Contacts of the helix formed by residues 540 - 556 (chain A) in PDB entry 3UGM
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 GLY 540 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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505A GLY* 4.4 1.1 - - - -
509A ALA* 4.0 20.0 - - - -
534A ILE 4.6 6.3 + - - +
535A ALA* 4.6 9.4 - - - -
537A HIS* 2.8 17.5 + - - +
538A ASP 2.7 4.6 + - - -
539A GLY* 1.3 66.1 - - - -
541A LYS* 1.3 69.4 + - - +
543A ALA* 3.2 13.5 + - - +
544A LEU* 3.3 16.5 + - - +
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Residues in contact with LYS 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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508A GLN* 2.8 44.5 + - + +
509A ALA* 4.1 6.3 - - - +
511A GLU* 5.4 2.2 + - - +
512A THR* 2.6 37.4 + - - +
515A ARG* 2.9 31.2 - - - +
539A GLY 3.2 2.2 + - - -
540A GLY* 1.3 71.5 - - - +
542A GLN* 1.3 71.7 - - - +
543A ALA 3.0 1.9 + - - -
544A LEU* 3.2 1.6 + - - +
545A GLU* 3.1 43.0 + - - +
7B C 3.5 18.8 + - - +
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Residues in contact with GLN 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A GLY 3.6 12.3 + - - +
541A LYS* 1.3 85.7 - - - +
543A ALA* 1.3 54.5 + - - +
545A GLU* 3.5 17.1 + - - +
546A THR* 2.6 32.4 + - - -
575A LYS* 3.7 29.6 - - + +
7B C 2.8 43.8 + - - +
8B C 3.3 32.8 - - - +
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Residues in contact with ALA 543 (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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534A ILE* 3.8 13.2 - - + +
539A GLY* 4.6 3.4 - - - -
540A GLY 3.2 10.1 + - - +
541A LYS 3.0 3.6 + - - -
542A GLN* 1.3 72.8 - - - +
544A LEU* 1.3 70.4 + - - +
545A GLU 2.5 4.7 + - - -
546A THR* 2.5 17.4 + - - -
547A VAL* 2.9 9.8 + - + -
569A ALA* 3.8 26.5 - - + +
574A GLY* 4.1 4.3 - - - -
575A LYS 4.0 19.7 - - - +
578A LEU* 6.2 0.7 - - + -
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Residues in contact with LEU 544 (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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509A ALA 4.6 1.1 - - - +
512A THR* 3.8 24.0 - - + +
513A VAL* 3.2 35.0 - - + +
516A LEU* 4.7 4.5 - - + -
520A LEU* 3.8 24.9 - - + +
531A VAL* 3.7 24.9 - - + -
534A ILE* 3.8 29.0 - - + +
535A ALA* 3.5 14.1 - - + -
540A GLY 3.3 7.8 + - - +
541A LYS 3.2 7.7 + - - +
543A ALA* 1.3 76.3 - - - +
545A GLU* 1.3 57.0 + - - +
547A VAL* 3.2 6.7 + - + +
548A GLN* 2.8 27.3 + - - +
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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
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512A THR* 4.4 11.0 - - + -
515A ARG* 4.0 15.3 + - - +
516A LEU* 4.7 8.7 - - + +
541A LYS* 3.1 34.6 + - - +
542A GLN* 3.5 25.3 + - - +
543A ALA 2.5 3.8 + - - -
544A LEU* 1.3 70.7 - - - +
546A THR* 1.3 55.2 + - - +
547A VAL 2.7 5.4 + - - -
548A GLN* 2.7 26.8 + - - +
549A ARG* 3.0 46.9 + - - +
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Residues in contact with THR 546 (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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542A GLN 2.6 21.6 + - - -
543A ALA* 2.5 10.7 + - - -
545A GLU* 1.3 73.5 - - - +
547A VAL* 1.3 57.3 + - - -
549A ARG* 4.2 12.5 - - - +
550A LEU* 3.3 37.3 + - + +
575A LYS* 3.1 46.4 - - + +
578A LEU* 3.7 17.1 - - + +
579A GLU* 4.7 6.7 - - + -
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Residues in contact with VAL 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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520A LEU* 4.1 20.9 - - + -
526A LEU* 4.5 5.6 - - + -
534A ILE* 3.6 19.1 - - + -
543A ALA* 2.9 12.1 + - + +
544A LEU* 3.3 9.9 - - - +
545A GLU 2.7 0.6 + - - -
546A THR* 1.3 76.1 - - - +
548A GLN* 1.3 71.7 + - - +
549A ARG 3.2 0.2 + - - -
551A LEU* 2.9 39.3 + - + +
565A VAL* 4.4 7.2 - - + -
566A VAL* 4.8 2.7 - - + -
569A ALA* 3.5 32.3 - - + -
578A LEU* 3.7 15.5 - - + -
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Residues in contact with GLN 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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516A LEU* 4.4 18.3 - - + +
519A VAL* 3.3 33.0 + - - +
520A LEU* 3.8 15.4 - - + +
524A HIS* 3.3 35.9 + - - -
544A LEU 2.8 13.1 + - - +
545A GLU* 2.7 15.3 + - - +
547A VAL* 1.3 77.4 - - - +
549A ARG* 1.3 77.1 + - + +
551A LEU* 3.6 9.8 + - - +
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Residues in contact with ARG 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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516A LEU* 5.6 1.0 - - - +
545A GLU* 3.0 63.0 + - - +
546A THR* 4.2 9.6 - - - +
548A GLN* 1.3 96.6 - - + +
550A LEU* 1.3 69.9 + - + +
551A LEU 3.2 3.5 + - - -
552A PRO* 3.7 7.8 - - - +
553A VAL* 3.4 14.8 - - - +
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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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546A THR* 3.3 31.9 + - + +
547A VAL* 3.8 1.8 - - - -
549A ARG* 1.3 85.2 - - + +
551A LEU* 1.3 66.5 + - - +
552A PRO 3.6 0.4 - - - -
553A VAL* 3.6 34.1 - - + -
554A LEU* 3.1 30.8 + - + +
565A VAL* 5.1 1.9 - - - +
578A LEU* 4.7 4.7 - - + +
579A GLU* 4.5 16.8 - - + +
582A GLN* 4.2 28.0 - - + +
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Residues in contact with LEU 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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520A LEU* 5.0 0.9 - - + -
524A HIS* 3.1 48.9 - - + +
526A LEU* 4.8 9.9 - - + -
547A VAL* 2.9 32.2 + - + +
548A GLN 3.8 1.1 - - - +
549A ARG 3.2 2.2 - - - -
550A LEU* 1.3 78.6 - - - +
552A PRO* 1.4 68.7 - - + +
554A LEU* 3.8 1.2 - - - +
555A CYS* 2.9 46.0 + - - -
562A PRO* 4.2 12.1 - - + +
565A VAL* 3.5 28.9 - - + -
566A VAL* 5.4 0.9 - - + -
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Residues in contact with PRO 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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524A HIS* 3.6 19.3 - - + +
549A ARG 3.7 10.1 - - - +
551A LEU* 1.4 90.9 - - + +
553A VAL* 1.3 64.0 + - + +
554A LEU 2.9 2.0 - - - -
555A CYS* 2.5 18.4 + - + -
556A GLN* 2.5 60.4 + - + +
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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
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549A ARG 3.4 21.8 - - - +
550A LEU* 3.6 32.8 - - + +
552A PRO* 1.3 79.4 - - + +
554A LEU* 1.3 57.1 + - - +
556A GLN* 5.0 2.7 - - - -
557A THR* 3.2 27.6 - - - +
558A HIS* 4.0 3.3 + - + -
582A GLN* 4.5 18.2 - - + +
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Residues in contact with LEU 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 LEU* 3.1 28.8 + - + +
551A LEU 4.0 1.3 - - - +
552A PRO 2.7 4.4 + - - -
553A VAL* 1.3 74.1 - - - +
555A CYS* 1.3 63.4 + - - +
558A HIS* 3.2 49.6 - - + +
560A LEU* 3.3 27.7 + - + +
565A VAL* 4.1 10.3 - - + -
578A LEU* 3.7 27.4 - - + +
581A VAL* 3.5 32.3 - - + -
582A GLN* 3.4 23.8 - - + -
585A LEU* 5.1 0.4 - - + -
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Residues in contact with CYS 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 LEU* 2.9 44.3 + - - +
552A PRO* 2.5 11.4 + - + +
554A LEU* 1.3 74.6 - - - +
556A GLN* 1.3 69.1 + - + +
557A THR 3.0 1.4 + - - -
559A GLY* 3.4 16.6 + - - -
560A LEU 3.3 26.0 + - - +
561A THR 4.0 2.7 - - - -
562A PRO* 3.9 22.2 - - + -
565A VAL* 5.0 2.5 - - - -
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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
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552A PRO* 2.5 41.6 + - + +
553A VAL* 5.0 1.6 - - - -
555A CYS* 1.3 76.8 - - + +
557A THR* 1.3 63.0 + - - +
559A GLY* 5.5 0.2 - - - -
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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