Contacts of the helix formed by residues 614 - 631 (chain A) in PDB entry 5CGD
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 614 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613A SER* 1.3 75.8 + - - +
615A ARG* 1.3 63.6 + - - +
616A GLU* 3.5 3.6 - - - -
617A LEU* 3.7 28.9 - - - +
618A CYS* 3.3 26.6 + - - -
665A LYS* 4.5 6.8 + - - +
668A ARG* 3.1 28.8 + - - +
693A GLN* 3.8 10.2 + - - -
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Residues in contact with ARG 615 (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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601A PHE 5.6 0.2 - - - -
605A ARG* 3.3 51.6 + - - +
606A ASP* 5.6 1.0 + - - +
610A VAL* 3.3 44.6 + - + +
611A LYS* 4.2 22.2 + - - +
613A SER 3.1 5.1 + - - +
614A SER* 1.3 71.7 - - - +
616A GLU* 1.3 72.7 + - - +
618A CYS* 3.4 9.1 + - + +
619A TYR* 3.4 41.0 + - + +
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Residues in contact with GLU 616 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A SER* 3.5 2.9 - - - -
615A ARG* 1.3 82.2 + - - +
617A LEU* 1.3 65.9 + - - +
619A TYR* 3.3 22.6 + - + +
620A ILE* 3.3 18.5 + - + +
690A ALA* 5.2 11.4 - - - +
694A LEU* 3.7 35.7 - - + +
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Residues in contact with LEU 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A SER* 3.7 23.5 + - - +
615A ARG 3.3 0.4 - - - -
616A GLU* 1.3 78.8 - - - +
618A CYS* 1.3 56.8 + - - +
620A ILE* 3.1 10.2 + - + +
621A ILE* 2.9 35.2 + - + +
661A ALA* 3.7 25.9 - - + +
664A THR* 3.6 20.9 - - - +
665A LYS* 4.0 13.2 - - + -
693A GLN* 3.4 35.0 - - + +
694A LEU* 3.8 23.3 - - + -
697A ALA* 4.4 10.3 - - + -
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Residues in contact with CYS 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A PHE* 5.6 5.4 - - + -
610A VAL* 6.4 2.0 - - - -
613A SER* 4.3 9.2 - - - -
614A SER 3.3 19.5 - - - -
615A ARG* 3.4 11.8 + - + +
616A GLU 3.2 0.6 - - - -
617A LEU* 1.3 80.5 - - - +
619A TYR* 1.3 55.4 + - + +
621A ILE* 3.1 13.3 + - - +
622A LEU* 2.7 43.8 + - + +
665A LYS* 4.9 6.3 - - - -
818A PHE* 4.4 16.3 - - + -
821A LYS* 4.2 22.0 - - - -
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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
----------------------------------------------------------
598A THR* 5.0 9.2 - - + -
601A PHE* 4.1 25.7 + + + +
602A ILE* 4.0 28.3 - - + +
605A ARG* 5.1 8.8 + - - +
615A ARG* 3.4 29.7 + - + -
616A GLU* 3.3 14.5 + - + +
617A LEU 3.3 0.4 - - - -
618A CYS* 1.3 80.1 - - + +
620A ILE* 1.3 58.6 + - + +
622A LEU* 3.8 16.0 - - + +
623A ALA* 2.9 28.9 + - - +
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Residues in contact with ILE 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A GLU 3.4 14.4 - - - +
617A LEU* 3.1 16.0 + - + +
619A TYR* 1.3 76.5 - - + +
621A ILE* 1.3 64.4 + - - +
623A ALA* 3.7 5.3 - - - +
624A GLY* 3.1 18.9 + - - -
657A MET* 3.3 33.7 - - + +
661A ALA* 3.9 7.9 - - + -
694A LEU* 4.5 21.3 - - + +
697A ALA* 5.0 8.1 - - + -
701A ILE* 4.3 16.6 - - + -
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Residues in contact with ILE 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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617A LEU* 2.9 24.6 + - + +
618A CYS* 3.1 14.1 + - - +
620A ILE* 1.3 77.7 - - - +
622A LEU* 1.3 59.7 + - - +
625A ILE* 3.1 22.7 + - + +
658A SER* 3.0 48.4 + - - +
661A ALA* 4.0 8.3 - - + +
662A LEU* 4.2 31.2 - - + +
665A LYS* 5.4 6.1 - - + -
817A MET* 4.2 11.9 - - + -
818A PHE* 3.5 29.8 - - + -
4005A 51E 5.1 0.4 - - - -
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Residues in contact with LEU 622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594A THR* 3.7 23.1 - - + +
597A VAL* 4.0 12.3 - - + -
598A THR* 3.7 31.6 - - + +
601A PHE* 4.0 25.1 - - + -
618A CYS* 2.7 26.6 + - + +
619A TYR* 3.8 14.6 - - + +
621A ILE* 1.3 72.5 - - - +
623A ALA* 1.3 58.5 + - - +
625A ILE* 3.4 3.8 + - + +
626A CYS* 3.0 27.2 + - - +
814A LEU* 4.2 9.6 - - + -
818A PHE* 3.8 28.5 - - + -
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Residues in contact with ALA 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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619A TYR 2.9 18.6 + - - +
620A ILE* 3.7 7.2 - - - +
621A ILE 3.3 0.2 - - - -
622A LEU* 1.3 75.8 - - - +
624A GLY* 1.3 59.7 + - - +
626A CYS* 3.2 7.0 + - - +
627A LEU* 2.9 33.2 + - + +
657A MET* 3.8 17.7 - - + -
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Residues in contact with GLY 624 (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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620A ILE 3.1 12.6 + - - -
621A ILE 3.4 0.2 + - - -
622A LEU 3.3 0.2 - - - -
623A ALA* 1.3 78.0 - - - +
625A ILE* 1.3 55.0 + - - +
627A LEU* 4.6 1.1 - - - -
628A GLY 3.0 20.4 + - - -
654A SER* 3.5 18.0 - - - -
657A MET* 3.8 12.9 - - - +
658A SER* 3.4 17.5 - - - -
4005A 51E 3.3 12.5 - - - -
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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
----------------------------------------------------------
594A THR* 3.9 10.3 - - + +
621A ILE* 3.1 21.3 + - + +
622A LEU* 3.7 7.0 - - - +
623A ALA 3.3 0.2 - - - -
624A GLY* 1.3 72.8 - - - +
626A CYS* 1.3 66.7 + - - +
628A GLY* 3.2 9.0 + - - -
629A TYR* 3.2 33.8 + - + -
810A ALA* 3.6 20.2 - - + +
813A ALA* 4.2 2.2 - - + -
814A LEU* 4.1 25.1 - - + +
818A PHE* 4.0 26.2 - - + -
4005A 51E 3.2 33.0 - - - -
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Residues in contact with CYS 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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591A LEU* 3.6 24.1 - - + +
594A THR* 4.4 13.4 - - + +
622A LEU 3.0 14.9 + - - +
623A ALA* 3.4 11.9 - - - +
625A ILE* 1.3 77.8 - - - +
627A LEU* 1.3 65.0 + - - +
629A TYR* 3.2 4.2 + - - -
630A LEU* 3.1 37.6 + - - +
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Residues in contact with LEU 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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623A ALA* 2.9 16.7 + - + +
624A GLY 3.9 2.5 - - - +
626A CYS* 1.3 77.6 - - + +
628A GLY* 1.3 61.6 + - - +
630A LEU* 3.2 26.1 + - + +
631A CYS* 3.1 25.3 + - - -
649A ILE 6.2 0.2 - - - +
650A GLY* 5.3 3.9 - - - -
653A LEU* 5.9 2.9 - - + -
654A SER* 3.2 19.7 - - - +
657A MET* 3.8 31.0 - - + -
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Residues in contact with GLY 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 GLY 3.0 15.3 + - - -
625A ILE 3.2 5.8 + - - -
626A CYS 3.1 0.8 - - - -
627A LEU* 1.3 75.9 - - - +
629A TYR* 1.3 62.3 + - - +
631A CYS* 3.1 14.2 + - - +
632A THR* 4.3 1.6 + - - +
654A SER* 3.8 0.4 + - - -
806A VAL* 3.1 23.7 - - - +
810A ALA* 4.9 3.6 - - - -
4005A 51E 3.8 24.5 - - - -
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Residues in contact with TYR 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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586A PHE* 4.4 5.4 - + - -
587A ALA* 3.4 34.0 - - - +
590A GLY* 3.5 42.7 - - - -
591A LEU* 3.7 20.4 - - + -
594A THR* 3.6 5.4 - - - -
625A ILE* 3.2 38.4 + - + -
626A CYS 3.2 1.8 + - - -
628A GLY* 1.3 75.5 - - - +
630A LEU* 1.3 62.5 + - - +
631A CYS 3.3 0.5 + - - -
632A THR* 3.5 11.4 + - - +
633A PHE* 3.7 3.3 - - - -
807A SER* 3.8 36.1 - - - -
810A ALA* 3.5 8.2 + - + +
811A THR* 2.9 35.6 + - - +
814A LEU* 4.2 7.8 - - + +
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Residues in contact with LEU 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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591A LEU* 3.7 29.2 - - + -
626A CYS* 3.1 27.4 + - - +
627A LEU* 3.5 34.8 - - + +
628A GLY 3.2 0.6 - - - -
629A TYR* 1.3 74.8 - - - +
631A CYS* 1.3 64.2 + - - +
632A THR 3.3 0.2 - - - -
633A PHE* 3.1 29.4 + - + +
634A CYS* 3.6 12.5 + - - -
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Residues in contact with CYS 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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627A LEU 3.1 22.3 + - - -
628A GLY* 3.2 16.4 - - - +
629A TYR 3.1 1.0 - - - -
630A LEU* 1.3 77.8 - - - +
632A THR* 1.3 54.6 + - - +
633A PHE 3.0 0.2 - - - -
634A CYS* 2.8 30.5 + - - +
635A LEU* 3.0 19.6 + - + +
646A LEU 6.1 0.2 - - - -
647A GLN* 5.0 2.1 - - - +
650A GLY* 3.3 40.2 - - - -
651A ILE* 3.7 17.7 - - + -
806A VAL* 4.2 8.5 - - + -
4005A 51E 4.2 4.9 - - - -
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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