Contacts of the helix formed by residues 505 - 522 (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 505 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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501A ILE 2.9 9.3 + - - -
504A ASN* 1.3 82.9 - - - +
506A GLY* 1.4 58.8 + - - +
508A GLN* 4.5 1.7 + - - +
509A ALA* 3.2 36.7 + - - +
535A ALA 3.7 4.7 - - - -
537A HIS 3.4 12.8 - - - -
538A ASP 4.1 7.9 - - - +
540A GLY* 4.5 1.0 - - - -
7B C 4.6 7.4 + - - -
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Residues in contact with GLY 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A GLY 6.0 2.0 - - - -
476A ALA* 5.1 7.0 - - - -
501A ILE 3.4 6.5 + - - -
502A ALA 3.6 14.6 + - - -
503A SER 5.4 0.4 - - - -
504A ASN 3.5 1.8 - - - -
505A GLY* 1.4 76.4 - - - +
507A LYS* 1.3 67.5 + - - +
509A ALA 3.2 8.1 + - - -
510A LEU* 3.2 22.9 + - - +
6B T 5.9 0.7 - - - -
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Residues in contact with LYS 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A GLN* 3.6 39.7 + - + +
476A ALA* 4.7 4.0 - - - +
478A GLU* 5.2 4.8 + - - +
479A THR* 3.1 33.1 + - - +
482A ARG* 4.9 12.5 - - - +
506A GLY* 1.3 70.4 - - - +
508A GLN* 1.3 70.2 + - - +
510A LEU* 3.4 6.1 + - - +
511A GLU* 2.9 55.1 + - - +
6B T 3.6 22.9 + - - +
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Residues in contact with GLN 508 (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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505A GLY 4.6 2.0 - - - +
506A GLY 3.3 0.4 - - - -
507A LYS* 1.3 92.6 - - - +
509A ALA* 1.3 54.6 + - - +
511A GLU* 4.0 11.0 - - - +
512A THR* 2.5 37.2 + - - -
541A LYS* 2.8 44.0 + - + +
6B T 2.9 46.9 + - - +
7B C 3.6 24.5 - - - +
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Residues in contact with ALA 509 (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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501A ILE* 3.8 5.8 - - + -
505A GLY* 3.2 40.6 + - - +
506A GLY 3.2 2.4 + - - +
508A GLN* 1.3 74.9 - - - +
510A LEU* 1.3 72.3 + - - +
512A THR* 3.2 3.4 + - - -
513A VAL* 2.8 24.0 + - - +
535A ALA* 3.5 16.8 - - + +
540A GLY* 4.0 10.1 - - - -
541A LYS 4.1 7.8 - - - +
544A LEU* 5.6 0.2 - - - -
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Residues in contact with LEU 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A ALA* 5.0 4.0 - - - +
479A THR* 3.8 29.8 - - + -
480A VAL* 4.7 10.5 - - + +
483A LEU* 3.9 19.7 - - + +
487A LEU* 4.7 10.2 - - + +
498A VAL* 3.7 39.7 - - + +
501A ILE* 3.9 12.3 - - + +
502A ALA* 4.0 20.0 - - + +
506A GLY 3.2 21.3 + - - +
507A LYS* 4.0 0.2 - - - -
509A ALA* 1.3 72.1 - - - +
511A GLU* 1.3 56.4 + - - +
513A VAL* 2.6 31.8 + - - +
514A GLN 2.9 8.1 + - - -
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Residues in contact with GLU 511 (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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479A THR* 4.0 17.9 - - + +
482A ARG* 4.7 6.9 + - - -
483A LEU* 3.9 12.6 - - + +
507A LYS* 2.9 48.1 + - - +
508A GLN* 4.0 14.5 - - - +
510A LEU* 1.3 77.3 - - - +
512A THR* 1.3 65.5 + - - +
514A GLN* 2.7 16.9 + - - +
515A ARG* 3.0 25.3 + - - +
541A LYS* 5.4 0.8 + - - +
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Residues in contact with THR 512 (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 2.5 30.3 + - - -
509A ALA 3.8 2.9 - - - -
510A LEU 3.1 0.2 + - - -
511A GLU* 1.3 73.4 - - - +
513A VAL* 1.3 56.1 + - - +
515A ARG* 3.3 27.0 + - - +
516A LEU* 3.0 32.2 + - + +
541A LYS* 2.6 39.5 + - + +
544A LEU* 3.8 29.1 - - + +
545A GLU* 4.4 7.6 - - + -
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Residues in contact with VAL 513 (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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487A LEU* 4.5 17.7 - - + -
491A HIS* 4.5 0.4 + - + -
493A LEU* 4.8 7.2 - - + -
501A ILE* 4.4 16.4 - - + -
509A ALA 2.8 6.5 + - - +
510A LEU* 2.6 19.1 + - - +
512A THR* 1.3 69.9 - - - +
514A GLN* 1.3 67.3 + - - +
516A LEU* 4.4 1.1 - - - +
517A LEU* 3.0 37.2 + - + +
531A VAL* 4.2 13.2 - - + +
532A VAL* 5.9 1.1 - - + -
535A ALA* 3.5 19.1 - - + -
544A LEU* 3.2 30.1 - - + -
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Residues in contact with GLN 514 (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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483A LEU* 3.8 20.5 - - + +
486A VAL* 3.1 36.4 - - - +
487A LEU* 3.4 21.7 - - - +
491A HIS* 4.6 9.2 + - - -
510A LEU 2.9 6.2 + - - +
511A GLU* 2.7 21.3 + - - +
513A VAL* 1.3 75.2 - - - +
515A ARG* 1.3 71.3 + - + +
516A LEU 2.9 0.3 + - - -
517A LEU* 3.5 4.5 + - - +
518A PRO* 4.1 7.4 - - - +
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Residues in contact with ARG 515 (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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511A GLU* 3.0 29.5 + - - +
512A THR* 3.3 36.1 + - - +
514A GLN* 1.3 84.1 - - + +
516A LEU* 1.3 77.5 + - + +
518A PRO* 4.6 4.3 - - - +
519A VAL* 3.6 11.6 - - - +
541A LYS* 2.9 36.3 - - - +
545A GLU* 4.0 10.9 + - - +
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Residues in contact with LEU 516 (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* 3.0 35.9 + - + +
513A VAL* 4.0 1.6 - - - -
514A GLN 2.9 3.2 + - - -
515A ARG* 1.3 93.8 - - + +
517A LEU* 1.3 67.4 + - - +
518A PRO 3.4 2.0 - - - -
519A VAL* 3.9 18.8 - - + -
520A LEU* 3.1 41.9 + - + +
531A VAL* 5.9 0.7 - - - -
544A LEU* 4.6 8.5 - - + +
545A GLU* 4.7 9.6 - - + -
548A GLN* 4.4 25.8 - - + +
549A ARG* 5.6 0.9 - - - +
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Residues in contact with LEU 517 (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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491A HIS* 3.1 48.0 - - + +
493A LEU* 5.6 3.1 - - + -
513A VAL* 3.0 32.5 + - + +
516A LEU* 1.3 74.2 - - - +
518A PRO* 1.4 66.2 - - + +
520A LEU* 3.7 1.0 - - - +
521A CYS* 2.8 41.4 + - + +
522A GLN* 3.6 21.1 - - - +
528A PRO* 4.3 25.1 - - + +
531A VAL* 4.3 22.7 - - + -
532A VAL* 6.2 1.1 - - + -
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Residues in contact with PRO 518 (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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491A HIS* 3.9 12.3 - - + -
514A GLN 4.1 6.3 - - - +
515A ARG 4.6 4.0 - - - +
516A LEU 3.7 0.2 - - - -
517A LEU* 1.4 93.2 - - + +
519A VAL* 1.3 67.5 + - + +
520A LEU 2.7 15.9 + - - -
522A GLN* 3.0 53.0 + - - +
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Residues in contact with VAL 519 (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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515A ARG 3.6 23.6 - - - +
516A LEU* 3.4 17.2 + - + +
518A PRO* 1.3 80.6 - - + +
520A LEU* 1.3 57.6 + - - +
523A ALA* 3.1 23.1 - - + +
524A HIS* 4.1 8.5 - - - -
548A GLN* 3.3 26.2 - - - +
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Residues in contact with LEU 520 (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* 3.1 32.5 + - + +
517A LEU 3.7 0.7 - - - +
518A PRO 2.7 1.6 + - - -
519A VAL* 1.3 76.7 - - - +
521A CYS* 1.3 69.7 + - - +
522A GLN 3.0 1.3 - - - -
523A ALA 2.7 14.0 + - - -
524A HIS* 3.1 25.7 + - + +
526A LEU* 3.8 31.3 + - + -
531A VAL* 4.8 7.6 - - + -
544A LEU* 3.8 39.7 - - + +
547A VAL* 4.1 15.5 - - + -
548A GLN* 3.8 24.7 - - - +
551A LEU* 5.0 0.4 - - + -
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Residues in contact with CYS 521 (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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517A LEU* 2.8 26.7 + - + +
520A LEU* 1.3 75.6 - - - +
522A GLN* 1.3 95.8 + - - +
523A ALA 3.7 1.6 + - - -
525A GLY* 4.3 2.8 + - - -
526A LEU* 2.6 43.8 + - - +
527A THR 4.2 1.3 - - - -
528A PRO* 3.8 27.8 - - + -
531A VAL* 4.3 6.7 - - + +
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Residues in contact with GLN 522 (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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491A HIS* 5.1 1.8 + - - +
517A LEU* 3.6 14.8 - - - +
518A PRO* 3.0 35.1 + - - +
520A LEU 3.0 0.6 - - - -
521A CYS* 1.3 103.9 - - - +
523A ALA* 1.3 61.3 + - - +
528A PRO* 5.4 0.4 - - - +
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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