Contacts of the strand formed by residues 1302 - 1310 (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 GLU1302 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1273A PRO* 3.4 5.5 - - - +
1274A VAL* 2.7 56.9 + - + +
1275A LYS 4.7 0.3 + - - -
1300A GLY 4.3 0.2 + - - -
1301A THR* 1.3 75.4 - - - +
1303A TYR* 1.3 59.8 + - - +
1322A ARG* 3.4 33.0 + - - +
1323A GLN* 3.7 17.2 + - - +
1324A LYS* 3.5 21.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1303 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1252A MET* 4.0 12.8 - - + -
1271A TYR* 4.3 14.6 - + - -
1272A SER* 3.2 21.5 - - - +
1273A PRO* 3.7 18.3 - - + +
1274A VAL* 4.0 0.7 - - - -
1294A LEU* 5.9 0.7 - - + -
1297A LEU* 3.5 28.1 - - + -
1298A LEU* 2.8 44.5 + - - +
1301A THR* 3.3 43.1 - - + -
1302A GLU* 1.3 75.0 - - - +
1304A VAL* 1.3 64.9 + - - +
1305A VAL* 4.0 9.1 + - + +
1322A ARG* 3.2 6.8 - - - +
1323A GLN 2.9 35.5 + - - +
1325A THR* 3.9 10.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1304 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1270A ARG 4.0 0.2 - - - +
1271A TYR* 3.0 25.5 - - - +
1272A SER* 2.7 21.2 + - - +
1273A PRO 5.0 0.2 - - - -
1274A VAL* 3.4 32.8 - - + -
1303A TYR* 1.3 72.5 - - - +
1305A VAL* 1.3 63.3 - - - +
1306A SER* 5.7 0.7 - - - -
1320A ARG* 3.6 35.0 - - + +
1321A GLY 3.7 4.9 - - - +
1322A ARG* 3.9 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1242A LEU* 3.8 3.2 - - + +
1244A PHE* 3.8 26.7 - - + -
1252A MET* 4.5 6.3 - - - -
1254A VAL* 4.0 28.5 - - + -
1269A VAL* 4.3 16.4 - - + -
1270A ARG 3.5 7.0 - - - +
1271A TYR* 3.8 12.3 - - + -
1294A LEU* 4.0 13.7 - - + -
1303A TYR* 4.5 9.9 - - + +
1304A VAL* 1.3 80.3 - - - +
1306A SER* 1.3 66.5 + - - +
1307A VAL* 4.8 1.6 - - + -
1319A LEU 3.7 0.7 - - - +
1320A ARG* 3.4 3.1 - - - +
1321A GLY 2.8 38.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1268A LEU 3.6 1.2 - - - +
1269A VAL* 3.3 4.5 - - - +
1270A ARG* 2.8 57.1 + - - +
1304A VAL* 5.7 0.7 - - - -
1305A VAL* 1.3 75.3 - - - +
1307A VAL* 1.3 63.5 + - - +
1308A SER* 5.2 1.1 + - - -
1318A PRO* 3.8 22.1 - - - +
1319A LEU 3.0 10.1 - - - -
1320A ARG* 4.1 21.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1307 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1239A PRO* 3.6 11.1 - - + +
1242A LEU* 3.8 19.5 - - + -
1254A VAL* 4.6 4.9 - - + -
1256A TRP* 3.4 59.9 - - + +
1267A PHE* 4.0 16.2 - - + -
1268A LEU 3.5 1.8 - - - -
1269A VAL* 3.8 13.5 - - + -
1305A VAL* 4.8 3.1 - - + -
1306A SER* 1.3 78.4 - - - +
1308A SER* 1.3 63.7 + - - +
1319A LEU* 2.8 39.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1239A PRO* 4.4 0.4 - - - -
1267A PHE* 3.2 9.3 - - - -
1268A LEU* 2.7 44.6 + - - +
1270A ARG* 4.1 5.5 + - - -
1306A SER* 5.2 1.0 + - - -
1307A VAL* 1.3 73.6 - - - +
1309A SER* 1.3 61.0 + - - +
1315A GLU* 3.5 36.5 + - - -
1316A SER* 4.2 7.9 - - - -
1317A THR 4.4 0.7 - - - -
1318A PRO* 3.3 27.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1309 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1236A VAL* 3.9 4.5 - - - -
1237A PRO 2.9 22.8 + - - -
1239A PRO* 2.9 25.4 - - - +
1259A PRO* 3.4 8.7 - - - +
1264A LEU* 3.9 20.0 - - - -
1266A ASN 4.1 0.4 - - - -
1267A PHE* 3.9 9.7 - - - -
1308A SER* 1.3 73.5 - - - +
1310A VAL* 1.3 66.5 + - - +
1315A GLU* 3.3 1.6 - - - +
1316A SER* 3.0 31.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1236A VAL* 4.9 0.4 - - - -
1264A LEU* 3.3 10.7 - - - +
1265A THR* 2.8 29.8 + - + -
1266A ASN* 3.1 36.5 + - - +
1268A LEU* 4.1 23.8 - - + -
1308A SER 4.1 1.6 - - - +
1309A SER* 1.3 82.9 - - - +
1311A TYR* 1.3 60.5 + - - +
1312A GLU 4.0 17.5 - - - +
1313A GLN 4.8 3.4 - - - +
1314A HIS 3.2 11.2 - - - +
1315A GLU* 4.0 17.0 - - + +
----------------------------------------------------------
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