Contacts of the helix formed by residues 623 - 641 (chain A) in PDB entry 3DPK
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 HIS 623 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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593A PHE* 5.5 0.2 - - - -
621A THR 3.9 4.9 + - - +
622A ALA* 1.3 78.3 + - - +
624A ALA* 1.3 63.0 + - - +
625A ASP* 3.1 5.8 - - + +
626A GLU* 2.8 30.2 + - + +
627A LYS* 3.2 19.2 + - - +
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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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623A HIS* 1.3 79.4 + - - +
625A ASP* 1.3 63.1 + - - +
627A LYS* 3.8 16.3 - - + +
628A GLU* 3.1 23.6 + - - +
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Residues in contact with ASP 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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623A HIS* 3.0 4.4 + - + +
624A ALA* 1.3 78.3 - - - +
626A GLU* 1.3 70.9 + - + +
628A GLU* 3.5 14.8 - - - +
629A ALA* 3.2 22.3 + - - +
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Residues in contact with GLU 626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A PHE* 3.3 44.0 - - + +
618A LEU* 3.5 14.7 - - + +
622A ALA* 3.6 21.8 - - + -
623A HIS* 2.8 26.6 + - - +
625A ASP* 1.3 86.2 - - - +
627A LYS* 1.3 65.9 + - - +
628A GLU 3.1 2.2 - - - -
629A ALA* 3.4 8.9 + - - +
630A LEU* 3.0 17.5 + - - +
799A LEU* 5.1 7.9 - - + +
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Residues in contact with LYS 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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618A LEU* 3.0 31.6 - - + +
622A ALA* 3.4 23.4 + - - +
623A HIS* 3.2 14.5 + - - +
624A ALA* 3.4 17.6 + - + +
626A GLU* 1.3 76.6 - - - +
628A GLU* 1.3 58.1 + - - +
630A LEU* 3.4 4.2 + - - +
631A MET* 3.1 32.5 + - + +
659A VAL* 5.6 7.3 - - + +
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Residues in contact with GLU 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 16.5 + - - +
625A ASP* 3.5 12.6 - - - +
626A GLU 3.1 0.2 - - - -
627A LYS* 1.3 75.8 - - - +
629A ALA* 1.3 63.1 + - - +
631A MET* 3.2 7.8 + - - +
632A SER* 2.8 30.9 + - - -
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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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549A ARG* 5.6 13.9 - - - +
625A ASP 3.2 11.6 + - - +
626A GLU* 3.4 12.1 + - - +
628A GLU* 1.3 80.3 - - - +
630A LEU* 1.3 57.4 + - - +
632A SER* 3.5 8.2 + - - -
633A GLU* 3.0 27.0 + - - +
799A LEU* 4.0 20.5 - - + +
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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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616A LYS* 3.8 30.3 - - + -
617A MET* 4.5 4.5 - - - -
618A LEU* 4.0 30.3 - - + +
626A GLU 3.0 14.0 + - - +
627A LYS 3.6 9.0 - - - +
629A ALA* 1.3 77.4 - - - +
631A MET* 1.3 62.4 + - - +
633A GLU* 3.2 6.9 + - - +
634A LEU* 3.0 19.9 + - - +
659A VAL* 3.7 39.9 - - + +
661A VAL* 3.9 19.3 - - + -
799A LEU* 4.0 14.3 - - + +
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Residues in contact with MET 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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571A TYR* 4.1 22.9 - - + -
627A LYS* 3.1 21.8 + - + +
628A GLU* 3.7 7.9 - - - +
630A LEU* 1.3 75.8 - - - +
632A SER* 1.3 57.9 + - - +
634A LEU* 3.2 23.2 + - + +
635A LYS* 2.9 51.2 + - + +
654A THR* 4.2 11.7 - - + -
659A VAL* 4.0 35.7 - - + -
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Residues in contact with SER 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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549A ARG* 5.8 1.9 + - - -
566A PRO 5.8 1.3 - - - -
628A GLU* 2.8 21.2 + - - -
629A ALA* 3.6 9.2 - - - -
631A MET* 1.3 76.4 - - - +
633A GLU* 1.3 64.0 + - - +
635A LYS* 3.5 12.7 + - - +
636A ILE* 3.2 33.7 + - - +
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Residues in contact with GLU 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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549A ARG* 6.0 0.3 - - - +
616A LYS* 2.5 37.3 + - - +
629A ALA 3.0 13.6 + - - +
630A LEU* 3.2 11.1 + - + +
632A SER* 1.3 76.3 - - - +
634A LEU* 1.3 63.3 + - - +
636A ILE* 3.4 8.7 + - - +
637A MET* 3.1 35.5 + - + +
661A VAL* 5.5 3.0 - - + +
796A ASP* 3.8 33.0 - - + +
799A LEU* 3.1 27.7 + - + +
923A 8C5 3.3 13.0 - - - +
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Residues in contact with LEU 634 (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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571A TYR* 3.6 36.6 - - + -
575A TRP* 5.4 0.2 - - + -
630A LEU 3.0 12.6 + - - +
631A MET* 3.2 28.5 + - + +
633A GLU* 1.3 76.8 - - - +
635A LYS* 1.3 58.2 + - - +
637A MET* 3.5 5.3 + - - +
638A SER* 2.9 26.7 + - - -
649A LEU* 3.8 32.1 - - + -
652A ALA* 3.9 19.1 - - + -
654A THR* 4.1 6.7 - - + -
659A VAL* 5.2 0.2 - - + -
661A VAL* 3.9 24.7 - - + +
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Residues in contact with LYS 635 (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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566A PRO* 3.6 34.7 + - + +
571A TYR* 4.4 30.1 - - + +
631A MET* 2.9 44.1 + - + +
632A SER* 3.8 9.5 - - - +
633A GLU 3.2 0.2 - - - -
634A LEU* 1.3 75.6 - - + +
636A ILE* 1.3 66.3 + - - +
638A SER* 3.0 20.9 + - - +
639A HIS* 3.2 11.4 + - - +
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Residues in contact with ILE 636 (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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550A TRP* 3.6 36.8 - - + +
551A LYS* 4.6 2.7 - - - -
552A ILE* 4.4 28.7 - - + +
566A PRO* 4.5 13.9 - - + -
632A SER* 3.2 25.8 + - - +
633A GLU* 3.4 7.6 + - - +
635A LYS* 1.3 76.4 - - + +
637A MET* 1.3 64.6 + - + +
639A HIS* 3.0 5.6 + - - +
640A LEU* 3.0 43.5 + - + +
774A CYS* 4.8 5.4 - - - -
796A ASP* 5.7 1.1 - - - +
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Residues in contact with MET 637 (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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550A TRP* 6.0 8.1 - - + -
575A TRP* 5.5 0.5 - - - -
633A GLU* 3.1 28.5 + - + +
634A LEU 3.6 5.4 - - - +
636A ILE* 1.3 80.3 - - + +
638A SER* 1.3 62.3 + - - +
639A HIS 3.3 0.7 + - - -
640A LEU* 3.5 16.6 + - + +
641A GLY* 3.9 9.0 + - - +
646A ILE* 5.5 2.5 - - + -
647A VAL 3.2 27.4 - - - +
649A LEU* 3.7 40.4 - - + +
661A VAL* 4.6 6.5 - - - -
663A THR* 3.7 12.6 - - + -
795A GLY* 6.2 0.7 - - - -
796A ASP* 5.9 4.7 - - + +
923A 8C5 3.2 34.8 - - - +
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Residues in contact with SER 638 (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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571A TYR* 5.6 4.2 - - - -
572A ASN* 5.4 7.0 + - - +
574A LYS* 5.4 4.0 + - - -
575A TRP* 3.3 40.5 + - - +
634A LEU* 2.9 17.0 + - - -
635A LYS* 3.0 21.0 + - - +
637A MET* 1.3 77.1 - - - +
639A HIS* 1.3 61.0 + - - +
641A GLY* 4.2 5.2 + - - -
649A LEU* 3.7 10.9 - - - +
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Residues in contact with HIS 639 (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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552A ILE* 5.1 15.0 - - + +
562A THR* 6.4 0.4 - - + -
564A ILE* 3.6 36.1 - - + +
566A PRO* 3.2 31.3 - - + +
635A LYS 3.5 13.2 - - - +
636A ILE 3.0 3.8 + - - +
638A SER* 1.3 80.4 + - - +
640A LEU* 1.3 69.1 + - + +
641A GLY* 3.3 2.8 + - - -
772A LYS* 5.1 8.4 + - + -
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Residues in contact with LEU 640 (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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550A TRP* 4.0 17.0 - - + -
552A ILE* 4.0 20.9 - - + -
636A ILE* 3.0 33.5 + - + +
637A MET* 3.5 9.1 + - + +
639A HIS* 1.3 81.6 - - + +
641A GLY* 1.3 67.5 + - - +
646A ILE* 5.9 2.9 - - + -
768A PHE* 3.6 13.0 - - + -
769A LEU* 3.9 24.5 - - + -
772A LYS* 3.2 59.6 + - + +
774A CYS* 4.2 4.9 - - + -
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Residues in contact with GLY 641 (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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637A MET 3.9 9.1 + - - +
638A SER 4.2 4.7 + - - -
639A HIS 3.3 3.8 - - - -
640A LEU* 1.3 88.0 - - - +
642A GLN* 1.3 67.4 + - - -
646A ILE* 5.6 2.4 - - - +
648A ASN* 4.1 4.0 - - - +
768A PHE* 3.8 8.9 - - - -
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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
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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