Contacts of the strand formed by residues 1211 - 1219 (chain A) in PDB entry 1FNF
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 GLU1211 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1181A PRO* 3.2 10.2 - - - +
1182A THR* 2.9 52.8 + - - +
1210A LEU* 1.3 74.7 - - - +
1212A TYR* 1.3 62.2 + - - +
1231A THR* 3.2 32.1 - - - +
1232A ILE* 3.5 6.7 + - - +
1233A ILE* 3.4 31.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1179A THR* 4.1 5.8 - - - -
1180A THR 3.2 27.6 - - - +
1181A PRO* 3.4 22.0 - - + -
1182A THR* 3.6 1.3 - - - -
1187A GLY* 4.0 1.8 - - - -
1188A ASN* 3.0 35.1 + - - +
1206A LEU* 3.9 32.1 - - + -
1207A SER* 2.9 52.9 + - - -
1210A LEU* 3.9 16.6 - - + +
1211A GLU* 1.3 75.8 - - - +
1213A ASN* 1.3 57.8 + - - +
1214A VAL* 4.0 3.0 + - + -
1231A THR* 2.6 22.3 + - - -
1232A ILE* 2.8 31.4 + - + +
1234A PRO* 4.3 5.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1178A THR* 3.4 5.2 + - - +
1179A THR* 3.6 0.2 - - - -
1180A THR* 2.7 46.6 + - + +
1182A THR* 3.7 11.9 + - + +
1212A TYR* 1.3 72.3 - - - +
1214A VAL* 1.3 74.5 + - - +
1215A SER* 3.5 7.0 + - - -
1229A SER* 3.3 21.5 - - - -
1230A ASP* 3.6 9.1 - - - +
1231A THR* 3.9 11.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1149A LEU* 4.1 3.2 - - + +
1151A LEU* 4.0 27.6 - - + -
1160A LEU* 4.5 10.1 - - + -
1162A VAL* 3.9 22.4 - - + -
1177A ILE* 3.8 20.9 - - + -
1178A THR 3.1 10.1 - - - +
1179A THR* 4.1 17.5 - - + -
1206A LEU* 6.0 0.4 - - + -
1212A TYR* 4.6 7.4 - - + +
1213A ASN* 1.3 76.4 - - - +
1215A SER* 1.3 63.5 + - - +
1216A VAL* 4.7 1.1 - - + -
1228A ILE 3.7 0.9 - - - +
1229A SER* 3.0 4.3 - - - -
1230A ASP 2.8 37.2 + - - +
1232A ILE* 4.6 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1176A ARG 3.7 1.0 - - - +
1177A ILE* 3.2 5.2 - - - +
1178A THR* 2.9 44.2 + - - -
1213A ASN* 3.5 7.5 + - - -
1214A VAL* 1.3 70.9 - - - +
1216A VAL* 1.3 63.5 + - - +
1217A TYR* 3.8 19.8 + - - -
1227A PRO* 3.8 7.0 - - - +
1228A ILE 3.3 4.3 - - - -
1229A SER* 2.7 26.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1146A PRO* 3.7 24.3 - - + +
1149A LEU* 3.9 14.6 - - + -
1162A VAL* 3.8 19.1 - - + -
1164A TRP* 3.9 25.1 - - + -
1175A TYR* 4.3 2.5 - - + -
1176A ARG 3.4 2.9 - - - +
1177A ILE* 3.6 32.3 - - + -
1214A VAL* 4.7 0.9 - - + -
1215A SER* 1.3 78.1 - - - +
1217A TYR* 1.3 68.8 + - - +
1227A PRO* 3.2 3.3 - - - +
1228A ILE* 2.9 37.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1146A PRO* 4.4 0.7 - - - -
1175A TYR* 3.2 12.5 - - - -
1176A ARG* 2.8 70.0 + - - +
1178A THR* 4.0 11.2 + - + +
1215A SER* 3.8 27.0 + - - -
1216A VAL* 1.3 75.9 - - - +
1218A THR* 1.3 60.5 + - - +
1219A VAL* 3.9 0.6 - - + +
1224A GLU* 4.0 27.8 - - + +
1225A SER* 3.6 21.3 - - - +
1227A PRO* 3.4 33.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1143A LEU* 3.5 9.1 - - + +
1144A SER 2.9 16.8 + - - +
1146A PRO* 3.2 18.8 - - - +
1167A SER* 3.4 29.0 - - - +
1172A ILE* 3.9 24.5 - - + -
1175A TYR* 3.5 13.7 - - + -
1217A TYR* 1.3 71.5 - - - +
1219A VAL* 1.3 61.1 + - - +
1224A GLU* 3.2 6.4 - - - +
1225A SER* 3.0 39.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1143A LEU* 4.2 1.3 - - - -
1172A ILE* 3.4 5.4 - - - +
1173A THR* 2.8 32.7 + - - +
1174A GLY* 3.0 24.1 + - - +
1175A TYR* 4.2 2.5 - - - +
1176A ARG* 3.9 26.7 - - + +
1217A TYR 3.9 1.1 - - - +
1218A THR* 1.3 76.5 - - - +
1220A LYS* 1.3 57.2 + - - +
1221A ASP 3.4 21.3 - - - +
1222A ASP 5.6 0.2 - - - -
1223A LYS 3.4 6.7 - - - +
1224A GLU* 3.4 31.4 - - + +
----------------------------------------------------------
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