Contacts of the helix formed by residues 499 - 508 (chain C) in PDB entry 5HP1
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 499 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478C GLU* 2.6 45.2 + - - +
497C THR* 2.8 16.0 + - - +
498C ASP* 1.3 74.9 + - - +
500C GLN* 1.3 63.1 + - - +
501C TYR* 3.6 2.6 + - - +
502C ALA* 2.9 30.4 + - - +
503C LEU* 3.1 22.2 + - - +
535C TRP* 4.3 3.4 - - - -
17E T 5.5 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 500 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498C ASP 3.4 3.8 + - - +
499C SER* 1.3 72.6 - - - +
501C TYR* 1.3 63.7 + - - +
503C LEU* 3.4 0.7 + - - +
504C GLY* 2.9 22.7 + - - -
535C TRP* 3.6 25.7 - - - +
422D LEU* 3.6 32.4 - - + +
16E T 3.7 35.1 + - - +
17E T 4.9 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 501 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361C HIS* 4.4 0.7 + - - -
475C GLN* 3.5 42.7 - - + +
478C GLU* 4.2 5.4 - - - +
479C LEU* 3.9 25.0 - - + +
499C SER* 3.7 7.6 - - - +
500C GLN* 1.3 80.4 - - - +
502C ALA* 1.3 66.6 + - + +
504C GLY* 3.5 1.4 + - - -
505C ILE* 3.4 39.6 + - + +
16E T 3.5 47.3 + + - +
17E T 4.6 0.6 + - - +
20E C 3.2 28.1 + - - -
21E A 2.5 27.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 502 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478C GLU 4.6 4.7 - - - +
479C LEU* 3.8 25.4 - - + -
482C ILE* 3.6 28.7 - - + -
499C SER* 2.9 28.0 + - - +
501C TYR* 1.3 73.9 - - + +
503C LEU* 1.3 64.6 + - - +
505C ILE* 3.1 5.0 + - - +
506C ILE* 3.0 29.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 503 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482C ILE* 5.2 0.7 - - + -
497C THR* 3.8 20.9 - - + -
499C SER 3.1 12.7 + - - +
500C GLN 4.0 1.6 - - - +
502C ALA* 1.3 75.9 - - - +
504C GLY* 1.3 67.1 + - - +
506C ILE* 4.5 2.7 - - + +
507C GLN* 2.9 55.3 + - - +
533C LEU* 3.7 37.0 - - + -
534C ALA* 4.3 4.5 - - - +
535C TRP* 3.5 41.1 - - + +
422D LEU* 3.8 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 504 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406C TRP* 4.1 7.3 - - - -
500C GLN 2.9 16.5 + - - -
501C TYR* 3.9 2.5 - - - -
502C ALA 3.2 0.2 - - - -
503C LEU* 1.3 78.5 - - - +
505C ILE* 1.3 62.6 + - - +
507C GLN 3.7 3.5 + - - -
508C ALA* 3.7 13.0 + - - +
420D PRO* 3.8 27.2 - - - +
422D LEU* 5.2 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 505 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361C HIS* 3.5 48.5 - - + +
479C LEU* 4.6 12.3 - - + -
501C TYR* 3.4 52.1 + - + +
502C ALA 3.1 6.9 + - - +
504C GLY* 1.3 77.7 - - - +
506C ILE* 1.3 70.7 + - + +
507C GLN 3.3 0.3 + - - -
508C ALA* 3.4 6.6 + - - +
510C PRO* 3.1 22.9 - - + +
518C VAL* 4.2 19.1 - - + -
21E A 3.9 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 506 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C TYR* 4.0 3.6 + - - +
429C LEU* 4.1 10.8 - - + +
479C LEU* 5.0 7.6 - - + -
482C ILE* 3.9 39.5 - - + -
502C ALA* 3.0 18.8 + - + +
503C LEU* 4.4 1.8 - - + +
505C ILE* 1.3 82.0 - - + +
507C GLN* 1.3 61.4 + - - +
509C GLN* 3.1 14.2 + - - +
510C PRO* 3.7 8.6 - - + +
518C VAL* 6.4 0.7 - - + -
521C ILE* 4.5 16.4 - - + -
525C LEU* 3.8 25.8 - - + -
533C LEU* 3.5 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 507 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405C TYR* 5.5 0.5 - - - -
406C TRP* 3.5 26.7 - - + -
429C LEU* 4.0 22.0 - - + +
503C LEU* 2.9 49.3 + - + +
505C ILE 3.2 0.2 - - - -
506C ILE* 1.3 77.0 - - - +
508C ALA* 1.3 57.4 + - - +
509C GLN* 3.1 13.6 + - - +
533C LEU* 5.1 8.8 + - + +
420D PRO* 4.2 10.6 - - - +
421D PRO* 4.6 7.7 + - - +
422D LEU* 3.8 17.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 508 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363C ASN* 3.2 16.6 + - - -
366C LYS* 3.7 25.3 + - - +
401C TRP* 3.8 8.3 - - - -
405C TYR* 4.4 7.0 - - + +
406C TRP* 3.5 22.4 - - + -
504C GLY 3.7 5.1 + - - +
505C ILE* 3.4 10.4 + - - +
506C ILE 3.2 1.4 - - - -
507C GLN* 1.3 75.7 - - - +
509C GLN* 1.3 67.4 + - - +
510C PRO* 3.3 4.4 - - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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