Contacts of the helix formed by residues 615 - 629 (chain A) 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 SER 615 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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613A ALA 3.2 4.4 + - - -
614A THR* 1.3 75.6 - - - +
616A GLU* 1.3 69.0 + - - +
617A LEU* 4.5 3.1 - - - -
618A VAL* 3.7 17.9 - - - -
619A GLN* 2.9 25.2 + - - +
656A GLU* 3.3 25.4 + - - +
657A TRP* 6.2 0.4 - - - -
554O GLN 3.7 14.7 + - - -
555O ASN* 4.2 13.3 + - - +
556O GLN* 4.7 1.3 - - - -
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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
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615A SER* 1.3 73.1 - - - +
617A LEU* 1.3 57.1 + - - +
619A GLN* 3.7 6.0 - - + +
620A THR* 2.2 39.7 + - - +
779A MET* 3.2 26.5 - - + +
555O ASN 3.6 17.3 + - - +
556O GLN* 3.9 21.6 - - + +
557O MET 3.3 4.3 + - - -
558O SER* 2.6 54.5 + - - -
559O GLU* 4.3 5.3 + - - -
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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
----------------------------------------------------------
615A SER* 3.3 3.5 - - - -
616A GLU* 1.3 77.2 - - - +
618A VAL* 1.3 62.9 + - + +
620A THR* 3.5 5.0 - - - -
621A CYS* 3.0 31.4 + - - -
657A TRP* 3.8 34.5 - - + -
773A LEU* 3.3 32.1 - - + -
779A MET* 4.7 11.7 - - + -
782A GLY* 3.3 44.6 - - - +
785A SER* 4.4 5.4 - - - -
786A LEU* 4.9 3.4 - - + -
555O ASN* 6.2 2.9 - - - +
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Residues in contact with VAL 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A ALA* 4.9 1.8 - - - +
615A SER* 3.1 26.7 + - - +
617A LEU* 1.3 77.4 - - + +
619A GLN* 1.3 66.2 + - - +
621A CYS* 3.4 4.0 + - - +
622A LEU* 3.0 26.4 + - + +
641A TRP* 3.9 24.2 - - + -
656A GLU* 4.0 10.5 - - + +
657A TRP* 3.8 41.5 - - + +
660A PHE* 3.7 27.8 - - + -
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Residues in contact with GLN 619 (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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612A ILE* 5.4 4.9 - - + +
613A ALA* 3.4 27.5 - - + +
614A THR 4.7 0.5 + - - -
615A SER 2.9 14.6 + - - +
616A GLU* 3.7 7.2 - - + +
618A VAL* 1.3 75.8 - - - +
620A THR* 1.3 67.3 + - - +
622A LEU* 3.0 8.3 + - - +
623A GLN* 3.0 42.8 + - + +
556O GLN* 2.7 34.7 + - - +
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Residues in contact with THR 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A GLU* 2.2 35.5 + - - +
617A LEU* 3.5 7.8 - - - -
619A GLN* 1.3 77.9 - - - +
621A CYS* 1.3 64.4 + - - +
623A GLN* 3.2 10.5 + - - +
624A ALA* 3.2 20.4 + - - +
769A VAL* 4.1 20.6 - - + -
773A LEU* 4.6 9.5 - - + +
779A MET* 4.8 5.2 - - - +
866A ILE* 3.1 42.6 - - + +
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Residues in contact with CYS 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* 3.0 22.8 + - - +
618A VAL 3.8 3.8 - - - +
620A THR* 1.3 78.7 - - - +
622A LEU* 1.3 59.6 + - - +
624A ALA* 3.2 3.0 + - - +
625A ILE* 2.7 47.3 + - + +
657A TRP* 3.9 23.1 - - + -
660A PHE* 4.4 9.2 - - + -
766A LEU* 4.6 14.8 - - + -
769A VAL* 4.0 28.3 - - - -
786A LEU* 4.3 7.4 - - - -
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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
----------------------------------------------------------
612A ILE* 4.3 20.4 - - + +
613A ALA* 4.8 1.3 - - + -
618A VAL* 3.0 21.6 + - + +
619A GLN* 3.0 11.7 + - - +
621A CYS* 1.3 76.1 - - - +
623A GLN* 1.3 66.1 - - - +
625A ILE* 3.2 7.1 + - + +
626A LYS* 2.9 28.8 + - - +
637A MET* 4.5 22.7 - - + -
638A LEU* 4.9 13.0 - - + +
641A TRP* 3.5 41.5 - - + -
660A PHE* 3.6 24.9 - - + -
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Residues in contact with GLN 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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612A ILE* 4.7 10.7 - - - +
619A GLN* 3.0 42.0 + - + +
620A THR* 3.5 9.6 - - - +
622A LEU* 1.3 76.4 - - - +
624A ALA* 1.3 58.7 + - + +
626A LYS* 3.4 33.6 + - - +
627A PHE* 2.9 29.5 + - - +
865A GLY* 5.9 3.6 - - - -
866A ILE* 5.0 13.7 - - + +
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Residues in contact with ALA 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 THR 3.2 8.6 + - - +
621A CYS 3.2 6.6 + - - +
623A GLN* 1.3 81.4 - - - +
625A ILE* 1.3 62.9 + - + +
627A PHE* 3.3 7.7 + - - +
628A ILE* 3.1 24.8 + - - +
765A VAL* 3.8 25.0 - - + +
766A LEU* 5.6 0.4 - - - -
769A VAL* 3.9 22.0 - - + -
863A LEU* 4.4 4.0 - - + -
866A ILE* 4.2 13.7 - - + -
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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
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621A CYS* 2.7 36.1 + - + +
622A LEU* 3.5 10.8 - - + +
624A ALA* 1.3 73.6 - - + +
626A LYS* 1.3 62.2 + - - +
628A ILE* 3.2 19.4 - - - +
629A LEU* 3.1 24.9 - - + +
637A MET* 4.0 32.8 - - + -
660A PHE* 4.0 23.8 - - + -
664A LEU* 4.4 7.4 - - + -
762A ILE* 4.1 24.9 - - + -
765A VAL* 4.5 5.2 - - + -
766A LEU* 4.1 18.2 - - + -
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Residues in contact with LYS 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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436A LEU 3.1 20.9 + - - -
437A CYS* 3.9 24.7 - - + +
612A ILE* 5.4 5.1 - - - +
622A LEU* 2.9 15.6 + - - +
623A GLN* 3.4 39.0 + - - +
625A ILE* 1.3 76.8 - - + +
627A PHE* 1.3 65.3 + - - +
629A LEU* 3.3 28.6 - - - +
630A PRO 4.2 2.1 - - - +
634A ALA* 4.1 18.0 - - + +
637A MET* 6.1 1.6 - - + -
638A LEU* 3.9 25.6 - - + +
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Residues in contact with PHE 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 GLN 2.9 16.7 + - - +
624A ALA* 3.6 7.0 - - - +
626A LYS* 1.3 79.3 - - - +
628A ILE* 1.3 72.6 + - + +
629A LEU 3.4 4.9 - - - +
863A LEU* 4.0 28.3 - - + -
864A PRO* 3.9 33.7 - - + -
865A GLY* 5.7 2.7 - - - -
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Residues in contact with ILE 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 ALA 3.1 7.8 + - - +
625A ILE 3.2 10.3 - - - +
627A PHE* 1.3 91.1 - - + +
629A LEU* 1.3 75.5 + - + +
630A PRO* 4.9 0.2 - - - +
758A HIS* 5.2 3.5 + - + -
761A ALA* 3.5 21.2 - - + +
762A ILE* 3.5 49.6 - - + +
765A VAL* 3.6 35.9 - - + -
863A LEU* 4.7 1.6 - - + -
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Residues in contact with LEU 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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625A ILE* 3.1 25.6 - - + +
626A LYS* 3.3 18.9 - - - +
627A PHE 3.4 4.9 - - - +
628A ILE* 1.3 89.0 - - + +
630A PRO* 1.4 80.7 - - + +
633A ILE* 3.6 27.8 - - + +
634A ALA* 3.1 40.4 - - + +
637A MET* 4.2 13.0 - - + -
758A HIS* 4.4 15.9 - - + -
762A ILE* 5.3 4.7 - - + -
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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