Contacts of the strand formed by residues 4016 - 4022 (chain C) in PDB entry 4O2W
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 ASN4016 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4003C GLY 3.7 4.9 - - - -
4004C ALA* 5.0 1.9 - - - +
4005C GLY 4.9 1.0 + - - -
4006C ARG* 3.9 12.3 - - - +
4014C GLY 3.7 0.2 - - - -
4015C ARG* 1.3 106.1 - - - +
4017C VAL* 1.3 63.8 + - - +
4018C MET* 4.2 5.2 + - + +
4320C GLU* 4.5 13.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL4017 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4001C LEU 3.7 15.9 - - - +
4002C TRP* 3.8 2.0 - - - -
4003C GLY* 2.7 44.3 + - - +
4010C LEU* 3.8 19.3 - - + -
4013C ALA 3.5 24.5 - - - +
4014C GLY* 4.0 8.7 - - - -
4016C ASN* 1.3 80.5 - - - +
4018C MET* 1.3 60.5 + - - +
4019C VAL* 3.0 29.6 - - + +
4021C ALA* 3.8 11.4 - - + -
4320C GLU 4.0 3.1 + - - +
4321C GLY 3.7 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET4018 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4002C TRP* 4.9 0.2 - - - -
4016C ASN* 4.2 3.3 + - + +
4017C VAL* 1.3 77.6 - - - +
4019C VAL* 1.3 62.3 + - + +
4320C GLU 5.4 1.1 - - - +
4321C GLY* 4.2 10.2 - - - +
4324C GLY* 3.2 15.9 + - - -
4325C LEU 3.4 0.2 + - - -
4326C GLY* 2.8 50.5 + - - +
4327C HIS* 3.8 12.9 - - - +
4328C THR* 3.8 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL4019 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4002C TRP* 3.9 4.3 - - - -
4017C VAL* 3.0 22.1 - - + +
4018C MET* 1.3 86.3 - - + +
4020C PRO* 1.3 83.2 - - + +
4021C ALA* 4.0 1.6 - - + +
4324C GLY 4.4 3.6 - - - +
4325C LEU 4.4 1.1 - - - -
4326C GLY* 3.5 21.3 - - - +
4339C GLY* 5.8 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO4020 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4000C TYR* 4.1 10.7 - - + -
4001C LEU 3.9 0.4 - - - +
4002C TRP* 3.7 28.7 - - + -
4019C VAL* 1.3 91.5 - - + +
4021C ALA* 1.3 58.1 + - - +
4022C ALA 4.4 0.2 + - - -
4324C GLY* 3.6 18.8 - - - +
4337C VAL* 3.9 11.2 - - + -
4339C GLY* 4.4 16.6 - - - +
4340C LEU* 3.7 38.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA4021 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4000C TYR* 3.3 4.2 - - - -
4001C LEU* 2.9 37.7 + - - +
4013C ALA* 3.9 23.6 - - + +
4017C VAL* 3.8 16.2 - - + -
4019C VAL* 3.1 2.0 + - + +
4020C PRO* 1.3 74.8 - - - +
4022C ALA* 1.3 65.3 + - - +
4023C ALA 3.6 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA4022 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3998C ASP* 6.5 0.2 - - + -
3999C VAL 3.5 8.5 - - - +
4000C TYR* 4.0 20.2 - - + -
4012C GLU* 5.1 0.7 - - - +
4013C ALA* 3.9 12.1 + - - +
4021C ALA* 1.3 74.8 - - - +
4023C ALA* 1.3 60.8 + - - +
4024C PRO* 3.4 15.8 - - + +
----------------------------------------------------------
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