Contacts of the helix formed by residues 544 - 565 (chain A) in PDB entry 5LUQ
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 ILE 544 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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466A LEU* 3.7 32.8 - - + -
469A ALA* 5.2 8.1 - - + -
541A MSE 5.6 7.2 - - + -
543A SER* 1.3 81.6 - - - +
545A LEU* 1.3 54.2 + - - -
546A ALA* 2.9 19.8 + - - +
547A ASP* 4.2 3.8 + - - +
548A GLU* 3.0 40.5 + - - +
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Residues in contact with LEU 545 (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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462A VAL* 5.2 6.3 - - + -
537A SER 3.2 20.9 - - - +
538A ASP* 2.9 30.7 - - - +
539A GLN* 3.9 15.9 - - - +
540A MSE 4.2 1.3 - - + +
541A MSE 3.0 30.1 - - + +
542A ASP* 3.3 16.6 - - + -
543A SER* 2.3 27.6 + - - +
544A ILE* 1.3 66.0 - - - +
546A ALA* 1.3 65.4 + - - +
548A GLU* 3.2 19.8 + - - +
549A ALA* 2.8 26.2 + - - +
628A GLU* 3.6 4.7 - - - +
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Residues in contact with ALA 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A SER* 4.4 1.3 - - - +
544A ILE* 2.9 11.6 - - - +
545A LEU* 1.3 81.1 - - - +
547A ASP* 1.3 81.3 + - - +
548A GLU 2.9 1.3 - - - -
549A ALA* 2.8 8.3 + - - +
550A PHE* 3.0 30.7 + - + -
628A GLU* 4.0 5.6 - - - -
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Residues in contact with ASP 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A ILE* 4.2 3.8 + - - +
546A ALA* 1.3 86.5 - - - +
548A GLU* 1.3 61.0 + - - +
550A PHE* 3.3 14.2 + - - +
551A PHE* 2.9 55.8 + - + -
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Residues in contact with GLU 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A VAL* 5.4 6.2 - - - +
465A PHE* 5.4 18.6 - - + -
466A LEU* 4.6 10.0 + - - +
469A ALA* 4.5 17.1 - - + +
537A SER 4.9 1.0 - - - +
538A ASP* 4.4 7.5 - - - +
544A ILE* 3.0 39.4 + - - +
545A LEU* 3.2 30.2 + - - +
547A ASP* 1.3 79.1 - - - +
549A ALA* 1.3 54.2 - - - +
551A PHE* 3.4 9.4 + - - +
552A SER* 2.2 39.5 + - - +
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Residues in contact with ALA 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A ASP* 3.0 35.3 + - + +
545A LEU 2.9 16.2 - - - +
546A ALA 2.8 6.3 + - - -
548A GLU* 1.3 76.8 - - - +
550A PHE* 1.3 56.2 + - - -
552A SER* 3.3 2.4 - - - -
553A VAL* 2.9 35.6 + - - +
627A VAL* 4.2 9.0 - - + -
628A GLU* 3.2 20.4 - - + +
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Residues in contact with PHE 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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546A ALA* 3.0 46.0 + - + -
547A ASP* 3.6 14.1 - - - +
549A ALA* 1.3 72.4 - - - +
551A PHE* 1.3 71.7 + - + +
553A VAL* 3.0 10.4 + - + +
554A ASN* 3.0 28.0 + - - +
628A GLU* 3.8 18.4 - - + -
633A ILE* 3.6 42.6 - - + -
636A GLU* 5.9 2.5 - - - -
637A LYS* 6.0 2.9 - - - -
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Residues in contact with PHE 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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469A ALA* 6.3 1.3 - - + -
476A ARG* 3.0 52.3 - - + -
477A ASN* 4.4 20.4 - - - +
480A SER* 5.0 5.6 - - - +
547A ASP* 2.9 46.5 + - + +
548A GLU* 3.7 7.0 - - - +
550A PHE* 1.3 76.7 - - + +
552A SER* 1.3 63.3 - - - +
554A ASN* 4.8 2.7 - - - +
555A SER* 2.4 39.2 + - - +
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Residues in contact with SER 552 (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 SER* 4.4 17.9 + - - -
538A ASP* 4.0 12.2 + - - -
548A GLU* 2.2 32.7 + - - +
549A ALA* 3.3 12.2 - - - -
551A PHE* 1.3 75.9 - - - +
553A VAL* 1.3 54.3 - - - +
555A SER* 3.9 0.7 - - - -
556A SER* 2.0 37.2 + - - -
623A PHE* 4.8 9.0 - - - -
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Residues in contact with VAL 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A ALA* 2.9 27.7 + - + +
550A PHE* 3.0 9.6 + - + +
552A SER* 1.3 73.2 - - - +
554A ASN* 1.3 69.3 + - - +
556A SER* 2.4 23.5 + - - -
557A SER* 2.9 17.6 + - - +
620A PHE* 4.8 5.5 - - + -
623A PHE* 4.5 15.0 - - + -
624A ILE* 4.3 24.7 - - + -
627A VAL* 5.3 10.1 - - + -
628A GLU* 5.6 6.5 - - + -
637A LYS* 3.8 26.0 - - - +
641A PHE* 5.5 1.8 - - + -
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Residues in contact with ASN 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 PHE* 3.0 15.9 + - - +
551A PHE* 4.5 2.0 - - - +
553A VAL* 1.3 78.7 - - - +
555A SER* 1.3 63.2 + - - +
557A SER* 3.0 10.5 + - - -
558A GLU* 2.9 48.4 + - - +
637A LYS* 3.9 19.8 + - - +
640A GLU* 4.5 15.8 + - - +
641A PHE* 5.4 2.6 - - - +
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Residues in contact with SER 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A ASN* 3.0 33.6 + - - -
480A SER* 4.0 18.8 - - - -
481A THR* 3.7 15.1 + - - -
551A PHE* 2.4 26.5 + - - +
552A SER 3.9 1.6 - - - -
554A ASN* 1.3 78.0 - - - +
556A SER* 1.3 63.9 + - - -
557A SER 3.1 0.9 + - - -
558A GLU* 4.1 6.0 + - - +
559A SER* 3.1 23.9 + - - -
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Residues in contact with SER 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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480A SER* 5.4 1.0 + - - -
481A THR* 5.3 0.6 - - - +
484A HIS* 3.1 43.5 - - - -
552A SER 2.0 35.2 + - - -
553A VAL* 2.4 12.1 + - - -
555A SER* 1.3 72.2 - - - +
557A SER* 1.3 62.2 + - - +
559A SER* 3.7 1.9 - - - -
560A LEU* 3.0 5.1 + - - -
616A LYS* 2.5 28.0 + - - -
620A PHE* 5.1 4.3 - - - -
623A PHE* 4.0 11.1 - - - -
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Residues in contact with SER 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 VAL* 2.9 14.0 + - - +
554A ASN* 3.0 15.8 + - - -
556A SER* 1.3 72.0 - - - +
558A GLU* 1.3 65.0 + - - -
560A LEU* 2.4 42.4 + - - +
561A ASN* 2.7 20.0 + - - +
620A PHE* 3.7 18.9 - - - -
641A PHE* 4.3 10.8 - - - -
645A TRP* 5.0 4.9 + - - -
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Residues in contact with GLU 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 ASN* 2.9 52.0 + - - +
555A SER* 4.1 5.0 + - - +
557A SER* 1.3 79.0 - - - +
559A SER* 1.3 62.1 + - - +
561A ASN* 3.2 21.9 + - - +
562A HIS* 3.0 22.7 + - - +
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Residues in contact with SER 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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481A THR* 2.9 37.3 + - - +
484A HIS* 6.0 0.9 - - - -
485A GLN* 3.1 20.4 + - - -
555A SER 3.1 15.9 + - - -
556A SER* 3.7 4.7 - - - -
557A SER 2.7 3.2 + - - -
558A GLU* 1.3 76.1 - - - +
560A LEU* 1.3 61.9 + - - -
562A HIS* 3.1 7.4 + - - +
563A LEU* 2.8 24.0 + - - +
616A LYS* 4.7 0.4 - - - -
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Residues in contact with LEU 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 SER 3.0 12.3 + - - +
557A SER* 2.4 30.6 + - - +
559A SER* 1.3 69.7 - - - +
561A ASN* 1.3 63.2 + - - +
563A LEU* 2.5 37.0 + - + +
564A LEU* 3.2 21.7 + - + +
613A HIS* 6.4 0.7 - - + -
616A LYS* 2.8 54.2 - - + +
617A PRO* 4.8 3.8 - - + -
620A PHE* 3.3 29.8 - - + -
645A TRP* 3.8 27.6 - - + -
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Residues in contact with ASN 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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557A SER* 2.7 28.7 - - - +
558A GLU* 3.2 35.0 + - - +
560A LEU* 1.3 89.5 - - - +
562A HIS* 1.3 57.8 + - - +
564A LEU* 3.7 9.5 - - - +
565A TYR* 3.0 21.9 + - - +
644A PRO* 5.0 15.4 - - - +
645A TRP* 5.2 5.7 + - - -
648A SER* 5.7 6.8 - - - -
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Residues in contact with HIS 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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558A GLU 3.0 12.3 + - - +
559A SER* 3.9 6.5 - - - +
561A ASN* 1.3 75.3 - - - +
563A LEU* 1.3 59.5 + - - +
565A TYR* 3.5 38.0 - + - -
566A ASP* 3.0 36.8 + - - +
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Residues in contact with LEU 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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485A GLN* 3.4 27.8 - - - +
488A ILE* 3.3 32.5 - - + -
559A SER 2.8 20.8 + - - +
560A LEU* 2.5 29.8 + - + +
562A HIS* 1.3 68.4 - - - +
564A LEU* 1.3 63.8 + - + +
566A ASP* 2.7 38.2 + - - +
609A ALA* 3.7 7.7 - - - +
612A LEU* 3.9 30.5 - - + -
613A HIS* 5.3 1.8 - - + -
616A LYS* 4.3 4.5 - - + -
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Residues in contact with LEU 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 LEU* 3.8 18.4 - - + +
561A ASN* 3.7 16.2 - - - +
563A LEU* 1.3 77.5 - - - +
565A TYR* 1.3 75.1 + - + +
566A ASP 2.9 5.9 + - - -
568A PHE* 3.3 29.7 + - + -
569A VAL* 3.2 25.8 + - + -
609A ALA* 4.1 4.3 - - - -
613A HIS* 3.7 35.1 - - + +
617A PRO* 5.2 6.5 - - + -
645A TRP* 5.7 3.1 - - + -
648A SER* 4.9 11.9 - - - +
656A GLN* 3.8 37.0 - - + +
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Residues in contact with TYR 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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561A ASN 3.0 21.5 - - - +
562A HIS* 3.3 44.7 - + - +
564A LEU* 1.3 83.7 - - + +
566A ASP* 1.3 63.9 + - - +
569A VAL* 3.3 18.8 - - + +
570A LYS* 3.7 4.9 + - - -
647A TYR* 6.5 0.4 - + - -
651A TYR* 5.4 15.3 - + - -
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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
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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