Contacts of the helix formed by residues 540 - 559 (chain B) in PDB entry 4OSI
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 540 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505B ILE* 3.2 14.7 + - - +
539B GLY* 1.3 73.6 - - - +
541B GLY* 1.3 65.2 + - - +
542B LYS 3.2 3.1 - - - -
543B GLN* 3.3 15.6 + - - +
544B ALA* 3.5 8.7 + - - +
572B HIS 5.6 0.5 - - - +
574B GLY 5.7 0.2 + - - -
575B GLY 5.9 0.5 + - - -
10G A 3.2 42.1 + - - -
11G T 3.9 6.0 + - - +
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Residues in contact with GLY 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B GLY 4.7 1.2 + - - -
510B ALA* 4.3 7.5 - - - +
535B ILE 4.3 6.1 - - - -
536B ALA* 4.1 13.9 - - - -
538B ASN* 3.2 16.6 + - - -
539B GLY 4.5 0.2 - - - -
540B GLY* 1.3 75.1 - - - +
542B LYS* 1.3 66.1 + - - +
544B ALA* 2.9 10.3 + - - +
545B LEU* 2.9 32.7 + - - +
10G A 4.6 0.2 + - - -
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Residues in contact with LYS 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509B GLN* 2.9 42.9 + - + +
510B ALA* 4.2 7.3 - - - +
512B GLU* 6.3 0.7 - - - -
513B THR* 3.1 36.7 - - - +
516B ARG* 4.9 2.5 - - - +
541B GLY* 1.3 75.6 - - - +
543B GLN* 1.3 63.5 + - - +
545B LEU* 3.5 1.2 + - - +
546B GLU* 3.0 53.0 + - - +
10G A 3.5 23.1 + - - +
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Residues in contact with GLN 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B GLY 3.3 2.0 + - - +
541B GLY 3.2 0.6 - - - -
542B LYS* 1.3 83.7 - - - +
544B ALA* 1.3 61.5 + - - +
546B GLU* 4.4 12.1 + - - +
547B THR* 2.7 36.1 + - - -
576B LYS* 3.0 46.2 - - + +
10G A 3.0 46.8 + - - +
11G T 3.7 23.3 - - - +
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Residues in contact with ALA 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B ILE* 3.7 11.7 - - + +
538B ASN* 6.3 0.4 - - + -
540B GLY 3.5 4.8 + - - +
541B GLY* 2.9 17.4 + - - +
543B GLN* 1.3 79.0 - - - +
545B LEU* 1.3 59.0 + - - +
547B THR* 3.7 2.3 - - - -
548B VAL* 2.9 31.7 + - - +
570B ALA* 3.2 29.8 - - - +
572B HIS 5.0 4.5 - - - +
575B GLY* 4.9 3.1 - - - +
576B LYS* 4.2 15.4 - - - +
11G T 5.4 0.2 + - - -
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Residues in contact with LEU 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510B ALA 4.2 8.1 - - - +
513B THR* 3.5 28.0 - - + -
514B VAL* 4.3 9.6 - - + +
517B LEU* 4.3 13.2 - - + +
521B LEU* 4.6 12.8 - - + +
532B VAL* 4.0 26.7 - - + +
535B ILE* 3.6 29.6 - - + -
536B ALA* 3.6 22.0 - - + +
541B GLY 2.9 17.7 + - - +
542B LYS 3.9 2.0 - - - +
544B ALA* 1.3 76.7 - - - +
546B GLU* 1.3 63.6 + - - +
548B VAL* 3.0 10.1 + - + +
549B GLN* 2.9 21.7 + - - +
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Residues in contact with GLU 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513B THR* 4.7 0.7 - - + -
516B ARG* 3.2 34.1 + - - +
517B LEU* 4.5 11.2 - - + -
542B LYS* 3.0 47.0 + - + +
543B GLN* 4.3 15.5 + - - +
545B LEU* 1.3 74.8 - - - +
547B THR* 1.3 62.8 + - - +
549B GLN* 3.1 9.0 + - - +
550B ARG* 3.0 26.7 + - - +
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Residues in contact with THR 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B GLN 2.7 22.4 + - - -
544B ALA 3.7 2.2 - - - -
546B GLU* 1.3 77.1 - - - +
548B VAL* 1.3 57.7 + - - +
550B ARG* 3.6 18.5 + - - +
551B LEU* 3.0 31.9 + - + +
576B LYS* 3.1 38.3 - - + +
579B LEU* 3.4 34.2 - - + +
580B GLU* 4.3 9.2 - - + -
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Residues in contact with VAL 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B LEU* 4.6 19.3 - - + -
527B LEU* 5.1 4.9 - - + -
535B ILE* 4.6 11.7 - - + -
544B ALA 2.9 10.2 + - - +
545B LEU* 3.0 11.2 + - - +
547B THR* 1.3 72.4 - - - +
549B GLN* 1.3 68.9 + - - +
550B ARG 3.0 1.7 + - - -
551B LEU 4.4 0.4 - - - +
552B LEU* 2.9 64.2 + - + +
566B VAL* 5.0 2.7 - - + -
567B VAL* 5.3 2.7 - - + -
570B ALA* 3.5 32.3 - - + -
579B LEU* 3.5 9.2 - - + -
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Residues in contact with GLN 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516B ARG* 4.5 5.7 + - - +
517B LEU* 3.3 33.8 - - + +
520B VAL* 4.1 11.4 - - + +
521B LEU* 4.2 11.2 - - + -
525B HIS* 3.6 31.6 + - + -
545B LEU 2.9 15.1 + - - +
546B GLU* 3.7 11.0 - - - +
548B VAL* 1.3 76.6 - - - +
550B ARG* 1.3 62.0 + - - +
553B PRO* 4.1 5.2 - - - +
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Residues in contact with ARG 550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B GLU 3.0 13.4 + - - +
547B THR* 3.6 21.0 + - - +
549B GLN* 1.3 78.1 - - - +
551B LEU* 1.3 102.2 + - + +
552B LEU 3.5 0.2 - - - -
553B PRO* 3.2 17.8 - - - +
554B VAL* 4.7 4.3 - - - +
576B LYS* 5.8 0.4 - - - +
580B GLU* 2.9 30.7 + - - +
583B GLN* 5.1 6.3 + - - +
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Residues in contact with LEU 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547B THR* 3.0 26.1 + - + +
548B VAL* 5.2 0.7 - - - -
550B ARG* 1.3 121.4 - - + +
552B LEU* 1.3 63.7 + - - +
553B PRO 3.1 3.4 - - - -
554B VAL* 3.5 16.1 + - + -
555B LEU* 3.3 38.6 + - + +
566B VAL* 5.7 0.7 - - - -
579B LEU* 4.4 6.1 - - + -
580B GLU* 4.2 18.8 - - - +
583B GLN* 4.1 34.3 - - + +
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Residues in contact with LEU 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B HIS* 3.1 43.1 - - + +
527B LEU* 4.5 15.3 - - + -
548B VAL* 2.9 38.9 + - + +
551B LEU* 1.3 75.2 - - - +
553B PRO* 1.3 67.7 - - + +
555B LEU* 5.1 1.6 - - - -
556B CYS* 2.9 34.4 - - + +
563B PRO* 5.0 11.2 - - + +
566B VAL* 3.7 34.5 - - + -
567B VAL* 5.1 5.4 - - + +
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Residues in contact with PRO 553 (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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525B HIS* 4.6 8.3 - - + +
549B GLN 4.1 7.4 - - - +
550B ARG 3.2 19.7 - - - +
552B LEU* 1.3 101.8 - - + +
554B VAL* 1.3 56.9 + - + +
557B GLN* 2.0 65.1 + - + +
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Residues in contact with VAL 554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550B ARG 4.7 4.9 - - - +
551B LEU* 3.5 24.4 + - + +
553B PRO* 1.3 76.9 - - + +
555B LEU* 1.3 57.6 + - + +
557B GLN* 4.6 0.7 - - - -
558B ALA* 2.6 46.0 + - + +
559B HIS* 3.8 22.2 - - + -
583B GLN* 4.1 20.0 - - + +
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Residues in contact with LEU 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551B LEU* 3.3 26.6 + - + +
552B LEU* 5.1 0.2 - - - -
554B VAL* 1.3 74.0 - - + +
556B CYS* 1.3 58.9 + - - +
557B GLN 3.0 2.4 + - - -
559B HIS* 2.9 56.5 + - + +
560B GLY 3.1 12.8 + - - -
561B LEU* 3.8 17.7 + - + -
566B VAL* 3.7 28.7 - - + -
569B ILE* 6.4 0.7 - - + -
579B LEU* 5.3 10.3 - - + +
582B VAL* 4.4 13.0 - - + -
583B GLN* 3.3 38.6 - - + +
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Residues in contact with CYS 556 (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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552B LEU* 2.9 25.5 + - + +
554B VAL 3.3 0.6 - - - -
555B LEU* 1.3 75.0 - - - +
557B GLN* 1.3 68.8 + - - +
560B GLY* 5.7 0.9 - - - -
561B LEU 2.6 32.8 - - - -
562B THR 3.6 1.8 - - - -
563B PRO* 3.4 35.9 - - - -
566B VAL* 3.9 9.9 - - - -
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Residues in contact with GLN 557 (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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553B PRO* 2.0 50.6 + - + +
554B VAL* 3.7 1.8 - - - +
555B LEU 3.0 0.8 + - - -
556B CYS* 1.3 80.7 - - - +
558B ALA* 1.3 65.1 + - + +
559B HIS 3.9 0.4 - - - -
560B GLY 5.2 1.1 - - - +
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Residues in contact with ALA 558 (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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554B VAL* 2.6 23.5 + - + +
557B GLN* 1.3 79.2 - - + +
559B HIS* 1.3 72.7 + - + +
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Residues in contact with HIS 559 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554B VAL* 3.8 20.8 - - + +
555B LEU* 2.9 46.2 + - + +
558B ALA* 1.3 84.8 + - + +
560B GLY* 1.3 62.0 + - - +
561B LEU* 4.0 17.4 - - + +
583B GLN* 4.3 16.8 + - + -
586B LEU* 4.0 33.9 - - + +
587B PRO* 4.9 8.4 - - + +
597B PRO* 5.4 8.1 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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