Contacts of the helix formed by residues 210 - 219 (chain V) in PDB entry 5GJQ
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 210 (chain V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24U ASN* 5.6 7.7 - - - -
179U ILE* 5.4 0.5 - - - +
208V ARG* 5.4 2.3 - - - +
209V LYS* 1.3 95.8 - - - +
211V GLU* 1.3 63.7 + - - +
212V LEU* 3.1 13.5 + - + +
213V GLU* 3.2 23.3 + - + +
214V GLN* 3.4 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 211 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574N LYS* 4.4 22.6 - - + +
179U ILE* 5.5 6.2 - - + +
210V ASN* 1.3 72.0 - - - +
212V LEU* 1.3 56.0 + - + +
214V GLN* 2.5 26.7 - - + +
215V LYS* 2.9 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 212 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20U VAL* 5.7 10.3 - - + -
126U VAL* 3.0 27.8 - - + +
127U LYS* 3.5 10.1 - - - +
128U PRO* 3.5 33.7 - - + -
210V ASN* 3.1 9.4 - - + +
211V GLU* 1.3 76.2 - - + +
213V GLU* 1.3 62.4 + - - +
214V GLN 3.1 1.1 - - - -
215V LYS* 2.5 43.1 + - + +
216V MET* 2.8 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 213 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17U LEU* 4.0 24.2 - - + -
20U VAL* 6.1 5.0 - - + +
175U LEU* 3.8 13.2 - - - +
35V SER* 2.4 43.6 + - - +
208V ARG 4.0 5.9 - - - +
209V LYS* 3.6 12.2 - - - +
210V ASN* 3.2 37.4 + - + +
212V LEU* 1.3 78.0 - - - +
214V GLN* 1.3 66.6 + - - +
216V MET* 3.0 13.5 + - - +
217V LEU* 3.1 22.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 214 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176U LEU* 3.1 26.9 - - + +
179U ILE* 3.5 35.9 - - + -
209V LYS* 4.2 3.1 - - - +
210V ASN 3.4 6.6 + - - +
211V GLU* 2.5 41.7 - - + +
213V GLU* 1.3 80.2 - - - +
215V LYS* 1.3 62.3 + - + +
217V LEU* 2.8 23.0 + - - +
218V LEU* 2.8 16.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 215 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127U LYS 5.4 0.2 + - - -
128U PRO* 4.0 26.0 + - + +
129U LYS* 5.4 3.8 - - - +
134U PRO* 6.0 0.4 - - - -
211V GLU* 2.9 40.1 + - - +
212V LEU* 2.5 40.1 + - + +
214V GLN* 1.3 79.4 - - + +
216V MET* 1.3 59.9 + - - +
218V LEU* 3.5 27.7 + - + +
219V ASN* 3.5 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 216 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16U LEU* 3.6 39.2 - - + +
17U LEU* 4.7 4.7 - - + -
20U VAL* 4.2 20.2 - - + -
124U ILE* 3.3 26.0 - - + -
125U ASP 3.2 26.7 - - - +
126U VAL* 5.0 0.2 - - - -
128U PRO* 4.2 10.3 - - + +
134U PRO* 3.5 21.3 - - + -
162U ILE* 5.8 0.7 - - - +
212V LEU 2.8 17.3 + - - +
213V GLU* 3.4 8.5 - - - +
215V LYS* 1.3 72.1 - - - +
217V LEU* 1.3 68.7 + - + +
219V ASN* 2.4 42.9 - - - +
220V LEU* 3.7 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 217 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13U PRO* 4.1 19.1 - - + -
16U LEU* 5.9 2.2 - - + -
17U LEU* 4.1 29.2 - - + -
162U ILE* 6.3 1.1 - - + -
172U VAL* 4.1 36.1 - - + +
175U LEU* 5.2 5.8 - - + -
176U LEU* 3.1 42.6 - - + +
35V SER* 5.5 1.1 - - - -
39V LEU* 5.3 1.8 - - + -
213V GLU* 3.2 19.3 - - + +
214V GLN 2.8 6.0 + - - +
216V MET* 1.3 79.4 - - + +
218V LEU* 1.3 55.6 + - - +
220V LEU* 2.7 33.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 218 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176U LEU* 3.7 16.1 - - + +
179U ILE* 3.4 36.1 - - + +
180U LYS* 4.2 7.4 - - + -
181U ASP* 4.4 19.4 - - - +
214V GLN* 2.8 15.8 + - + +
215V LYS* 3.5 26.9 - - + +
217V LEU* 1.3 77.6 - - - +
219V ASN* 1.3 58.7 + - - +
220V LEU 3.0 5.5 + - - -
221V HIS* 3.6 9.7 + - - +
222V LYS* 4.1 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 219 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132U GLY* 4.1 11.5 - - - -
133U LEU* 3.8 16.6 - - - +
134U PRO* 3.5 28.4 - - - +
162U ILE* 3.7 22.9 + - - +
215V LYS 3.5 8.5 + - - +
216V MET* 2.4 32.8 + - - +
218V LEU* 1.3 75.9 - - - +
220V LEU* 1.3 67.0 + - - +
221V HIS 3.3 0.4 - - - -
222V LYS* 3.0 30.1 + - + +
----------------------------------------------------------
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