Contacts of the strand formed by residues 1224 - 1228 (chain U) in PDB entry 6FF7
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 ILE1224 (chain U).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1211U PHE* 6.1 5.8 - - + -
1214U MET* 6.3 3.1 - - + -
1219U TYR* 6.3 2.2 - - + -
1220U PRO 3.8 3.1 + - - +
1221U ALA* 3.2 12.5 + - - +
1222U ASP 3.1 2.3 - - - -
1223U LYS* 1.3 79.8 - - - +
1225U SER* 1.3 61.1 + - - +
1254U PRO* 3.2 11.6 - - + +
1255U ASN 3.0 24.3 + - - -
1268U ASN* 4.8 0.2 - - - -
1270U TYR* 3.4 15.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1225 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1223U LYS 4.1 0.4 + - - -
1224U ILE* 1.3 76.4 - - - +
1226U ILE* 1.3 63.4 + - - +
1227U LEU 4.1 0.4 + - - -
1254U PRO* 4.5 1.3 - - - -
1255U ASN* 4.8 3.1 - - - -
1256U LYS* 3.6 23.1 - - - -
1268U ASN* 4.0 19.9 - - - +
1270U TYR 2.9 7.7 + - - +
1271U ILE* 3.3 9.6 - - - +
1272U LEU* 3.0 22.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1226 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1207U VAL* 6.2 3.1 - - + -
1225U SER* 1.3 74.5 - - - +
1227U LEU* 1.3 61.0 + - - +
1237U ILE* 5.9 6.3 - - + -
1254U PRO* 4.7 7.1 - - + +
1256U LYS* 2.9 15.0 + - - +
1257U VAL* 3.4 11.5 - - + -
1258U THR 3.0 26.0 + - - +
1272U LEU* 3.4 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1227 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1225U SER* 4.1 1.7 + - - +
1226U ILE* 1.3 75.8 - - - +
1228U THR* 1.3 62.3 + - - +
1258U THR 3.2 7.9 - - - +
1259U THR 5.0 0.7 - - - -
1260U VAL* 4.7 16.2 - - + +
1271U ILE* 5.7 7.0 - - + -
1272U LEU 2.7 17.2 + - - +
1273U LEU* 3.3 9.4 - - + -
1274U SER* 3.0 22.3 + - - -
1296U ARG* 6.2 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1228 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1227U LEU* 1.3 77.4 - - - +
1229U THR* 1.3 61.7 + - - +
1230U TYR 3.3 13.7 - - - -
1233U GLN* 4.3 14.6 - - - -
1234U LYS* 4.8 7.2 - - - -
1258U THR 3.2 7.4 + - - -
1259U THR* 3.1 9.0 - - - -
1260U VAL* 3.0 24.7 + - - -
1273U LEU* 6.0 0.2 - - - -
1274U SER* 3.3 25.1 - - - +
1276U VAL* 6.1 0.2 - - - -
----------------------------------------------------------
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