Contacts of the helix formed by residues 508 - 518 (chain A) in PDB entry 5IYB
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 SER 508 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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390A PHE* 4.5 3.4 - - - -
506A PRO 4.9 0.2 - - - -
507A GLN* 1.3 81.1 + - - +
509A LEU* 1.3 62.2 + - - +
510A GLU* 2.7 24.5 + - - +
511A THR* 3.1 19.2 + - - +
512A ARG* 3.1 21.8 + - - +
1105B GLU* 4.7 0.8 + - - -
71F LEU* 5.9 5.8 - - - -
62G GLY* 5.6 8.8 - - - -
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Residues in contact with LEU 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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390A PHE* 4.6 14.1 - - + -
393A ILE* 5.3 3.8 - - + -
508A SER* 1.3 72.1 + - - +
510A GLU* 1.3 60.9 + - - +
512A ARG* 3.7 23.1 - - - +
513A ALA* 2.9 30.8 + - - +
67F GLY* 4.3 2.3 - - - -
70F ALA* 3.6 25.6 - - + +
71F LEU* 4.4 18.3 - - + +
74F ALA* 3.6 30.7 - - + -
88F ASP* 5.7 2.0 - - - +
89F PRO* 3.8 21.8 - - + -
90F LEU* 5.1 7.0 - - + +
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Residues in contact with GLU 510 (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 SER* 2.7 15.8 + - - +
509A LEU* 1.3 74.4 - - - +
511A THR* 1.3 62.0 + - + +
513A ALA* 3.5 1.6 + - - +
514A GLU* 3.1 24.1 + - - +
1101B GLN* 3.3 31.3 + - + +
64F ARG* 3.6 4.7 + - - -
67F GLY* 3.2 28.3 - - - +
68F THR* 3.0 32.3 + - - +
71F LEU* 4.3 13.5 - - + +
60G GLN 5.1 0.5 - - - +
61G PRO* 3.7 2.3 - - - +
62G GLY* 2.7 38.1 + - - -
64G GLY 5.6 0.3 + - - -
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Residues in contact with THR 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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506A PRO* 3.5 20.8 - - - +
507A GLN 3.6 1.6 + - - -
508A SER* 3.1 30.8 + - - +
510A GLU* 1.3 73.1 - - + +
512A ARG* 1.3 65.2 + - - +
514A GLU* 3.8 5.8 - - - +
515A ILE* 2.9 28.6 + - - +
1101B GLN* 3.7 13.5 - - + +
1102B PHE* 3.7 36.6 - - - +
1105B GLU* 4.2 12.1 - - + -
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Residues in contact with ARG 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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390A PHE* 3.2 41.5 - - + -
448A ARG* 5.3 0.4 - - - +
453A GLY 4.3 5.7 + - - -
454A ASP* 2.8 46.8 + - - +
455A ILE* 4.1 26.8 + - + +
505A LEU* 5.7 1.0 - - - +
506A PRO* 4.5 10.2 - - + +
508A SER 3.1 18.1 + - - +
509A LEU* 3.7 17.7 - - - +
511A THR* 1.3 77.5 + - - +
513A ALA* 1.3 62.7 + - - +
515A ILE* 4.0 4.0 - - - +
516A GLN* 3.0 26.5 + - - +
88F ASP* 4.8 10.7 + - - -
90F LEU* 4.3 14.6 - - + -
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Residues in contact with ALA 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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509A LEU 2.9 11.4 + - - +
510A GLU 3.9 0.2 - - - +
511A THR 3.3 0.2 - - - -
512A ARG* 1.3 77.8 - - - +
514A GLU* 1.3 57.4 + - - +
516A GLN* 3.7 1.0 - - - +
517A GLU* 2.9 37.3 + - + +
63F ALA 4.1 2.5 - - - +
66F LEU* 4.1 4.0 - - + -
67F GLY* 3.4 37.2 - - - +
90F LEU* 3.9 28.4 - - + +
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Residues in contact with GLU 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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510A GLU 3.1 14.8 + - - +
511A THR* 3.8 4.2 - - - +
513A ALA* 1.3 76.4 - - - +
515A ILE* 1.3 60.2 + - + +
518A LEU* 2.9 51.6 + - + +
1468A THR* 2.5 29.1 + - + +
1099B ALA* 3.2 21.5 - - + +
1101B GLN* 2.5 30.4 + - - +
1102B PHE* 3.0 30.7 + - - +
63F ALA* 4.0 12.5 + - + +
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Residues in contact with ILE 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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455A ILE* 3.7 23.8 - - + -
456A VAL 5.1 0.4 - - - +
457A ILE* 3.6 23.1 - - + -
471A GLY* 4.0 20.0 - - - -
506A PRO* 3.6 22.9 - - + -
511A THR 2.9 16.8 + - - +
512A ARG* 4.1 2.7 - - - +
514A GLU* 1.3 74.4 - - - +
516A GLN* 1.3 62.0 + - - +
519A ALA* 2.9 34.8 + - + +
520A MET* 3.2 8.7 + - - -
1099B ALA* 5.7 3.4 - - + -
1102B PHE* 3.5 39.3 - - + -
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Residues in contact with GLN 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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455A ILE* 3.3 21.5 - - + +
512A ARG* 3.0 17.9 + - - +
513A ALA* 3.7 4.7 - - - +
515A ILE* 1.3 76.9 - - - +
517A GLU* 1.3 64.5 + - + +
520A MET* 3.6 37.9 - - + +
523A ARG* 4.8 1.9 - - - +
90F LEU* 3.1 21.4 - - - +
94F MET* 3.4 31.1 - - + +
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Residues in contact with GLU 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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513A ALA* 2.9 20.6 + - - +
516A GLN* 1.3 82.4 - - - +
518A LEU* 1.3 63.3 + - + +
523A ARG* 3.2 33.0 + - - +
59F LYS 5.4 0.4 - - - +
62F ARG* 2.4 45.6 + - - +
63F ALA* 3.8 24.0 - - + +
66F LEU* 3.6 21.7 - - + +
94F MET* 3.4 24.4 - - + +
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Residues in contact with LEU 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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514A GLU* 2.9 33.2 + - + +
517A GLU* 1.3 80.9 - - + +
519A ALA* 1.3 65.0 + - + +
520A MET 3.3 2.8 + - - -
523A ARG* 3.5 10.0 - - - +
524A MET* 3.4 19.0 - - - +
1468A THR* 4.4 4.0 - - + -
1097B HIS* 4.1 14.4 - - + +
1098B GLY 3.9 22.9 - - - +
1099B ALA* 4.6 4.0 - - + +
59F LYS* 3.9 49.6 - - + +
60F TYR* 3.9 17.7 - - + -
62F ARG* 6.3 0.4 - - - +
63F ALA* 4.1 7.0 - - + -
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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
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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