Contacts of the helix formed by residues 540 - 559 (chain A) in PDB entry 3IKM
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 GLN 540 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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538A GLU* 5.6 1.3 - - + +
539A PHE* 1.3 117.8 - - + +
541A GLN* 1.3 71.6 + - - +
542A ASP* 2.8 21.9 + - - +
543A VAL* 2.7 35.2 - - - +
544A MET* 3.2 4.7 + - - +
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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
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540A GLN* 1.3 86.0 + - + +
542A ASP* 1.3 67.8 + - - +
544A MET* 2.9 22.4 - - + +
545A ALA* 2.3 44.6 + - + +
396C ARG* 4.3 16.2 - - - +
400C GLN* 4.3 21.8 - - + +
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Residues in contact with ASP 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A GLU* 2.5 46.1 - - + +
540A GLN* 2.8 21.1 - - - +
541A GLN* 1.3 85.6 - - - +
543A VAL* 1.3 58.0 + - - +
545A ALA* 3.0 3.3 + - - -
546A ARG* 2.2 52.4 + - + +
122B ARG* 5.6 1.2 + - - -
400C GLN* 4.8 5.1 + - - +
404C ASN* 2.9 21.7 + - - +
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Residues in contact with VAL 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A GLU* 3.8 34.3 - - + -
537A GLU 6.2 0.2 - - - +
538A GLU 3.3 23.3 + - - +
539A PHE* 4.6 1.8 - - - -
540A GLN 2.7 30.7 - - - +
542A ASP* 1.3 76.2 - - - +
544A MET* 1.3 73.0 + - + +
546A ARG* 4.2 8.2 - - - +
547A ALA* 2.6 35.5 + - + +
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Residues in contact with MET 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A GLN 3.9 2.5 - - - +
541A GLN* 2.9 27.6 - - + +
543A VAL* 1.3 88.1 - - + +
545A ALA* 1.3 58.4 + - - +
547A ALA* 4.2 1.7 - - - +
548A CYS* 2.9 27.2 + - + +
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Residues in contact with ALA 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A GLN* 2.3 35.0 + - + +
542A ASP 3.6 1.3 - - - +
544A MET* 1.3 66.6 - - - +
546A ARG* 1.3 68.0 + - - +
548A CYS* 2.6 32.4 + - - -
549A LEU* 2.7 9.5 + - - +
396C ARG* 6.0 0.2 - - - +
397C GLN* 5.2 8.7 - - + +
400C GLN* 2.8 36.3 - - + +
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Residues in contact with ARG 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A GLU* 2.9 56.8 + - - +
538A GLU* 4.7 10.2 + - - +
542A ASP* 2.2 54.8 + - + +
543A VAL* 3.9 5.2 - - - +
545A ALA* 1.3 69.9 - - - +
547A ALA* 1.3 62.7 + - - +
549A LEU* 3.1 15.5 + - - +
550A GLN* 2.8 28.0 + - - +
400C GLN* 4.6 3.1 + - - +
401C GLY* 5.6 5.4 - - - +
404C ASN* 4.5 14.3 - - + +
405C GLU* 4.3 13.8 - - + +
408C GLU* 2.8 39.4 + - - +
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Residues in contact with ALA 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A GLU* 5.2 8.7 - - + +
543A VAL* 2.6 32.6 + - + +
544A MET* 4.2 1.1 - - - +
546A ARG* 1.3 74.8 - - - +
548A CYS* 1.3 59.2 + - - +
549A LEU 3.4 0.2 + - - -
550A GLN* 3.1 20.5 - - - +
551A LYS* 3.4 15.2 + - - +
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Residues in contact with CYS 548 (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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544A MET* 2.9 14.4 + - + +
545A ALA* 2.6 45.1 + - - -
547A ALA* 1.3 70.1 - - - +
549A LEU* 1.3 63.3 + - - +
551A LYS* 3.1 16.4 - - + +
552A LEU* 2.8 36.9 + - + +
397C GLN* 5.0 10.1 - - - -
398C VAL* 4.3 17.9 - - - -
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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
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545A ALA 2.7 10.1 + - - +
546A ARG* 3.1 12.3 + - - +
548A CYS* 1.3 77.9 - - - +
550A GLN* 1.3 52.9 + - - +
552A LEU* 2.9 16.0 + - + +
553A LYS* 2.4 56.3 + - + +
398C VAL* 2.9 46.4 - - + +
401C GLY* 3.2 43.5 - - - +
402C LEU* 3.3 15.3 - - + -
405C GLU* 5.7 1.1 - - + -
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Residues in contact with GLN 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A ARG* 2.8 36.2 + - - +
547A ALA* 3.1 22.9 - - - +
548A CYS 3.5 0.2 - - - -
549A LEU* 1.3 72.9 - - - +
551A LYS* 1.3 58.8 + - - +
553A LYS* 3.9 17.0 - - - +
554A GLY* 2.2 38.1 + - - -
405C GLU* 6.1 3.4 - - - +
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Residues in contact with LYS 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 ALA 3.4 11.9 + - - +
548A CYS* 3.1 26.0 + - + +
549A LEU 3.1 0.2 - - - -
550A GLN* 1.3 76.0 - - - +
552A LEU* 1.3 82.2 + - + +
554A GLY* 5.0 0.2 - - - -
555A THR* 2.6 40.1 + - - +
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Residues in contact with LEU 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A CYS* 2.8 21.4 + - + +
549A LEU* 3.1 35.4 - - + +
551A LYS* 1.3 104.6 - - + +
553A LYS* 1.3 52.9 + - + +
555A THR* 4.0 3.4 - - - -
556A THR* 2.6 33.7 + - - -
397C GLN* 5.1 2.7 - - - +
398C VAL* 3.5 18.4 - - + -
448C LEU* 3.1 45.1 - - + -
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Residues in contact with LYS 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A LEU* 2.4 46.3 + - + +
550A GLN* 3.6 17.7 - - - +
552A LEU* 1.3 71.7 - - + +
554A GLY* 1.3 68.5 + - - +
556A THR* 2.7 26.1 + - - -
557A GLU* 3.3 8.8 + - - +
402C LEU* 5.0 1.2 - - + +
405C GLU* 4.3 25.2 + - - +
467C HIS* 3.6 10.2 + - + -
468C ILE* 2.9 37.0 - - + +
469C SER* 4.6 13.4 - - - +
472C LYS* 4.7 12.1 - - - +
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Residues in contact with GLY 554 (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 GLN* 2.2 27.8 + - - +
551A LYS* 3.7 0.4 - - - -
553A LYS* 1.3 67.0 - - - +
555A THR* 1.3 55.0 + - - -
557A GLU* 2.7 37.1 + - - +
558A LEU* 3.5 2.6 + - - +
566A LEU* 5.7 0.2 - - - +
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Residues in contact with THR 555 (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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551A LYS* 2.6 35.2 + - - +
552A LEU* 4.1 3.8 - - - -
554A GLY* 1.3 65.9 - - - -
556A THR* 1.3 52.1 + - - +
557A GLU 2.8 6.1 - - - -
558A LEU* 2.7 29.6 + - + +
559A LEU* 2.6 43.4 + - + +
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Residues in contact with THR 556 (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 LEU 2.6 20.8 + - - -
553A LYS* 2.7 18.9 + - - -
555A THR* 1.3 72.1 - - - +
557A GLU* 1.3 55.3 + - - +
559A LEU* 2.8 31.7 - - - +
560A PRO 3.5 1.0 - - - +
448C LEU* 6.0 0.9 - - - +
451C GLY* 4.3 0.9 - - - -
452C LEU* 2.7 55.0 + - + +
467C HIS* 2.8 30.1 + - + +
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Residues in contact with GLU 557 (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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553A LYS 3.4 6.9 - - - +
554A GLY* 2.7 29.0 - - - +
555A THR 2.8 1.4 - - - -
556A THR* 1.3 74.8 - - - +
558A LEU* 1.3 62.5 + - - +
559A LEU 2.7 16.6 - - - +
560A PRO 3.6 8.3 - - - +
561A LYS* 5.5 0.9 - - - +
562A ARG 5.4 2.9 - - - +
563A PRO* 5.6 5.7 - - - +
566A LEU* 4.3 29.8 - - + +
569A HIS* 4.7 16.0 - - - -
467C HIS* 2.8 35.0 + - - -
469C SER* 4.1 9.2 + - - -
470C LYS* 5.5 2.8 - - - +
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Residues in contact with LEU 558 (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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554A GLY 3.5 2.0 + - - +
555A THR* 2.7 35.6 + - + +
557A GLU* 1.3 75.4 - - - +
559A LEU* 1.3 72.2 + - + +
563A PRO* 5.8 9.7 - - - +
566A LEU* 5.8 0.4 - - - +
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Residues in contact with LEU 559 (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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555A THR* 2.6 18.2 + - + +
556A THR* 2.8 21.3 - - - +
557A GLU 2.7 11.4 - - - +
558A LEU* 1.3 93.0 - - + +
560A PRO* 1.4 74.9 - - + +
561A LYS 3.9 5.2 + - - +
451C GLY* 2.5 47.6 - - - +
452C LEU* 3.8 3.1 - - + -
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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