Contacts of the helix formed by residues 616 - 631 (chain H) in PDB entry 5A31
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 616 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587H ILE* 4.8 1.9 - - - +
611H PHE* 3.0 35.0 + - + +
614H THR* 3.9 30.6 - - + +
615H GLU* 1.3 76.8 - - - +
617H LEU* 1.3 59.3 + - - +
618H ASP 3.6 1.8 - - - -
619H LYS* 3.4 31.2 - - + +
620H ALA* 3.0 26.5 + - - +
27L SER* 5.0 8.0 + - - -
28L GLN* 4.1 21.7 + - - +
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Residues in contact with LEU 617 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1394A TYR* 4.2 18.4 - - + +
612H VAL* 3.8 46.2 - - + +
615H GLU* 3.3 15.3 + - + +
616H GLU* 1.3 72.5 - - - +
618H ASP* 1.3 61.9 + - - +
620H ALA* 3.2 3.8 + - - +
621H LEU* 2.9 32.1 + - - +
644H ILE* 3.9 31.1 - - + +
647H LYS* 4.0 22.7 - - + -
648H GLN* 3.9 20.6 - - + +
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Residues in contact with ASP 618 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1330A VAL* 6.0 1.6 - - - +
1331A GLY 5.7 1.2 - - - +
1398A PHE* 5.0 11.6 - - - -
617H LEU* 1.3 76.9 - - - +
619H LYS* 1.3 61.7 + - - +
621H LEU* 3.4 26.9 - - - +
622H ALA* 3.5 6.4 + - - +
625H ARG* 5.1 0.9 + - - -
648H GLN* 3.8 15.4 - - - +
510K ARG* 4.4 27.5 + - - +
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Residues in contact with LYS 619 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E GLU* 5.5 3.8 + - - -
105E PHE* 3.4 41.2 - - + -
611H PHE* 3.4 39.5 - - + -
616H GLU* 3.4 33.0 - - + +
618H ASP* 1.3 77.8 - - - +
620H ALA* 1.3 62.9 + - - +
622H ALA* 3.3 13.5 + - - +
623H CYS* 3.2 15.8 - - - -
510K ARG* 5.8 4.3 - - - +
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Residues in contact with ALA 620 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608H GLY 3.5 13.2 - - - +
611H PHE* 3.4 26.9 - - + -
612H VAL* 3.8 9.0 - - + -
616H GLU 3.0 10.1 + - - +
617H LEU* 3.2 5.6 + - - +
619H LYS* 1.3 77.1 - - - +
621H LEU* 1.3 66.0 + - - +
623H CYS* 3.1 9.5 + - - +
624H PHE* 3.1 25.1 + - - -
644H ILE* 3.7 14.8 - - + -
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Residues in contact with LEU 621 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617H LEU 2.9 17.9 + - - +
618H ASP* 3.4 21.8 - - - +
619H LYS 3.3 0.2 - - - -
620H ALA* 1.3 76.3 - - - +
622H ALA* 1.3 63.2 + - - +
624H PHE* 3.2 4.6 + - - +
625H ARG* 2.9 60.1 + - - +
641H LEU* 3.4 27.1 - - + -
644H ILE* 3.5 30.4 - - + +
645H TYR* 4.2 22.7 - - + +
648H GLN* 4.9 4.5 - - - +
650H LYS* 6.1 0.4 - - - +
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Residues in contact with ALA 622 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E LEU* 4.0 17.7 - - + +
105E PHE* 4.0 18.8 - - + -
618H ASP 3.5 5.6 + - - +
619H LYS 3.3 11.6 + - - +
620H ALA 3.2 0.4 - - - -
621H LEU* 1.3 79.2 - - - +
623H CYS* 1.3 57.6 + - - +
625H ARG* 3.2 12.2 + - - +
626H ASN* 2.9 35.5 + - - +
506K LEU 5.4 0.2 - - - +
507K GLY* 4.8 7.0 - - - +
510K ARG* 5.0 10.5 - - + -
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Residues in contact with CYS 623 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E LEU* 3.5 22.9 - - + -
604H TYR* 3.7 19.7 - - + +
607H LEU* 4.4 4.5 - - + -
608H GLY* 3.7 16.8 - - - +
611H PHE* 3.5 29.8 - - - -
619H LYS 3.2 18.2 - - - -
620H ALA 3.1 6.9 + - - +
622H ALA* 1.3 74.3 - - - +
624H PHE* 1.3 57.2 + - - +
626H ASN* 3.2 10.9 + - - +
627H ALA* 2.9 26.7 + - - +
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Residues in contact with PHE 624 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605H THR* 3.4 32.5 - - + -
608H GLY* 3.5 13.2 - - - -
609H HIS* 3.5 45.3 - + - -
612H VAL* 4.1 5.4 - - + -
620H ALA 3.1 18.8 + - - -
621H LEU 3.2 4.5 + - - +
623H CYS* 1.3 75.1 - - - +
625H ARG* 1.3 64.0 + - - +
627H ALA* 3.1 4.8 + - - +
628H ILE* 3.0 26.9 + - - +
637H ALA* 3.9 29.6 - - - +
640H GLY* 3.9 16.2 - - - -
641H LEU* 4.0 11.2 - - + -
644H ILE* 3.4 27.8 - - + -
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Residues in contact with ARG 625 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618H ASP 5.1 0.8 + - - -
621H LEU* 2.9 55.8 + - - +
622H ALA* 3.7 7.2 - - - +
624H PHE* 1.3 75.5 - - - +
626H ASN* 1.3 58.6 + - - +
628H ILE* 3.1 13.8 + - - +
629H ARG* 3.0 26.6 + - - +
641H LEU* 4.3 6.3 - - + -
645H TYR* 3.5 14.1 + - - -
503K HIS* 3.2 64.9 + - + +
504K THR* 4.8 3.1 - - - -
506K LEU* 3.7 37.5 + - - +
507K GLY* 3.8 10.3 - - - +
510K ARG* 6.2 1.6 - - - +
519K LEU* 4.6 0.4 - - - +
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Residues in contact with ASN 626 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102E LEU 4.3 4.5 - - - +
103E LEU* 3.1 39.0 + - - +
604H TYR* 3.4 26.0 - - + -
622H ALA 2.9 25.4 + - - -
623H CYS* 3.6 1.8 - - - +
625H ARG* 1.3 74.7 - - - +
627H ALA* 1.3 64.9 + - - +
629H ARG* 3.1 24.5 + - - +
630H VAL* 3.1 28.8 + - - +
507K GLY* 3.6 20.5 + - - +
508K LEU* 3.8 6.6 - - - +
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Residues in contact with ALA 627 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601H ALA* 4.1 8.3 - - - +
604H TYR* 3.7 17.6 - - + +
605H THR* 3.7 16.2 - - - +
623H CYS 2.9 13.9 + - - +
624H PHE* 3.1 11.6 + - - +
626H ASN* 1.3 78.3 - - - +
628H ILE* 1.3 57.1 + - - +
630H VAL* 3.4 4.9 + - - +
631H ASN* 2.9 30.0 + - - +
634H HIS* 4.5 3.5 - - - +
637H ALA* 3.6 18.8 - - + -
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Residues in contact with ILE 628 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624H PHE 3.0 18.1 + - - +
625H ARG* 3.1 13.0 + - - +
627H ALA* 1.3 74.7 - - - +
629H ARG* 1.3 66.9 + - - +
631H ASN 2.9 23.2 - - - +
632H PRO* 3.2 11.3 - - + +
634H HIS 4.4 2.5 - - - +
637H ALA* 3.4 28.0 - - + -
638H TRP* 3.8 48.9 - - + +
641H LEU* 4.5 10.3 - - + -
500K ASP* 3.5 26.5 - - - +
503K HIS* 5.1 5.2 - - + -
504K THR* 4.7 5.2 - - + -
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Residues in contact with ARG 629 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E LEU 4.5 4.9 + - - -
598H PRO 5.4 0.8 + - - -
599H ASN* 5.4 3.6 + - - -
604H TYR* 4.1 10.1 + - - -
625H ARG 3.0 13.7 + - - +
626H ASN* 3.1 36.1 + - - +
627H ALA 3.3 0.4 - - - -
628H ILE* 1.3 78.0 - - - +
630H VAL* 1.3 86.7 + - - +
631H ASN* 3.4 0.7 + - - -
632H PRO* 4.7 4.5 - - - +
477K GLN* 3.2 30.1 - - - +
482K TYR* 4.3 23.6 - - + +
504K THR* 4.0 28.9 - - + +
508K LEU* 3.2 32.3 - - - +
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Residues in contact with VAL 630 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598H PRO 3.9 17.0 - - - +
599H ASN* 2.9 48.7 + - - +
600H TYR 4.2 0.2 - - - -
601H ALA* 3.7 22.0 - - + +
604H TYR* 4.0 9.6 - - + -
626H ASN 3.1 18.8 + - - +
627H ALA* 3.7 4.0 - - - +
629H ARG* 1.3 98.5 - - - +
631H ASN* 1.3 60.3 + - - +
632H PRO* 4.5 1.7 - - - +
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Residues in contact with ASN 631 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157H GLU* 4.9 12.8 + - - +
601H ALA* 4.0 16.5 - - + +
627H ALA 2.9 12.0 + - - +
628H ILE* 2.9 11.8 - - - +
629H ARG 3.3 0.2 - - - -
630H VAL* 1.3 81.5 - - + +
632H PRO* 1.3 72.2 - - - +
633H ARG* 3.0 19.2 + - - +
634H HIS* 3.3 39.3 + - + +
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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