Contacts of the helix formed by residues 554 - 574 (chain A) in PDB entry 3KUT
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 PRO 554 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552A SER 4.1 2.2 - - - +
553A ALA* 1.3 85.3 - - + +
555A PRO* 1.3 76.7 - - + +
556A GLN* 4.3 6.1 - - + +
557A GLU* 2.8 53.1 + - + +
558A GLN 2.9 10.2 + - - -
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Residues in contact with PRO 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A ALA 3.3 3.8 - - - +
554A PRO* 1.3 83.4 - - + +
556A GLN* 1.3 62.5 + - - +
558A GLN* 3.1 22.0 + - - +
559A LYS* 3.1 27.5 + - - +
552B SER 5.8 3.6 - - - +
554B PRO* 3.8 25.6 - - + -
557B GLU* 4.0 20.6 - - - +
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Residues in contact with GLN 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A PRO* 3.1 5.8 - - + +
555A PRO* 1.3 79.1 - - - +
557A GLU* 1.3 62.6 + - + +
559A LYS* 3.4 7.0 + - - +
560A GLN* 3.1 23.9 + - - +
551B ALA* 3.0 30.6 + - - +
552B SER* 3.6 10.4 - - - +
553B ALA* 3.4 19.0 + - - -
554B PRO* 3.5 28.7 - - + +
555B PRO* 6.1 0.4 - - - +
558B GLN* 5.3 1.4 - - - +
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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
----------------------------------------------------------
553A ALA* 4.8 5.0 - - + +
554A PRO* 2.8 40.6 + - + +
556A GLN* 1.3 79.8 - - + +
558A GLN* 1.3 58.0 + - - +
559A LYS 3.2 0.4 - - - -
560A GLN* 3.6 9.4 - - + +
561A MET* 2.9 35.8 + - + +
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Residues in contact with GLN 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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550A LEU* 2.8 50.6 + - + +
551A ALA* 4.5 3.6 - - - +
552A SER 4.5 1.6 - - - +
553A ALA* 3.5 19.3 + - + +
554A PRO 2.9 13.3 + - - +
555A PRO* 3.1 22.2 + - - +
557A GLU* 1.3 76.5 - - - +
559A LYS* 1.3 58.0 + - - +
561A MET* 3.3 5.2 + - - +
562A LEU* 3.0 35.4 + - - +
590A ASN* 3.2 25.5 - - - +
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Residues in contact with LYS 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A PRO* 3.1 18.4 + - - +
556A GLN* 3.6 8.7 - - - +
557A GLU 3.2 0.2 - - - -
558A GLN* 1.3 76.1 - - - +
560A GLN* 1.3 57.3 + - - +
562A LEU* 4.6 0.9 - - + -
563A GLY* 2.8 26.3 + - - -
586A LEU* 2.8 49.2 + - + +
587A GLU 4.3 2.4 + - - -
588A ILE 2.8 25.5 + - - -
589A ASP* 4.6 1.0 - - - +
590A ASN* 2.8 34.2 - - - +
593A LEU* 4.1 1.0 - - - +
1B CL 3.8 17.2 - - + +
554B PRO* 4.5 16.8 - - + -
555B PRO* 5.6 2.2 - - + -
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Residues in contact with GLN 560 (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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556A GLN 3.1 13.9 + - - +
557A GLU* 3.2 13.9 + - + +
559A LYS* 1.3 75.3 - - - +
561A MET* 1.3 56.5 + - - +
563A GLY* 3.2 0.3 + - - -
564A GLU* 2.8 61.5 + - + +
118C PHE* 3.5 20.8 - - - -
119C VAL 3.2 20.6 + - - +
121C GLY 4.2 1.0 + - - -
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Residues in contact with MET 561 (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 LEU* 3.5 24.9 - - + -
549A MET* 3.6 34.3 - - + +
550A LEU* 3.9 14.8 - - + -
553A ALA* 4.8 11.7 - - + -
557A GLU* 2.9 18.3 + - + +
558A GLN 3.5 8.7 - - - +
560A GLN* 1.3 76.3 - - - +
562A LEU* 1.3 64.2 + - - +
564A GLU* 3.4 6.9 + - - -
565A ARG* 2.9 45.1 + - - +
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Residues in contact with LEU 562 (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 LEU* 3.5 25.8 - - + -
550A LEU* 4.1 7.6 - - + -
558A GLN 3.0 21.4 + - - +
559A LYS* 3.8 4.5 - - - +
561A MET* 1.3 76.9 - - - +
563A GLY* 1.3 57.9 + - - +
565A ARG* 3.1 5.4 + - - +
566A LEU* 2.9 36.7 + - + +
586A LEU* 4.0 8.1 - - + -
590A ASN* 3.3 42.2 - - + +
593A LEU* 4.0 22.4 - - + -
594A LEU* 3.9 16.2 - - + +
597A LEU* 3.8 16.6 - - + +
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Residues in contact with GLY 563 (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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559A LYS 2.8 21.6 + - - -
560A GLN 3.2 0.2 + - - -
562A LEU* 1.3 73.8 - - - +
564A GLU* 1.3 56.2 + - - +
566A LEU* 4.4 1.3 - - - -
567A PHE* 2.8 34.8 + - - +
582A THR* 4.2 5.6 - - - +
586A LEU* 3.6 13.9 - - - +
118C PHE* 3.3 22.1 - - - -
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Residues in contact with GLU 564 (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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560A GLN* 2.8 43.9 + - + +
561A MET* 3.8 7.9 - - - +
562A LEU 3.3 0.2 - - - -
563A GLY* 1.3 75.9 - - - +
565A ARG* 1.3 71.1 + - - +
567A PHE* 4.5 1.0 - - - +
568A PRO* 3.2 21.8 - - - +
118C PHE* 3.4 1.8 - - - -
120C PRO* 3.6 14.3 - - - +
121C GLY* 2.8 38.0 + - - +
122C VAL* 4.7 3.3 - - - +
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Residues in contact with ARG 565 (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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543A SER* 2.7 46.0 + - - +
544A PRO 4.8 0.2 + - - -
545A LEU* 3.9 31.3 - - + +
549A MET* 4.6 9.1 - - - +
561A MET* 2.9 44.1 + - - +
562A LEU 3.1 6.1 + - - +
564A GLU* 1.3 89.6 - - - +
566A LEU* 1.3 65.2 + - - +
567A PHE 3.4 0.2 - - - -
568A PRO* 3.4 10.8 - - - +
569A LEU* 3.9 11.1 - - - +
597A LEU* 3.7 24.8 - - + +
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Residues in contact with LEU 566 (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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562A LEU* 2.9 29.8 + - + +
563A GLY* 4.0 4.0 - - - +
565A ARG* 1.3 76.9 - - - +
567A PHE* 1.3 65.0 + - - +
569A LEU* 3.1 9.4 + - - +
570A ILE* 2.9 36.5 + - + +
582A THR* 4.5 3.6 - - + -
585A LEU* 5.2 3.6 - - + -
586A LEU* 4.1 16.2 - - + -
593A LEU* 4.0 31.2 - - + +
596A MET* 4.8 4.9 - - + -
597A LEU* 3.8 26.2 - - + +
603A LEU* 3.9 31.6 - - + -
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Residues in contact with PHE 567 (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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563A GLY 2.8 19.3 + - - +
564A GLU* 4.5 2.0 - - - +
566A LEU* 1.3 76.1 - - - +
568A PRO* 1.3 68.3 - - + +
570A ILE 3.3 0.6 + - - +
571A GLN* 2.7 66.7 + - - +
578A ALA* 3.5 25.1 - - + -
579A GLY* 3.8 13.9 - - - -
582A THR* 3.7 22.0 - - - +
118C PHE* 3.8 16.4 - + + -
120C PRO* 3.6 36.1 - - + -
122C VAL* 5.3 9.6 - - + -
124C TYR* 5.9 3.4 - + - -
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Residues in contact with PRO 568 (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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564A GLU 3.2 22.7 - - - +
565A ARG* 3.4 12.1 - - - +
567A PHE* 1.3 101.4 - - + +
569A LEU* 1.3 61.0 + - + +
571A GLN* 3.8 11.2 - - + +
572A ALA* 3.0 27.0 + - - +
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Residues in contact with LEU 569 (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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565A ARG 3.9 18.8 - - - +
566A LEU 3.1 6.0 + - - +
568A PRO* 1.3 80.0 - - + +
570A ILE* 1.3 65.7 + - - +
572A ALA* 3.2 12.9 + - + +
573A MET* 3.1 24.2 + - - +
596A MET 5.8 0.2 - - - +
597A LEU* 4.3 21.3 - - + +
603A LEU* 3.9 26.7 - - + -
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Residues in contact with ILE 570 (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 LEU* 2.9 32.6 + - + +
567A PHE 4.0 0.2 - - - +
569A LEU* 1.3 75.0 - - - +
571A GLN* 1.3 57.4 + - - +
573A MET* 3.1 10.4 + - - +
574A HIS* 2.9 28.6 + - + +
578A ALA* 4.0 7.6 - - - +
581A ILE* 3.6 31.9 - - + -
582A THR* 3.6 34.8 - - - +
585A LEU* 3.8 27.8 - - + -
603A LEU* 4.4 9.6 - - + -
607A VAL* 3.9 17.3 - - + -
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Residues in contact with GLN 571 (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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567A PHE* 2.7 49.9 + - + +
568A PRO* 3.8 10.3 - - - +
570A ILE* 1.3 70.7 - - - +
572A ALA* 1.3 63.3 + - - +
574A HIS 4.3 0.4 - - - -
575A PRO* 3.0 36.6 + - + +
578A ALA* 3.5 26.0 - - + +
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Residues in contact with ALA 572 (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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568A PRO 3.0 15.5 + - - +
569A LEU* 3.2 12.3 + - + +
571A GLN* 1.3 76.8 - - - +
573A MET* 1.3 65.9 + - + +
575A PRO* 3.9 8.7 - - - +
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Residues in contact with MET 573 (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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569A LEU* 3.1 24.9 - - - +
570A ILE* 3.1 11.4 + - - +
572A ALA* 1.3 80.2 - - + +
574A HIS* 1.3 82.4 + - + +
575A PRO* 3.8 3.6 - - - +
600A PRO 5.7 0.2 - - - +
603A LEU* 4.3 11.9 - - + -
604A ARG* 3.7 38.6 - - + +
607A VAL* 3.7 33.7 - - + -
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Residues in contact with HIS 574 (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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2A CL 3.6 15.0 - - + +
570A ILE* 2.9 9.4 + - + +
571A GLN 3.5 2.0 - - - -
573A MET* 1.3 98.6 + - + +
575A PRO* 1.3 68.9 - - - +
576A THR 3.2 2.7 - - - -
577A LEU* 3.0 29.0 + - + +
578A ALA* 3.2 13.3 + - - +
581A ILE* 5.3 2.9 - - + -
604A ARG* 6.4 0.2 - - - -
607A VAL* 3.5 30.1 - - + +
608A ASP* 4.6 9.8 + - - -
611A VAL* 3.8 30.0 - - + +
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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