Contacts of the strand formed by residues 2217 - 2223 (chain C) in PDB entry 1W21
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 ARG2217 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2213C TRP* 3.1 6.9 - - - -
2214C TYR 2.7 33.6 + - - +
2215C GLY 4.6 8.1 + - - +
2216C GLY* 1.3 81.9 - - - +
2218C PRO* 1.3 76.0 - - + +
2219C ILE* 3.5 9.0 - - + +
3131D ASP 2.9 27.7 + - - -
3132D PRO 3.1 20.4 + - - -
3133D GLN* 3.8 12.1 + - - +
3134D GLY* 3.6 14.6 - - - +
3135D CYS* 6.5 0.2 - - - -
3418D ASP* 2.7 37.5 + - - +
3420D TRP* 3.7 18.1 + - - +
3421D ALA* 4.0 12.8 - - + +
3422D ASN* 5.0 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO2218 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2211C VAL* 4.2 10.5 - - + -
2212C VAL 3.9 5.4 - - - +
2213C TRP* 3.5 22.8 - - + -
2217C ARG* 1.3 88.3 - - + +
2219C ILE* 1.3 63.1 + - - +
2221C GLU* 5.3 2.0 - - - +
3104D HIS* 3.8 29.8 - - + +
3106D LEU* 3.7 21.8 - - + -
3418D ASP* 5.4 4.5 - - + +
3423D LYS* 3.3 22.4 + - - +
3455D CYS* 5.3 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2219 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2212C VAL 2.8 14.2 + - - +
2213C TRP 4.4 0.4 - - - -
2214C TYR* 3.6 33.2 - - + +
2217C ARG* 3.5 22.9 - - + +
2218C PRO* 1.3 81.3 - - - +
2220C THR* 1.3 61.0 + - - +
2221C GLU* 4.2 7.4 - - - +
2266C GLU 3.6 17.5 - - - +
2267C GLY 3.7 16.8 - - - +
2268C LYS* 3.8 20.0 - - + -
3422D ASN* 5.7 12.3 - - + +
3423D LYS* 4.6 14.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR2220 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2211C VAL* 3.5 4.7 - - - +
2212C VAL* 2.7 39.0 + - + +
2219C ILE* 1.3 83.7 + - - +
2221C GLU* 1.3 78.3 + - - +
2222C ILE* 4.4 4.0 - - + -
2267C GLY 2.7 27.7 + - - -
2268C LYS* 3.8 7.4 - - - +
2269C ILE* 4.1 29.6 + - + +
3459D LYS* 4.2 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2221 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2210C ALA 3.2 8.7 - - - +
2211C VAL* 4.6 4.5 - - + +
2218C PRO 5.3 1.4 - - - -
2219C ILE 4.2 7.0 + - - +
2220C THR* 1.3 88.4 + - - +
2222C ILE* 1.3 64.0 + - - +
2223C PRO* 4.2 1.3 - - - -
3104D HIS* 3.8 40.9 + - + -
3423D LYS* 5.7 4.2 + - - -
3456D GLY 4.7 1.8 - - - +
3457D SER* 2.9 30.8 + - - +
3458D LYS 4.4 1.9 + - - -
3459D LYS* 2.8 37.4 + - + +
3461D LEU* 3.8 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2222 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2209C SER* 3.2 1.5 - - - -
2210C ALA* 2.7 45.7 + - + +
2212C VAL* 4.3 7.4 - - + -
2220C THR* 4.4 3.8 - - + -
2221C GLU* 1.3 78.6 - - - +
2223C PRO* 1.3 78.2 - - + +
2225C TRP* 3.9 22.9 - - + -
2230C LEU* 3.6 4.9 - - + +
2248C MET* 4.1 10.5 - - + -
2262C ILE* 3.9 24.2 - - + -
2264C PHE* 3.9 24.2 - - + -
2269C ILE* 4.0 20.2 - - + -
2272C ILE* 6.6 0.4 - - + -
3459D LYS* 4.9 0.9 - - - +
3461D LEU* 4.3 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO2223 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2208C ALA 4.1 4.7 - - - +
2209C SER* 4.3 0.7 - - - -
2221C GLU 4.0 5.6 - - - +
2222C ILE* 1.3 101.5 - - + +
2224C SER* 1.3 71.5 + - - +
2225C TRP* 3.4 8.0 + - - +
2230C LEU* 4.3 0.9 - - - -
3459D LYS* 4.4 17.5 - - + +
3460D ARG 4.0 21.3 - - - +
3461D LEU* 4.0 19.9 - - + -
3462D GLY 5.4 1.8 - - - +
----------------------------------------------------------
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