Contacts of the helix formed by residues 615 - 633 (chain A) in PDB entry 4MS0
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 SER 615 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613A THR 4.0 1.4 + - - -
614A LEU* 1.3 79.3 - - - +
616A SER* 1.3 64.5 + - - +
617A SER* 3.3 9.0 + - - -
618A GLU* 3.1 38.6 + - - +
619A TYR* 2.9 18.7 + - - +
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Residues in contact with SER 616 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A LEU 4.5 0.9 - - - -
615A SER* 1.3 75.0 - - - +
617A SER* 1.3 62.7 + - - +
619A TYR* 3.6 6.9 - - - +
620A GLU* 3.4 34.8 + - - +
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Residues in contact with SER 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A SER* 3.1 7.5 + - - -
616A SER* 1.3 79.8 - - - +
618A GLU* 1.3 62.5 + - - +
620A GLU* 3.4 13.3 + - - +
621A GLN* 3.0 46.7 + - - +
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Residues in contact with GLU 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A LEU* 3.7 30.7 - - + +
614A LEU* 4.1 17.4 - - + +
615A SER* 3.1 36.0 + - - +
617A SER* 1.3 73.8 - - - +
619A TYR* 1.3 60.9 + - - +
621A GLN* 3.1 11.4 + - - +
622A VAL* 2.8 28.6 + - - +
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Residues in contact with TYR 619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603A LEU* 5.0 6.9 - - - +
604A GLN* 5.6 5.5 + - - +
609A ASN* 3.4 26.8 + - - -
611A PHE* 3.4 43.5 - + + -
612A SER* 5.1 2.2 - - - -
614A LEU* 4.0 8.5 - - + +
615A SER 2.9 16.6 + - - +
616A SER* 3.6 9.2 - - - +
618A GLU* 1.3 76.5 - - - +
620A GLU* 1.3 66.9 - - + +
622A VAL* 3.3 8.6 - - + +
623A LEU* 3.1 56.3 + - + +
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Residues in contact with GLU 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A SER* 3.4 25.7 + - - +
617A SER* 3.7 11.2 - - - +
618A GLU 3.4 0.2 - - - -
619A TYR* 1.3 82.5 - - + +
621A GLN* 1.3 65.8 + - + +
623A LEU* 4.2 4.6 - - - +
624A GLU* 3.1 29.0 + - - +
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Residues in contact with GLN 621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551A LEU* 3.8 18.0 - - + +
617A SER* 3.0 37.9 + - - +
618A GLU* 3.1 15.2 + - - +
620A GLU* 1.3 78.3 - - + +
622A VAL* 1.3 57.0 + - - +
624A GLU* 3.3 6.6 + - - +
625A ILE* 2.8 35.7 + - + +
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Residues in contact with VAL 622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A LEU* 4.0 24.0 - - + +
555A GLY* 3.7 28.7 - - - -
611A PHE* 3.7 45.8 - - + -
614A LEU* 3.9 5.4 - - + -
618A GLU 2.8 14.8 + - - +
619A TYR* 3.3 11.9 - - + +
621A GLN* 1.3 74.4 - - - +
623A LEU* 1.3 65.9 + - + +
625A ILE* 3.1 8.9 + - + +
626A ILE* 2.8 34.9 + - + +
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Residues in contact with LEU 623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596A PHE* 3.7 15.9 - - + -
599A THR* 6.0 0.2 - - + -
600A VAL* 4.2 26.0 - - + -
603A LEU* 4.0 26.7 - - + -
611A PHE* 5.5 1.1 - - + -
619A TYR* 3.1 45.6 + - + +
620A GLU* 4.2 4.7 - - - +
622A VAL* 1.3 84.0 - - + +
624A GLU* 1.3 57.9 + - - +
626A ILE* 3.3 12.0 + - + +
627A ARG* 2.8 31.2 + - - +
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Residues in contact with GLU 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A PHE* 5.9 0.2 - - - -
620A GLU* 3.1 22.3 + - + +
621A GLN* 3.5 6.5 - - - +
622A VAL 3.2 0.2 - - - -
623A LEU* 1.3 73.9 - - + +
625A ILE* 1.3 65.9 + - - +
627A ARG* 2.9 46.2 + - - +
628A LYS* 3.0 50.5 + - - +
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Residues in contact with ILE 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551A LEU* 4.1 16.6 - - + +
552A GLU* 4.0 36.8 - - + +
555A GLY* 4.4 14.8 - - - -
556A LEU* 4.0 25.4 - - + +
621A GLN* 2.8 26.3 + - + +
622A VAL* 3.3 15.7 - - - +
624A GLU* 1.3 72.6 - - - +
626A ILE* 1.3 59.0 + - - +
628A LYS* 3.6 6.5 + - - +
629A ALA* 3.0 26.5 + - - +
659A GLN* 6.2 1.6 - - - +
666A ILE* 5.4 8.6 - - + +
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Residues in contact with ILE 626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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555A GLY* 3.5 26.7 - - - +
558A ILE* 4.2 9.9 - - + -
559A ALA* 4.2 12.1 - - + -
596A PHE* 3.8 13.7 - - + -
599A THR* 4.5 12.8 - - + -
603A LEU* 5.3 0.7 - - + -
611A PHE* 3.7 36.1 - - + -
622A VAL 2.8 25.0 + - - +
623A LEU* 3.6 13.5 - - + +
625A ILE* 1.3 70.2 - - - +
627A ARG* 1.3 60.4 + - - +
629A ALA* 3.8 0.7 - - - +
630A ILE* 2.9 49.6 + - + +
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Residues in contact with ARG 627 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596A PHE* 3.7 39.5 - - + -
623A LEU 2.8 17.8 + - - +
624A GLU* 2.9 41.1 + - - +
626A ILE* 1.3 73.8 - - - +
628A LYS* 1.3 88.5 + - - +
629A ALA 3.3 0.2 + - - -
630A ILE* 3.4 1.4 + - - +
631A ILE* 3.0 50.2 + - + +
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Residues in contact with LYS 628 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624A GLU* 3.0 45.8 + - - +
625A ILE* 4.0 5.6 - - - +
627A ARG* 1.3 94.9 - - - +
629A ALA* 1.3 57.3 + - - +
631A ILE* 3.4 7.2 + - - +
632A ALA* 3.0 29.9 + - - +
659A GLN* 4.7 8.1 - - - +
663A ASP* 2.9 45.6 + - + +
666A ILE* 5.9 2.2 - - + -
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Residues in contact with ALA 629 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556A LEU* 3.6 27.6 - - + -
559A ALA* 4.0 5.6 - - + -
625A ILE 3.0 18.5 + - - +
626A ILE 3.9 3.6 - - - +
627A ARG 3.3 0.2 - - - -
628A LYS* 1.3 73.2 - - - +
630A ILE* 1.3 67.5 + - - +
632A ALA* 3.3 9.3 + - - +
633A THR* 3.6 4.5 + - - +
666A ILE* 4.4 7.1 - - + +
667A GLY* 5.8 0.2 - - - -
670A MET* 3.6 39.1 - - + +
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Residues in contact with ILE 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559A ALA* 3.8 26.2 - - + +
562A CYS* 4.2 3.1 - - + +
563A HIS* 3.9 29.4 - - + +
592A GLU* 3.5 29.5 - - - +
595A HIS* 4.0 3.8 - - + -
596A PHE* 4.1 14.6 - - + +
599A THR* 3.7 23.1 - - - +
626A ILE* 2.9 36.3 + - + +
627A ARG 4.1 2.2 - - - +
629A ALA* 1.3 75.7 - - - +
631A ILE* 1.3 61.9 + - + +
633A THR* 2.7 30.3 + - - -
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Residues in contact with ILE 631 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589A SER* 4.3 9.0 - - - +
592A GLU* 4.2 7.6 - - + +
593A GLN* 3.7 44.2 - - + +
596A PHE* 5.6 2.9 - - + -
627A ARG* 3.0 44.4 + - + +
628A LYS* 3.8 6.1 - - - +
630A ILE* 1.3 76.5 - - + +
632A ALA* 1.3 62.8 + - - +
634A ASP* 3.1 23.4 + - - +
637A LEU* 3.5 20.0 - - + +
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Residues in contact with ALA 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628A LYS 3.0 17.5 + - - +
629A ALA 3.7 7.2 - - - +
630A ILE 3.2 0.6 - - - -
631A ILE* 1.3 76.9 - - - +
633A THR* 1.3 55.9 + - - +
634A ASP 3.1 13.6 + - - +
637A LEU* 4.7 11.2 - - - +
638A TYR* 5.1 3.3 + - - +
641A ASN* 6.0 0.4 - - - +
667A GLY* 3.6 34.5 - - - +
670A MET* 4.5 1.6 - - + -
671A THR* 4.1 13.7 + - - -
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Residues in contact with THR 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533A VAL* 6.2 0.4 - - + -
563A HIS* 3.8 28.2 + - + -
592A GLU* 3.9 13.1 - - - +
629A ALA 3.6 14.6 - - - +
630A ILE* 2.7 17.6 + - - +
632A ALA* 1.3 73.5 - - - +
634A ASP* 1.3 61.0 + - - +
635A LEU* 3.3 9.4 + - - +
670A MET* 3.8 37.2 - - + +
671A THR* 5.4 3.8 - - - +
674A ASP* 3.7 25.7 - - + +
902A NI 4.1 3.6 - - - +
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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
------------------------------------------------------------
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