Contacts of the helix formed by residues 537 - 553 (chain A) in PDB entry 4CQ8
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 LYS 537 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A PRO* 3.4 22.9 + - - +
164A GLU* 3.7 25.6 - - + +
169A ASP* 2.9 34.0 + - - +
533A PHE 5.3 0.4 + - - -
534A ASN* 2.8 40.2 + - + +
536A MET* 1.3 75.6 - - - +
538A SER* 1.4 62.4 + - - +
539A ALA 3.3 1.4 + - - -
540A VAL* 3.3 4.6 + - - +
541A GLN* 2.9 59.5 + - + +
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Residues in contact with SER 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A PHE* 4.3 7.0 - - - -
527A LEU* 4.7 2.0 - - - -
530A CYS* 2.9 42.9 + - - -
531A LEU* 3.4 16.0 - - - -
534A ASN* 3.5 9.6 + - - +
535A GLY 2.7 20.6 + - - -
536A MET 3.2 1.7 - - - -
537A LYS* 1.4 77.0 - - - +
539A ALA* 1.4 58.0 + - - +
541A GLN* 4.0 2.6 - - - +
542A ILE* 3.0 33.7 + - - +
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Residues in contact with ALA 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A PHE* 5.6 1.3 - - + -
240A LEU* 3.6 19.3 - - + +
241A GLY* 3.6 23.3 - - - +
242A PHE* 3.8 28.5 - - + -
536A MET 4.6 2.4 + - - -
537A LYS 3.5 0.4 - - - -
538A SER* 1.4 75.1 - - - +
540A VAL* 1.3 66.6 + - - +
542A ILE* 3.6 7.7 - - - +
543A LYS* 3.0 33.6 + - + +
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Residues in contact with VAL 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ASN* 5.6 0.9 - - - +
163A PRO* 3.9 24.5 - - + -
164A GLU* 3.5 18.4 - - + +
200A ASP* 3.6 33.2 - - - +
202A SER* 5.4 3.4 - - - +
240A LEU 3.9 10.7 + - - +
537A LYS 3.3 6.4 + - - +
539A ALA* 1.3 76.1 - - - +
541A GLN* 1.3 62.5 + - - +
543A LYS* 3.9 9.2 - - - +
544A ARG* 3.2 46.8 + - - +
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Residues in contact with GLN 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A GLU* 4.2 12.2 + - - +
509A PHE 5.7 0.3 - - - +
534A ASN* 4.4 15.3 + - - +
537A LYS* 2.9 54.3 + - + +
538A SER* 4.0 3.4 - - - +
540A VAL* 1.3 74.3 - - - +
542A ILE* 1.3 63.7 + - - +
544A ARG* 3.3 18.0 + - - +
545A GLU* 3.0 49.8 + - + +
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Residues in contact with ILE 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A PHE* 3.7 39.9 - - + -
508A ILE* 3.7 23.1 - - + -
509A PHE 3.8 15.3 - - - +
510A SER* 3.5 35.7 - - - +
511A GLY 3.8 0.7 - - - +
527A LEU* 4.1 17.0 - - + -
530A CYS* 4.9 0.4 - - - -
538A SER 3.0 22.7 + - - +
539A ALA* 3.6 11.0 - - - +
541A GLN* 1.3 75.8 - - - +
543A LYS* 1.4 60.6 + - - +
545A GLU* 3.4 7.1 + - - +
546A LEU* 3.0 28.8 + - - +
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Residues in contact with LYS 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A ASP* 2.8 29.5 + - - -
202A SER* 5.4 1.3 - - - -
204A ASP* 2.8 26.4 + - - +
219A ASN* 3.6 27.1 - - + +
220A PRO* 5.0 1.3 - - + -
221A PHE* 3.6 26.5 - - + -
241A GLY* 2.8 25.7 + - - +
539A ALA 3.0 25.5 + - - +
540A VAL* 3.9 5.2 - - - +
542A ILE* 1.4 72.3 - - - +
544A ARG* 1.3 64.0 + - - +
546A LEU* 3.5 1.7 + - - +
547A ASN* 3.1 36.4 + - - +
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Residues in contact with ARG 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A GLU* 2.8 42.6 + - - -
540A VAL* 3.2 24.6 + - - +
541A GLN* 3.3 21.3 + - - +
543A LYS* 1.3 77.8 - - - +
545A GLU* 1.4 63.1 + - + +
547A ASN* 3.4 9.8 + - - +
548A HIS* 3.1 24.6 + - + +
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Residues in contact with GLU 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A PHE 4.4 1.7 - - - +
510A SER* 3.3 16.6 - - - -
511A GLY* 3.0 30.3 + - - +
541A GLN* 3.0 45.9 + - + +
542A ILE* 3.8 5.1 - - - +
544A ARG* 1.4 77.5 - - + +
546A LEU* 1.3 57.2 + - - +
548A HIS* 3.6 6.0 + - - +
549A LEU* 3.1 28.9 + - - +
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Residues in contact with LEU 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ALA* 5.2 2.5 - - + -
220A PRO* 3.7 31.0 - - + -
221A PHE* 3.7 16.2 - - + -
511A GLY* 3.9 24.8 - - - +
514A ALA* 4.6 0.4 - - + -
515A LEU* 4.1 24.7 - - + +
518A ILE* 4.2 9.0 - - + -
542A ILE 3.0 17.3 + - - +
543A LYS 4.1 3.1 - - - +
544A ARG 3.3 0.2 - - - -
545A GLU* 1.3 74.8 - - - +
547A ASN* 1.4 56.0 + - - +
549A LEU* 3.2 4.2 + - + +
550A LEU* 2.8 51.8 + - + +
558A LEU* 3.8 14.4 - - + -
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Residues in contact with ASN 547 (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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205A SER* 3.7 27.0 + - - +
207A TYR* 5.4 0.3 - - - +
208A ALA* 3.4 27.7 - - - +
543A LYS* 3.1 28.8 + - - +
544A ARG* 3.7 7.9 - - - +
546A LEU* 1.4 74.3 - - - +
548A HIS* 1.3 62.3 + - - +
550A LEU* 3.6 9.2 + - - +
551A TYR* 3.3 21.8 + - - +
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Residues in contact with HIS 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A ARG* 3.1 14.5 + - + +
545A GLU* 3.8 7.0 - - - +
546A LEU 3.3 0.2 - - - -
547A ASN* 1.3 77.5 - - - +
549A LEU* 1.3 58.4 + - + +
551A TYR* 3.2 9.9 + + - +
552A GLN* 3.0 71.1 + - + +
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Residues in contact with LEU 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511A GLY 3.6 7.9 - - - +
512A LEU* 3.5 46.9 - - + +
515A LEU* 3.7 26.7 - - + -
545A GLU 3.1 16.7 + - - +
546A LEU* 3.5 5.8 - - + +
548A HIS* 1.3 75.4 - - + +
550A LEU* 1.4 59.0 - - - +
552A GLN* 3.7 19.8 - - - +
553A ARG* 2.9 60.4 + - - +
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Residues in contact with LEU 550 (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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207A TYR* 4.4 8.1 - - + +
208A ALA* 4.6 8.7 - - + -
515A LEU* 4.2 15.3 - - + -
518A ILE* 6.4 0.2 - - + -
546A LEU* 2.8 46.0 + - + +
547A ASN* 3.9 8.1 - - - +
548A HIS 3.4 0.2 - - - -
549A LEU* 1.4 72.0 - - - +
551A TYR* 1.3 59.7 + - - +
553A ARG 3.5 0.7 + - - -
554A GLY 3.3 3.8 + - - -
555A TYR* 3.0 65.9 + - + +
557A ASN* 4.3 2.0 - - - +
558A LEU* 4.0 39.5 - - + +
561A ALA* 4.3 2.5 - - + -
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Residues in contact with TYR 551 (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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547A ASN 3.3 10.5 + - - +
548A HIS* 3.2 12.9 + + + +
550A LEU* 1.3 76.9 - - - +
552A GLN* 1.4 63.0 + - + +
554A GLY* 3.1 15.2 + - - -
555A TYR 4.7 8.1 - - - -
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Residues in contact with GLN 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A HIS* 3.0 52.2 + - + +
549A LEU* 3.4 23.8 + - + +
551A TYR* 1.4 75.3 - - + +
553A ARG* 1.3 66.2 + - + +
554A GLY 3.3 0.9 + - - -
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Residues in contact with ARG 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A LEU* 3.5 29.3 - - - +
515A LEU* 3.8 25.0 - - + +
519A GLU* 4.6 11.5 + - - +
549A LEU* 2.9 36.7 + - + +
551A TYR 3.3 0.2 - - - -
552A GLN* 1.3 79.4 - - - +
554A GLY* 1.3 60.6 + - - +
555A TYR* 3.5 28.6 - - + -
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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
------------------------------------------------------------
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