Contacts of the helix formed by residues 614 - 630 (chain D) in PDB entry 5MS0
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 LEU 614 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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487D THR 5.2 8.9 - - - +
488D ASN* 5.2 11.7 - - - +
609D TYR* 6.0 1.8 - - + +
613D GLY* 1.3 69.8 - - - -
615D LYS* 1.3 62.2 + - - +
616D PRO 3.3 0.7 - - - -
617D THR* 2.9 24.4 + - - -
618D VAL* 3.2 12.5 + - - +
6O VAL* 6.0 5.6 - - + -
7O GLN* 4.8 10.0 - - + +
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Residues in contact with LYS 615 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613D GLY* 3.6 0.6 - - - -
614D LEU* 1.3 75.0 - - - +
616D PRO* 1.4 61.9 - - - +
617D THR 3.5 0.2 + - - -
618D VAL* 3.8 10.5 + - - +
619D ILE* 4.0 12.8 + - - +
3O ARG 5.0 11.4 - - - +
5O THR 6.0 1.3 - - - +
6O VAL* 5.5 9.0 - - + +
7O GLN* 5.2 14.4 - - + +
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Residues in contact with PRO 616 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587D LEU* 5.2 12.7 - - + +
608D CYS* 4.9 2.5 - - + +
612D LEU* 3.8 23.3 - - + -
613D GLY* 3.7 16.5 - - - +
614D LEU 3.3 0.2 - - - -
615D LYS* 1.4 75.9 - - - +
617D THR* 1.3 52.2 + - - +
619D ILE* 4.9 1.0 - - + +
620D PHE* 2.6 41.1 + - + +
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Residues in contact with THR 617 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487D THR 5.8 4.0 - - - -
490D ILE* 5.8 7.4 - - - -
605D LEU* 6.1 3.4 - - - -
608D CYS* 5.5 6.3 - - - -
609D TYR* 5.4 9.9 - - - -
613D GLY 4.1 7.9 - - - -
614D LEU* 2.9 23.5 + - - -
616D PRO* 1.3 75.1 - - - +
618D VAL* 1.3 57.2 + - - +
620D PHE* 3.7 5.7 - - - +
621D ALA* 2.9 28.9 + - - +
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Residues in contact with VAL 618 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363D LEU* 6.0 3.7 - - + +
487D THR* 4.8 17.5 + - - +
614D LEU 3.2 11.7 + - - +
615D LYS* 4.3 7.6 - - - +
616D PRO 3.3 0.6 - - - -
617D THR* 1.3 76.7 - - - +
619D ILE* 1.3 59.5 + - - +
621D ALA* 3.1 7.4 + - - +
622D ASP* 3.1 23.8 + - - +
2O ALA* 4.3 31.4 - - + +
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Residues in contact with ILE 619 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586D GLY 5.1 10.5 - - - +
615D LYS 4.0 9.0 + - - +
616D PRO* 3.9 2.1 + - + +
618D VAL* 1.3 75.4 - - - +
620D PHE* 1.3 59.4 + - - +
622D ASP* 3.6 10.1 - - + +
623D GLN* 2.9 31.2 + - - +
2O ALA 5.7 0.4 - - - +
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Residues in contact with PHE 620 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583D VAL* 6.0 2.6 - - - +
587D LEU* 5.3 11.5 - - + +
608D CYS* 6.1 4.9 - - + -
616D PRO 2.6 28.3 + - - +
617D THR* 3.7 6.5 - - - +
618D VAL 3.2 0.2 - - - -
619D ILE* 1.3 76.1 - - - +
621D ALA* 1.3 59.1 + - - +
623D GLN* 4.5 4.1 - - - +
624D ILE* 3.6 21.7 + - - +
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Residues in contact with ALA 621 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617D THR 2.9 18.3 + - - +
618D VAL* 3.1 6.0 + - - +
620D PHE* 1.3 74.5 - - - +
622D ASP* 1.3 59.8 + - - +
624D ILE* 3.9 3.8 - - - +
625D MET* 2.9 30.2 + - - +
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Residues in contact with ASP 622 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362D ARG* 5.5 11.0 - - + -
618D VAL 3.1 12.8 + - - +
619D ILE* 3.1 13.0 + - + +
621D ALA* 1.3 76.3 - - - +
623D GLN* 1.3 60.0 + - - +
625D MET* 3.3 7.6 - - - +
626D TYR* 2.9 28.6 + - - +
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Residues in contact with GLN 623 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582D ILE 4.9 4.0 - - - +
583D VAL* 4.4 27.8 - - + +
586D GLY* 6.4 1.6 - - - -
619D ILE 2.9 16.0 + - - +
620D PHE* 4.5 4.3 - - - +
622D ASP* 1.3 73.9 - - - +
624D ILE* 1.3 59.5 + - - +
626D TYR* 3.3 4.5 + - - +
627D THR* 2.9 32.8 + - - -
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Residues in contact with ILE 624 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506D VAL* 4.6 4.6 - - - +
583D VAL* 5.4 8.6 - - + +
620D PHE 3.6 17.6 + - - +
621D ALA* 4.2 4.3 - - - +
623D GLN* 1.3 75.3 - - - +
625D MET* 1.3 59.8 + - - +
627D THR* 4.7 2.5 - - - +
628D GLY* 2.9 28.2 + - - +
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Residues in contact with MET 625 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359D PRO 5.4 6.7 - - - +
506D VAL* 4.9 6.8 - - - +
621D ALA 2.9 21.7 + - - +
622D ASP* 3.3 11.2 - - - +
624D ILE* 1.3 75.7 - - - +
626D TYR* 1.3 58.5 + - - +
629D PHE* 2.9 33.8 + - - +
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Residues in contact with TYR 626 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B VAL* 5.7 9.2 - - + -
622D ASP 2.9 16.5 + - - +
623D GLN* 3.9 4.0 - - - +
625D MET* 1.3 75.3 - - - +
627D THR* 1.3 58.8 + - - +
629D PHE* 5.3 1.3 - - - -
630D ALA* 2.8 38.2 + - + +
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Residues in contact with THR 627 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509D GLY 5.3 0.2 - - - -
510D LEU* 5.0 7.5 + - - +
582D ILE* 5.3 13.2 - - - -
623D GLN 2.9 16.9 + - - -
624D ILE* 4.8 3.1 - - - -
626D TYR* 1.3 76.6 - - - +
628D GLY* 1.3 60.3 + - - +
630D ALA* 4.3 4.0 - - - -
631D TYR* 3.8 19.4 - - - +
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Residues in contact with GLY 628 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505D ASP 3.5 12.5 - - - +
506D VAL* 3.3 26.7 - - - +
509D GLY* 4.4 3.6 + - - -
510D LEU* 4.9 7.6 - - - -
624D ILE 2.9 20.0 + - - -
627D THR* 1.3 80.3 - - - +
629D PHE* 1.3 61.7 + - - +
630D ALA 3.3 0.7 + - - -
632D ALA* 3.7 13.0 + - - +
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Residues in contact with PHE 629 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806C PRO* 4.8 0.7 - - - +
807C TRP 4.4 1.9 - - - +
808C ASN* 3.6 20.7 - - + -
809C GLY* 3.7 28.6 + - - +
359D PRO* 5.3 4.7 - - + -
505D ASP* 4.4 7.0 - - + -
506D VAL* 3.9 12.1 - - + +
625D MET 2.9 16.7 + - - +
626D TYR* 4.7 0.9 - - - +
628D GLY* 1.3 75.2 - - - +
630D ALA* 1.3 61.8 + - - +
632D ALA* 4.0 9.6 + - - +
633D ALA 4.8 0.3 + - - -
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Residues in contact with ALA 630 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B HIS* 5.7 9.6 - - + -
807C TRP 4.8 1.7 - - - +
808C ASN* 4.9 9.6 - - + +
626D TYR* 2.8 24.0 + - + +
627D THR* 4.7 2.2 - - - -
629D PHE* 1.3 79.8 - - - +
631D TYR* 1.3 62.1 + - + +
632D ALA 3.5 0.7 + - - -
633D ALA* 3.8 11.8 + - - +
634D ARG* 4.1 5.0 + - - +
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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