.9 - - - +
436B GLN 3.3 0.6 - - - -
437B ASN* 1.3 74.7 - - - +
439B GLY* 1.3 53.5 + - - +
441B LYS* 3.1 6.9 + - - +
442B VAL* 2.7 54.4 + - + +
445B ARG* 5.1 6.5 - - - +
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Residues in contact with GLY 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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116B LEU* 3.7 30.2 - - - +
120B ILE* 3.2 23.3 - - - +
435B ASP 3.3 5.8 + - - -
436B GLN 3.2 8.2 + - - -
438B VAL* 1.3 78.0 - - - +
440B ILE* 1.3 61.4 + - - +
442B VAL* 3.4 5.0 + - - +
443B ALA* 3.1 19.2 + - - +
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Residues in contact with ILE 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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119B GLY* 3.1 20.9 - - - +
122B LYS* 4.7 6.1 - - + -
123B ALA* 3.8 19.5 - - + +
426B LEU* 5.9 0.2 - - + -
429B LEU* 3.7 44.9 - - + +
430B ARG* 3.7 26.2 - - - +
431B GLY* 3.8 7.6 - - - +
436B GLN 3.1 11.1 + - - +
437B ASN* 3.1 9.3 + - - +
439B GLY* 1.3 77.0 - - - +
441B LYS* 1.3 65.9 + - + +
443B ALA* 3.3 4.5 + - - +
444B LEU* 3.1 35.2 + - + +
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Residues in contact with LYS 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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426B LEU 4.5 2.0 + - - -
427B ALA* 2.8 18.6 + - - +
429B LEU 3.6 7.5 + - - -
430B ARG* 2.8 41.2 - - - +
437B ASN* 3.0 18.6 + - + +
438B VAL* 3.6 9.2 - - - +
440B ILE* 1.3 77.8 - - + +
442B VAL* 1.3 56.5 + - - +
444B LEU* 3.2 14.7 + - + +
445B ARG* 2.7 51.5 + - - +
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Residues in contact with VAL 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ILE* 3.9 24.5 - - + +
102B GLU* 3.6 38.6 - - + +
103B GLY* 4.1 6.1 - - - +
106B ALA* 4.9 3.1 - - + -
116B LEU* 5.6 1.1 - - + -
120B ILE* 4.8 5.4 - - + -
438B VAL* 2.7 42.6 + - + +
439B GLY* 3.6 9.6 - - - +
441B LYS* 1.3 74.0 - - - +
443B ALA* 1.3 57.6 + - - +
445B ARG* 3.7 18.9 - - - +
446B ALA* 3.0 26.5 + - - +
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Residues in contact with ALA 443 (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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99B ILE* 5.0 7.6 - - + -
120B ILE* 4.2 18.4 - - + +
123B ALA* 4.0 17.9 - - + -
124B VAL* 5.1 3.1 - - + -
439B GLY 3.1 13.0 + - - +
440B ILE 3.6 8.5 - - - +
441B LYS 3.2 0.2 - - - -
442B VAL* 1.3 76.3 - - - +
444B LEU* 1.3 59.7 + - - +
446B ALA* 3.0 8.5 + - - +
447B MET* 2.9 42.4 + - + +
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Residues in contact with LEU 444 (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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123B ALA* 5.0 3.6 - - + -
423B ALA* 3.9 26.8 - - + +
426B LEU* 3.7 46.0 - - + +
427B ALA* 4.2 6.1 - - - +
440B ILE* 3.1 23.6 + - + +
441B LYS* 3.7 17.9 - - + +
443B ALA* 1.3 76.3 - - + +
445B ARG* 1.3 63.3 + - - +
447B MET* 3.1 45.5 + - + +
448B GLU* 3.7 11.9 + - - +
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Residues in contact with ARG 445 (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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102B GLU* 2.6 51.5 + - + +
105B LYS* 5.7 1.6 - - - +
438B VAL* 5.1 5.1 + - - +
441B LYS* 2.7 33.2 + - - +
442B VAL* 3.7 24.7 - - - +
444B LEU* 1.3 73.9 - - - +
446B ALA* 1.3 60.1 + - - +
448B GLU* 3.6 26.7 - - - +
449B ALA* 4.2 2.3 + - - +
452B ARG* 5.6 1.0 + - - -
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Residues in contact with ALA 446 (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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95B LEU* 3.7 9.1 - - + +
98B ALA* 3.5 28.4 - - + +
99B ILE* 3.8 24.2 - - + +
102B GLU* 5.9 2.0 - - + -
442B VAL 3.0 17.3 + - - +
443B ALA 3.0 6.6 + - - +
445B ARG* 1.3 74.9 - - - +
447B MET* 1.3 56.5 + - - +
448B GLU 3.1 5.6 - - - -
449B ALA* 3.1 24.7 + - - +
450B PRO* 3.5 3.5 - - - +
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Residues in contact with MET 447 (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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95B LEU* 4.3 7.6 - - + -
123B ALA 4.5 7.4 - - - +
124B VAL* 5.0 1.8 - - + -
127B ALA* 4.0 13.9 - - + -
416B GLY 4.7 1.9 - - - +
419B LEU* 3.7 37.8 - - + +
420B ILE* 4.1 7.3 + - - +
422B VAL* 4.2 10.8 - - - -
423B ALA* 4.0 12.1 - - + -
443B ALA* 2.9 31.3 + - + +
444B LEU* 3.1 38.7 + - + +
446B ALA* 1.3 76.8 - - - +
448B GLU* 1.3 61.4 + - - +
449B ALA 3.3 0.4 - - - -
450B PRO* 3.4 10.0 - - - +
451B LEU* 5.1 0.3 + - - +
504B LEU* 4.0 36.1 - - + -
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Residues in contact with GLU 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B ILE* 4.0 28.2 - - + +
423B ALA* 5.6 1.8 - - + -
444B LEU 4.0 12.8 - - - +
445B ARG* 3.6 19.0 - - - +
446B ALA 3.1 0.2 - - - -
447B MET* 1.3 80.1 - - - +
449B ALA* 1.3 64.2 + - - +
450B PRO 3.4 0.2 - - - -
451B LEU* 3.2 14.4 + - - +
452B ARG* 2.9 50.7 + - - +
466B ALA* 5.1 0.4 - - + +
470B LYS* 3.2 33.0 + - - +
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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