Contacts of the helix formed by residues 613 - 631 (chain A) in PDB entry 5E2Q
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 VAL 613 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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582A ALA* 3.8 20.9 - - + +
583A GLY 4.1 4.3 - - - +
584A GLU* 3.7 45.3 - - + +
586A LEU* 4.2 7.2 - - + -
609A LYS* 3.2 22.5 + - + +
612A SER* 1.3 94.2 + - - +
614A GLY* 1.3 66.3 + - - +
616A PRO* 3.3 5.8 - - - +
617A ALA* 3.3 23.0 + - - +
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Residues in contact with GLY 614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A TRP* 3.9 16.3 - - - -
579A LEU* 4.2 5.9 - - - +
586A LEU* 3.7 19.9 - - - +
609A LYS 3.2 3.6 + - - -
610A ILE 3.0 11.3 + - - -
613A VAL* 1.3 79.7 - - - +
615A LYS* 1.3 56.7 + - - +
617A ALA* 3.3 3.6 + - - +
618A LEU* 2.8 31.0 + - - +
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Residues in contact with LYS 615 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A TYR* 2.7 41.3 + - + -
520A LEU* 3.8 27.6 - - + -
543A TRP* 4.1 5.3 - - - -
610A ILE 2.8 13.2 + - - +
611A ARG* 3.6 20.9 - - + +
614A GLY* 1.3 72.7 - - - +
616A PRO* 1.4 66.0 - - + +
618A LEU* 3.2 5.9 + - - +
619A GLU* 2.7 40.5 + - - +
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Residues in contact with PRO 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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611A ARG 3.5 14.4 - - - +
612A SER 3.3 19.1 - - - +
613A VAL* 3.3 16.6 - - - +
615A LYS* 1.4 95.7 - - + +
617A ALA* 1.3 54.5 + - - +
619A GLU* 3.6 13.6 - - + +
620A ARG* 3.0 28.6 + - - +
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Residues in contact with ALA 617 (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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578A VAL* 4.1 15.6 - - + +
579A LEU* 5.1 2.7 - - + -
582A ALA* 3.8 23.3 - - + -
613A VAL 3.3 18.3 + - - +
614A GLY* 3.3 4.6 + - - +
615A LYS 3.2 0.4 - - - -
616A PRO* 1.3 77.6 - - - +
618A LEU* 1.3 59.0 + - - +
620A ARG* 3.5 10.3 + - - +
621A PHE* 3.1 27.5 + - - +
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Residues in contact with LEU 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A SER* 3.6 47.6 - - - +
516A LEU* 3.8 13.7 - - + -
517A TYR* 3.7 27.1 - - + +
543A TRP* 3.9 14.6 - - + -
575A ILE* 4.8 15.5 - - + -
578A VAL* 5.0 4.7 - - + +
579A LEU* 4.9 8.0 - - + +
614A GLY 2.8 18.1 + - - +
615A LYS* 3.7 3.8 - - - +
617A ALA* 1.3 74.0 - - - +
619A GLU* 1.3 60.2 + - - +
621A PHE* 4.4 12.1 - - + -
622A LEU* 2.8 33.8 + - + +
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Residues in contact with GLU 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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358A PRO* 3.5 26.2 - - + +
517A TYR* 3.3 29.4 + - + +
615A LYS* 2.7 30.5 + - - +
616A PRO* 3.6 13.8 - - - +
618A LEU* 1.3 71.6 - - - +
620A ARG* 1.3 64.9 + - - +
622A LEU* 4.5 2.5 - - - -
623A ARG* 3.2 37.3 + - - +
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Residues in contact with ARG 620 (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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616A PRO 3.0 17.6 + - - +
617A ALA* 3.7 8.3 - - - +
618A LEU 3.3 0.2 - - - -
619A GLU* 1.3 76.8 - - - +
621A PHE* 1.3 63.1 + - - +
623A ARG* 3.4 27.5 + - - +
624A ARG* 3.3 38.1 + - + +
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Residues in contact with PHE 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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509A CYS* 3.7 24.7 - - - -
513A SER* 3.8 12.6 - - - -
574A VAL* 3.7 12.6 - - + -
575A ILE* 4.7 2.9 - - + -
578A VAL* 3.9 36.6 - - + -
617A ALA 3.1 14.9 + - - +
618A LEU* 3.8 11.4 - - + +
620A ARG* 1.3 80.8 - - - +
622A LEU* 1.3 64.4 + - - +
624A ARG* 3.4 7.1 + - + +
625A LEU* 3.2 60.0 + - + +
640A LEU* 4.6 12.6 - - + -
641A TYR* 5.1 2.2 - + - -
644A TYR* 4.1 24.0 - + - +
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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
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357A LEU* 4.5 0.4 - - + -
358A PRO* 3.7 33.0 - - + -
359A TRP* 3.9 7.9 - - + -
510A ARG* 3.7 36.1 - - + +
513A SER* 3.8 14.8 - - - +
514A VAL* 3.9 32.1 - - + +
517A TYR* 4.3 16.4 - - + -
618A LEU* 2.8 18.4 + - + +
621A PHE* 1.3 74.8 - - - +
623A ARG* 1.3 65.1 + - - +
625A LEU* 3.5 7.1 + - + +
626A GLN* 3.3 21.8 + - - +
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Residues in contact with ARG 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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358A PRO* 3.4 27.4 + - - +
359A TRP* 5.0 6.0 - - + +
360A PRO* 6.1 0.2 - - - -
479A PRO* 4.4 19.1 - - + -
480A GLU* 3.3 25.9 + - - +
619A GLU* 3.2 29.3 + - - +
620A ARG* 3.6 34.4 + - - +
621A PHE 3.3 0.2 - - - -
622A LEU* 1.3 75.6 - - - +
624A ARG* 1.3 63.0 + - - +
625A LEU 3.4 0.2 + - - -
626A GLN* 3.5 4.5 + - - +
627A VAL* 3.2 35.6 + - + +
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Residues in contact with ARG 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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480A GLU* 3.4 42.8 + - - +
620A ARG* 3.3 29.1 + - + +
621A PHE* 3.6 9.2 - - - +
622A LEU 3.3 0.2 - - - -
623A ARG* 1.3 77.2 - - - +
625A LEU* 1.3 61.6 + - - +
627A VAL* 3.4 6.2 + - - +
628A LEU* 3.2 65.2 + - - +
636A GLY 5.4 0.6 + - - -
640A LEU* 3.8 37.8 - - + +
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Residues in contact with LEU 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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506A TYR* 2.8 50.7 + - + +
509A CYS* 4.3 2.9 - - - +
510A ARG* 3.7 39.7 - - + +
513A SER* 4.5 0.2 - - - +
621A PHE* 3.2 52.1 + - + +
622A LEU* 3.7 14.6 - - + +
623A ARG 3.3 0.2 - - - -
624A ARG* 1.3 78.8 - - - +
626A GLN* 1.3 61.4 + - - +
629A LYS* 3.0 17.6 + - - +
640A LEU* 3.9 11.0 - - + -
641A TYR* 4.7 7.9 - - + -
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Residues in contact with GLN 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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359A TRP* 3.5 50.7 - - + +
363A PHE* 3.8 6.0 + - + +
458A GLY* 3.3 25.9 - - - -
459A LYS 3.8 2.4 - - - +
510A ARG* 2.8 38.9 + - - +
622A LEU 3.3 6.2 + - - +
623A ARG 4.0 2.9 - - - +
624A ARG 3.4 0.2 - - - -
625A LEU* 1.3 79.4 - - - +
627A VAL* 1.3 58.6 + - + +
629A LYS* 3.9 14.8 - - - +
630A SER* 2.9 60.5 + - - +
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Residues in contact with VAL 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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359A TRP* 5.9 3.4 - - + -
363A PHE* 4.0 16.4 - - + -
478A ASN* 3.2 33.7 - - - +
479A PRO* 4.2 15.9 - - + -
480A GLU* 4.2 18.8 - - + -
623A ARG* 3.2 23.5 + - + +
624A ARG* 3.7 4.9 - - - +
625A LEU 3.3 0.2 - - - -
626A GLN* 1.3 77.1 - - + +
628A LEU* 1.3 73.5 + - + +
630A SER* 4.0 1.0 - - - -
631A THR* 2.9 34.5 + - + +
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Residues in contact with LEU 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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499A PHE* 3.7 5.8 - - - -
506A TYR* 3.6 10.8 - - - +
624A ARG* 3.2 37.2 + - - +
627A VAL* 1.3 82.0 - - + +
629A LYS* 1.3 57.9 + - - +
631A THR* 3.6 4.3 - - - +
632A GLY* 3.1 5.5 + - - -
633A ASP* 2.9 61.5 + - + +
636A GLY* 3.4 29.4 - - - +
637A GLY* 3.7 4.7 - - - +
640A LEU* 3.8 26.2 - - + -
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Residues in contact with LYS 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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396A ASP* 6.0 0.9 - - - -
400A GLN* 5.1 0.2 - - - +
457A SER 4.4 5.1 + - - -
458A GLY 4.5 3.0 + - - -
460A LEU* 3.3 27.2 - - + +
489A TYR* 2.6 27.9 + - - -
495A TRP* 3.5 39.0 - - + -
499A PHE* 4.4 1.6 - - - -
506A TYR* 4.1 7.5 + - + -
507A GLU* 3.2 23.1 - - - +
510A ARG* 3.6 33.6 - - - +
625A LEU 3.0 18.9 + - - +
626A GLN* 3.6 20.1 - - - +
628A LEU* 1.3 75.8 - - - +
630A SER* 1.3 65.6 + - - +
632A GLY 3.1 2.6 + - - -
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Residues in contact with SER 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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363A PHE* 3.6 26.5 + - - -
459A LYS 2.6 27.2 + - - -
460A LEU* 4.4 2.7 - - - +
461A PHE* 3.1 36.9 + - - +
489A TYR* 3.4 7.4 - - - -
626A GLN* 2.9 35.3 + - - -
627A VAL 4.0 0.4 - - - -
629A LYS* 1.3 76.0 - - - +
631A THR* 1.3 59.2 + - - +
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Residues in contact with THR 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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363A PHE* 4.4 3.6 - - + -
461A PHE* 3.9 20.2 - - + -
478A ASN* 5.8 2.0 - - + +
485A ILE* 4.1 15.0 - - + -
486A GLN 5.8 0.2 - - - +
487A SER* 3.0 49.8 - - - +
488A TRP* 3.0 8.6 + - - +
489A TYR* 4.3 0.2 - - - -
627A VAL* 2.9 25.2 + - + +
628A LEU* 3.4 8.5 + - - +
630A SER* 1.3 75.7 - - - +
632A GLY* 1.3 61.8 + - - +
633A ASP* 3.5 13.7 - - - +
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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
------------------------------------------------------------
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