Contacts of the helix formed by residues 493 - 503 (chain C) in PDB entry 2W4T
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 PHE 493 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489C ASN* 3.0 16.4 + - - +
492C MET* 1.3 119.5 - - + +
494C ILE* 1.3 72.8 + - + +
495C LEU 3.1 1.4 + - - -
496C GLU* 3.6 9.3 + - - +
497C GLN* 3.7 13.7 + - - +
509C PHE* 5.5 5.3 - - + -
510C ILE* 5.6 1.6 - - - +
512C PHE* 2.5 78.2 - + + -
514C MET* 4.1 14.4 - - + -
698C GLU* 3.1 35.2 - - + -
699C GLY* 4.2 0.2 - - - -
702C ILE* 3.3 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 494 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486C GLN* 5.9 2.7 - - - +
489C ASN* 3.4 7.0 - - + +
490C HIS* 2.3 83.7 - - + +
493C PHE* 1.3 78.3 - - + +
495C LEU* 1.3 60.5 + - + +
497C GLN* 4.1 3.2 + - - +
498C GLU* 2.8 39.8 + - + +
509C PHE* 5.7 7.0 - - - -
514C MET 5.5 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 495 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487C PHE* 6.2 0.7 - - + -
490C HIS* 2.6 43.9 + - + +
491C HIS* 2.7 48.2 - - + +
493C PHE 3.1 0.2 - - - -
494C ILE* 1.3 78.6 - - + +
496C GLU* 1.3 59.8 + - - +
497C GLN 3.1 1.8 - - - -
498C GLU* 2.7 40.3 + - + +
499C GLU* 3.3 14.7 + - + +
661C TYR* 4.9 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 496 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C LEU* 5.4 8.4 - - - +
491C HIS* 3.9 14.7 + - - +
492C MET* 2.6 34.8 - - + +
493C PHE* 3.6 4.2 + - - +
495C LEU* 1.3 79.3 - - - +
497C GLN* 1.3 54.4 + - - +
499C GLU* 3.5 9.3 + - - +
500C TYR* 2.3 46.5 + - + -
702C ILE* 4.7 17.8 - - + +
710C ARG* 3.8 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 497 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493C PHE 3.7 11.3 + - - +
494C ILE 4.3 3.4 - - - +
495C LEU 2.9 1.0 + - - -
496C GLU* 1.3 78.4 - - - +
498C GLU* 1.3 77.6 + - - +
500C TYR* 3.1 23.2 + - - +
501C LYS* 3.2 15.3 + - - +
507C TRP* 3.7 47.4 + - + +
509C PHE* 4.4 33.2 - - + +
510C ILE* 5.0 6.7 - - + -
754C ARG* 5.5 2.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 498 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494C ILE* 2.8 36.8 - - + +
495C LEU* 2.7 23.0 + - + +
497C GLN* 1.3 82.5 - - - +
499C GLU* 1.3 53.2 + - + +
501C LYS* 2.9 13.6 + - - +
502C LYS* 2.7 63.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 499 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495C LEU* 3.3 18.3 + - + +
496C GLU* 3.7 10.5 - - - +
498C GLU* 1.3 73.9 - - + +
500C TYR* 1.3 64.4 + - - +
502C LYS* 3.9 21.1 - - - +
503C GLU* 2.9 14.8 + - - +
710C ARG* 5.2 14.4 + - - +
761C PHE* 2.9 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 500 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496C GLU* 2.3 54.3 + - + -
497C GLN* 3.1 16.2 - - + +
499C GLU* 1.3 78.4 - - + +
501C LYS* 1.3 59.7 + - - +
504C GLY 3.3 2.3 + - - -
505C ILE* 2.4 47.5 + - + +
507C TRP* 4.6 23.3 - + + -
706C GLY* 4.0 2.9 - - - -
707C PHE* 2.8 73.2 + + + -
708C PRO* 3.9 0.7 - - - +
710C ARG* 4.2 14.1 + - - -
754C ARG* 5.4 1.3 - - - -
761C PHE* 3.7 20.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 501 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497C GLN* 3.2 17.2 + - - +
498C GLU* 2.9 18.3 + - - +
500C TYR* 1.3 78.3 - - - +
502C LYS* 1.3 68.3 + - + +
504C GLY* 2.7 26.8 + - - -
505C ILE 5.9 0.2 - - - -
754C ARG* 5.7 6.3 - - - +
755C LEU* 3.7 5.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 502 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498C GLU* 2.7 63.4 + - - +
499C GLU* 3.4 23.8 - - - +
501C LYS* 1.3 82.8 - - + +
503C GLU* 1.3 51.1 - - + +
504C GLY 2.9 0.7 + - - -
756C GLY* 1.8 13.1 - - - +
757C THR* 1.5 63.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 503 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499C GLU* 2.9 8.1 + - + +
502C LYS* 1.3 70.8 - - + +
504C GLY 1.3 0.8 - - - +
713C TYR* 2.1 11.4 + - - -
755C LEU 1.8 23.6 - - - +
756C GLY* 0.6 167.2 + - - +
757C THR* 2.3 5.1 + - - +
758C THR* 2.6 24.2 + - - -
759C LYS* 1.0 120.2 + - - +
761C PHE* 1.9 50.7 - - + -
----------------------------------------------------------
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