Contacts of the helix formed by residues 199 - 212 (chain C) in PDB entry 1Y67
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 ASN 199 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C GLN 4.2 2.6 + - - +
87C ILE 2.7 22.8 + - - +
88C MET 3.8 17.8 + - - +
89C GLY* 4.1 6.7 - - - +
197C VAL 3.3 1.2 + - - -
198C VAL* 1.3 70.7 - - - +
200C TRP* 1.3 58.8 + - - +
201C ASP* 3.2 15.3 + - - +
202C GLU* 3.0 27.9 + - + +
203C VAL* 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 200 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C ASN* 3.6 44.8 + - - +
99C GLN* 3.6 14.7 - - - +
100C PRO* 3.6 32.3 - - + -
104C LEU* 3.7 22.3 - - + +
108C ILE* 4.4 7.0 - - + -
115C PHE* 3.6 20.8 - + - -
118C PHE* 3.8 17.0 - + - -
137C LEU* 4.9 1.8 - - + -
170C LEU* 3.7 23.3 - - + -
195C TRP* 4.0 15.3 + + - -
198C VAL* 3.5 21.2 + - + +
199C ASN* 1.3 69.0 + - - +
201C ASP* 1.3 62.6 + - - +
203C VAL* 3.7 24.5 - - + +
204C SER* 2.8 33.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 201 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B GLN* 4.9 8.0 - - - +
199C ASN* 3.2 11.3 + - - +
200C TRP* 1.3 78.4 - - - +
202C GLU* 1.3 57.0 + - - +
204C SER* 3.5 5.7 + - - -
205C LYS* 3.1 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 202 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C GLN* 3.1 41.6 - - - +
87C ILE* 3.9 9.9 - - + -
199C ASN* 3.0 23.6 + - - +
201C ASP* 1.3 75.0 - - - +
203C VAL* 1.3 59.2 + - - +
205C LYS* 3.3 27.5 + - - +
206C ARG* 3.0 56.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 203 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C ILE* 4.1 12.1 - - + -
104C LEU* 3.6 17.5 - - + -
137C LEU* 4.9 0.9 - - + -
169C ILE* 3.5 41.6 - - + +
170C LEU* 4.1 11.0 - - + -
198C VAL* 4.0 21.1 - - + -
199C ASN 3.0 14.9 + - - +
200C TRP* 3.4 21.3 + - + +
202C GLU* 1.3 75.5 - - - +
204C SER* 1.3 57.1 + - - +
206C ARG* 3.2 3.2 + - - +
207C TYR* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 204 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C PRO* 4.9 1.9 - - - +
101C SER 4.2 9.0 + - - -
103C GLU* 4.7 5.8 - - - +
104C LEU* 3.4 28.4 + - - +
200C TRP 2.8 23.0 + - - -
201C ASP* 3.7 7.0 - - - -
203C VAL* 1.3 69.9 - - - +
205C LYS* 1.3 60.0 + - - +
207C TYR* 3.2 7.3 + - - +
208C ALA* 2.9 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 205 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LYS* 4.1 39.6 - - + +
201C ASP 3.1 14.9 + - - +
202C GLU* 3.3 32.0 + - - +
204C SER* 1.3 75.2 - - - +
206C ARG* 1.3 64.4 + - + +
208C ALA* 3.3 7.2 + - - +
209C ALA* 3.1 23.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 206 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C GLU* 6.1 2.6 - - - +
83C MET* 2.9 48.4 - - - +
86C GLN* 2.6 32.5 + - - +
87C ILE* 3.8 16.5 - - - +
168C PRO 4.8 1.1 + - - +
169C ILE* 3.7 35.6 - - + +
202C GLU* 3.0 32.0 + - - +
203C VAL 3.6 7.2 - - - +
205C LYS* 1.3 77.6 - - + +
207C TYR* 1.3 57.8 + - - +
209C ALA* 3.4 6.6 + - - +
210C ALA* 2.8 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 207 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B PRO* 5.2 6.6 - - - +
103C GLU* 3.6 24.0 - - + -
104C LEU* 4.0 21.3 - - + -
107C ALA* 3.3 28.5 - - + +
139C VAL* 3.7 23.6 - - + -
142C GLY 4.7 9.3 + - - -
144C LEU* 4.0 24.2 - - + +
169C ILE* 3.7 14.7 - - + +
203C VAL 2.9 15.0 + - - +
204C SER* 3.5 8.7 - - - +
206C ARG* 1.3 76.4 - - - +
208C ALA* 1.3 61.3 + - - +
210C ALA* 3.3 1.1 + - - +
211C LYS* 3.1 64.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 208 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C GLU* 3.8 19.7 - - - +
204C SER 2.9 16.2 + - - +
205C LYS* 3.7 7.2 - - - +
207C TYR* 1.3 77.4 - - - +
209C ALA* 1.3 61.9 + - - +
211C LYS* 3.6 14.9 + - - +
212C LEU* 3.5 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 209 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B LYS* 6.5 0.9 - - + -
205C LYS* 3.1 14.5 + - + +
206C ARG* 3.7 10.1 - - - +
208C ALA* 1.3 76.4 - - - +
210C ALA* 1.3 60.5 + - - +
212C LEU* 3.2 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 210 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C VAL* 3.8 33.1 - - + +
167C THR* 4.0 29.8 + - + -
169C ILE* 4.0 3.4 - - + -
206C ARG 2.8 18.3 + - - +
207C TYR 3.3 4.7 + - - +
209C ALA* 1.3 74.5 - - - +
211C LYS* 1.3 64.7 + - - +
212C LEU 3.3 0.5 + - - -
213C VAL 3.9 16.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 211 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B PRO* 3.8 19.3 - - + +
54B GLU* 2.8 31.7 + - - +
103C GLU* 3.1 40.8 + - - +
139C VAL* 5.2 6.7 - - + -
142C GLY* 5.9 7.4 - - - +
207C TYR* 3.1 51.3 + - + +
208C ALA* 3.7 10.5 - - - +
209C ALA 3.3 0.6 - - - -
210C ALA* 1.3 75.8 - - - +
212C LEU* 1.3 61.6 + - + +
213C VAL 3.3 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 212 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B ALA* 3.5 41.7 - - + +
210B ALA* 6.1 0.2 - - - -
208C ALA 3.5 20.0 - - - +
209C ALA* 3.2 20.2 + - - +
210C ALA 3.1 1.2 - - - -
211C LYS* 1.3 76.9 - - + +
213C VAL* 1.3 70.3 + - - +
----------------------------------------------------------
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