Contacts of the helix formed by residues 443 - 458 (chain B) in PDB entry 5XOU
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 GLU 443 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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438B PRO 4.1 1.1 - - - +
439B LEU* 3.7 1.7 - - + +
440B ARG* 3.0 63.2 + - - +
442B GLU* 1.3 73.8 - - - +
444B ARG* 1.3 62.7 + - - +
445B HIS* 3.3 4.2 + - - -
446B ARG* 2.8 48.2 + - + +
447B TRP* 2.9 26.4 + - + -
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Residues in contact with ARG 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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329B LYS* 5.6 3.2 - - - +
335B ARG* 2.8 31.8 - - - +
441B GLU 4.3 4.3 - - - +
442B GLU* 2.8 12.7 + - - +
443B GLU* 1.3 73.2 - - - +
445B HIS* 1.3 82.5 + - + +
447B TRP* 3.3 21.8 - - + +
448B GLU* 2.9 62.0 + - + +
647B PHE* 4.7 5.7 - - - -
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Residues in contact with HIS 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B GLU 3.3 0.8 + - - -
444B ARG* 1.3 99.9 + - + +
446B ARG* 1.3 57.6 + - - +
449B ASN* 2.9 35.0 + - - +
647B PHE* 3.8 37.2 - + + -
2E G 3.9 27.7 + - + +
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Residues in contact with ARG 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B LEU* 3.9 7.3 - - + +
436B ASN* 2.9 22.8 + - - +
438B PRO 3.0 20.6 + - - -
439B LEU* 3.2 13.8 - - + +
443B GLU* 2.8 49.7 + - + +
445B HIS* 1.3 78.8 - - - +
447B TRP* 1.3 58.9 + - - +
449B ASN 3.2 2.1 + - - -
450B ALA* 2.9 24.1 + - - +
2E G 2.6 98.2 + - + +
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Residues in contact with TRP 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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334B LEU* 5.6 1.1 - - + -
360B PHE* 3.8 30.3 - + + -
361B LEU* 3.6 19.7 - - + -
364B ALA* 3.9 29.4 - - + -
367B ARG* 6.2 0.7 - - - -
435B LEU* 4.0 25.8 - - + -
439B LEU* 4.1 11.7 - - + -
440B ARG 3.9 10.8 - - - -
441B GLU* 3.0 31.8 + - + -
443B GLU 2.9 24.7 + - - -
444B ARG* 3.3 20.5 - - + +
446B ARG* 1.3 77.0 - - - +
448B GLU* 1.3 84.1 + - + +
450B ALA* 3.3 2.3 + - - +
451B LEU* 2.9 37.6 + - + +
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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
----------------------------------------------------------
331B ALA* 3.9 8.3 - - + +
334B LEU* 3.8 21.6 - - + +
335B ARG* 3.0 30.1 + - - -
367B ARG* 5.7 1.9 + - - -
444B ARG* 2.9 47.8 + - + +
445B HIS 4.1 2.2 - - - +
447B TRP* 1.3 95.8 - - + +
449B ASN* 1.3 58.7 + - - +
451B LEU* 3.1 7.8 + - - +
452B LEU* 3.0 32.5 + - - +
647B PHE* 3.2 25.5 - - + -
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Residues in contact with ASN 449 (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 GLN* 5.0 0.3 - - - +
445B HIS 2.9 18.8 + - - +
446B ARG 3.5 4.0 - - - +
448B GLU* 1.3 77.4 - - - +
450B ALA* 1.3 62.7 + - - +
452B LEU* 3.3 7.4 + - - +
453B GLY* 2.9 20.1 + - - -
644B ALA 3.8 11.4 - - - +
645B SER* 4.5 0.4 + - - +
646B GLY* 2.8 34.6 + - - +
647B PHE* 4.0 4.9 - - - +
2E G 3.0 33.1 + - - +
3E A 2.4 37.5 + - - +
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Residues in contact with ALA 450 (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 LEU* 4.9 1.3 - - + -
433B GLN* 3.3 29.3 - - + +
435B LEU* 3.7 39.0 - - + -
446B ARG 2.9 8.5 + - - +
447B TRP 3.3 9.4 + - - +
449B ASN* 1.3 75.7 - - - +
451B LEU* 1.3 60.4 + - + +
453B GLY 3.1 2.1 + - - -
454B LEU* 2.9 25.8 + - - +
2E G 4.2 8.4 + - - -
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Residues in contact with LEU 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B LEU* 4.8 15.3 - - + -
361B LEU* 3.7 34.3 - - + +
364B ALA* 4.3 15.0 - - + -
365B LEU* 3.7 38.4 - - + +
407B LEU* 4.5 17.9 - - + -
435B LEU* 5.2 1.1 - - + -
447B TRP* 2.9 23.0 + - + +
448B GLU* 3.1 11.2 + - - +
450B ALA* 1.3 80.8 - - + +
452B LEU* 1.3 63.1 + - - +
454B LEU* 3.3 9.5 + - + +
455B LEU* 3.0 31.7 + - - +
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Residues in contact with LEU 452 (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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330B PRO 3.9 9.0 - - - +
331B ALA* 3.9 15.3 - - + +
333B ALA* 5.3 0.7 - - + -
334B LEU* 4.3 22.7 - - + -
338B PHE* 5.4 0.2 - - + -
448B GLU 3.0 18.6 + - - +
449B ASN* 3.3 11.9 + - - +
451B LEU* 1.3 72.8 - - - +
453B GLY* 1.3 66.4 + - - +
455B LEU* 3.3 7.0 + - + +
456B ALA* 3.0 24.4 + - - +
462B VAL* 3.8 35.8 - - + +
643B PRO 3.6 18.3 - - - +
644B ALA* 4.4 5.2 - - - -
646B GLY* 3.6 32.3 - - - +
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Residues in contact with GLY 453 (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 GLN* 3.5 17.5 - - - -
449B ASN 2.9 13.4 + - - -
450B ALA 3.1 4.9 + - - -
452B LEU* 1.3 78.1 - - - +
454B LEU* 1.3 62.2 + - - +
456B ALA* 3.3 2.9 + - - +
457B LYS* 2.9 29.3 + - - +
644B ALA* 4.3 7.5 - - - +
685B VAL* 4.1 15.0 - - - +
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Residues in contact with LEU 454 (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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346B LEU* 3.6 34.3 - - + -
357B TRP* 4.6 4.9 - - + -
365B LEU* 4.9 6.3 - - + -
405B ALA* 4.0 7.2 - - + +
406B VAL* 3.4 40.8 - - - +
407B LEU* 3.7 27.8 - - + +
432B SER 5.1 0.2 - - - -
433B GLN* 3.8 17.3 - - + +
450B ALA 2.9 12.6 + - - +
451B LEU* 3.3 14.8 + - + +
453B GLY* 1.3 74.1 - - - +
455B LEU* 1.3 58.5 + - + +
457B LYS* 3.2 6.1 + - + +
458B ALA* 3.0 28.6 + - - +
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Residues in contact with LEU 455 (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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334B LEU* 4.2 14.1 - - + -
338B PHE* 3.3 33.4 - - + -
346B LEU* 4.4 19.1 - - + -
365B LEU* 4.5 11.9 - - + -
369B PHE* 4.0 29.6 - - + -
451B LEU 3.0 17.8 + - - +
452B LEU* 3.7 7.2 - - + +
453B GLY 3.2 0.2 - - - -
454B LEU* 1.3 78.1 - - + +
456B ALA* 1.3 61.2 + - - +
458B ALA* 3.1 9.2 + - - +
460B LEU* 3.1 44.8 + - + +
462B VAL* 4.3 8.7 - - + -
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Residues in contact with ALA 456 (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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452B LEU 3.0 16.6 + - - +
453B GLY* 3.8 3.6 - - - +
455B LEU* 1.3 76.2 - - - +
457B LYS* 1.3 60.4 + - - +
459B GLY* 3.3 11.8 + - - -
460B LEU 4.0 11.2 + - - +
462B VAL* 4.7 1.7 - - + +
643B PRO* 4.0 28.7 - - + -
644B ALA* 5.0 1.6 - - + -
680B GLU 3.9 0.5 - - - +
681B LYS* 3.9 0.2 - - - -
682B LEU* 3.0 36.0 + - + +
685B VAL* 4.5 9.4 - - + -
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Residues in contact with LYS 457 (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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405B ALA* 4.1 6.3 - - + +
422B LYS* 4.4 0.6 - - - +
431B PRO* 3.2 21.6 - - + +
432B SER 2.9 38.1 - - - +
433B GLN* 3.5 21.8 - - + +
453B GLY 2.9 18.7 + - - +
454B LEU* 3.5 6.3 - - + +
456B ALA* 1.3 75.7 - - - +
458B ALA* 1.3 56.1 + - - +
459B GLY 3.3 0.9 - - - -
681B LYS* 3.1 22.3 - - - +
682B LEU 3.2 21.0 + - - +
683B PHE* 2.8 30.1 + - - +
685B VAL* 3.0 29.5 + - + +
1E T 3.9 4.3 - - - -
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Residues in contact with ALA 458 (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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344B THR* 4.4 3.1 - - + -
346B LEU* 4.0 14.8 - - + -
404B GLN* 3.9 33.8 + - + +
405B ALA* 3.9 14.8 - - + -
454B LEU 3.0 14.6 + - - +
455B LEU* 3.1 8.0 + - - +
457B LYS* 1.3 78.8 - - - +
459B GLY* 1.3 59.6 + - - +
460B LEU* 3.8 14.4 + - + +
681B LYS* 4.0 7.8 - - - +
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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