Contacts of the helix formed by residues 1200 - 1218 (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 ASN1200 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1189U GLY 3.8 14.8 - - - +
1191U SER* 5.8 0.2 - - - -
1199U GLN* 1.3 80.5 - - - +
1201U LEU* 1.3 59.7 + - - +
1202U GLY 3.2 2.5 - - - -
1203U GLU* 3.0 14.8 + - + +
1204U ALA* 2.8 31.1 + - - +
1233U GLN* 4.9 4.8 - - + +
1236U LEU* 5.9 0.6 - - - +
1276U VAL* 3.5 31.6 - - + +
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Residues in contact with LEU1201 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1185U PHE* 5.2 6.1 - - + +
1188U VAL* 6.5 1.1 - - + -
1189U GLY 4.4 4.2 + - - -
1191U SER* 6.0 1.6 - - - -
1199U GLN* 5.1 1.6 - - - +
1200U ASN* 1.3 71.6 - - - +
1202U GLY* 1.3 57.5 + - - +
1204U ALA* 3.9 6.2 - - - +
1205U GLU* 2.9 34.0 + - - +
1236U LEU* 6.6 0.2 - - - -
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Residues in contact with GLY1202 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1182U VAL* 5.0 6.4 - - - +
1183U GLU 5.2 6.3 - - - -
1185U PHE* 4.0 25.5 - - - +
1188U VAL 5.8 0.8 + - - -
1189U GLY 5.3 2.0 + - - -
1200U ASN 3.2 0.8 - - - -
1201U LEU* 1.3 78.7 - - - +
1203U GLU* 1.3 60.3 + - - +
1205U GLU* 4.2 2.4 - - - +
1206U TYR* 3.3 23.0 + - - +
1358U MET* 3.8 13.0 - - - +
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Residues in contact with GLU1203 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1182U VAL* 4.8 14.1 - - + +
1200U ASN* 3.0 22.3 + - + +
1202U GLY* 1.3 74.8 - - - +
1204U ALA* 1.3 60.1 + - - +
1206U TYR* 3.2 6.7 + - - +
1207U VAL* 2.9 30.4 + - - +
1274U SER* 4.6 14.4 - - - -
1276U VAL* 5.3 4.3 - - - +
1304U PHE* 4.5 23.8 - - + +
1305U ALA* 6.0 0.7 - - - -
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Residues in contact with ALA1204 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1200U ASN 2.8 21.5 + - - +
1201U LEU* 3.9 7.2 - - - +
1203U GLU* 1.3 73.8 - - - +
1205U GLU* 1.3 62.1 + - - +
1207U VAL* 3.2 7.9 + - - +
1208U VAL* 3.0 25.6 + - - +
1233U GLN* 5.3 4.3 - - + +
1236U LEU* 4.9 11.0 - - + +
1237U ILE* 4.6 27.2 - - + +
1240U ILE* 5.6 5.6 - - + -
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Residues in contact with GLU1205 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1201U LEU 2.9 18.4 + - - +
1202U GLY* 4.2 3.8 - - - +
1204U ALA* 1.3 75.6 - - - +
1206U TYR* 1.3 58.7 + - - +
1208U VAL* 3.6 5.8 + - - +
1209U ALA* 2.9 31.1 + - - +
1240U ILE* 5.6 4.9 - - - +
1358U MET* 5.4 4.7 - - + -
1362U ALA* 5.7 6.3 - - + +
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Residues in contact with TYR1206 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1202U GLY 3.3 17.0 + - - +
1203U GLU* 3.2 7.3 + - - +
1204U ALA 3.2 0.6 - - - -
1205U GLU* 1.3 76.7 - - - +
1207U VAL* 1.3 60.3 + - - +
1209U ALA* 3.3 7.0 + - - +
1210U LEU* 2.9 29.5 + - - +
1304U PHE* 5.4 7.0 - - + -
1358U MET* 3.8 22.6 - - + +
1361U MET* 5.7 3.6 - - + +
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Residues in contact with VAL1207 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1203U GLU 2.9 13.5 + - - +
1204U ALA* 3.5 10.8 - - - +
1206U TYR* 1.3 76.3 - - - +
1208U VAL* 1.3 57.5 + - - +
1210U LEU* 3.1 8.3 + - - +
1211U PHE* 2.9 28.0 + - - +
1237U ILE* 6.0 4.0 - - + -
1272U LEU* 5.0 20.6 - - + +
1273U LEU 6.0 1.6 - - - +
1274U SER* 5.3 10.3 - - - -
1304U PHE* 5.6 4.5 - - + -
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Residues in contact with VAL1208 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1204U ALA 3.0 16.3 + - - +
1205U GLU* 3.9 6.3 - - - +
1207U VAL* 1.3 76.6 - - - +
1209U ALA* 1.3 57.3 + - - +
1211U PHE* 3.2 9.9 + - - +
1212U MET* 2.9 29.0 + - - +
1237U ILE* 5.3 4.7 - - + +
1240U ILE* 4.7 22.9 - - + +
1241U ILE* 5.2 5.2 - - + +
1244U ARG* 5.9 4.3 - - + -
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Residues in contact with ALA1209 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1205U GLU 2.9 20.2 + - - +
1206U TYR* 3.5 7.9 - - - +
1208U VAL* 1.3 76.7 - - - +
1210U LEU* 1.3 57.1 + - - +
1212U MET* 3.4 7.4 + - - +
1213U TYR* 2.9 27.9 + - - +
1358U MET 5.6 0.2 - - - +
1361U MET* 4.7 10.1 - - + +
1362U ALA* 4.5 27.6 - - + +
1365U VAL* 4.3 10.6 - - + +
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Residues in contact with LEU1210 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1206U TYR 2.9 13.4 + - - +
1207U VAL* 3.1 10.5 + - - +
1209U ALA* 1.3 73.8 - - - +
1211U PHE* 1.3 60.9 + - - +
1213U TYR* 3.2 9.3 + - - +
1214U MET* 2.9 29.1 + - - +
1302U TYR* 6.4 2.0 - - + -
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Residues in contact with PHE1211 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1207U VAL 2.9 12.7 + - - +
1208U VAL* 3.2 13.2 + - - +
1210U LEU* 1.3 77.6 - - - +
1212U MET* 1.3 56.2 + - - +
1214U MET* 3.4 7.3 + - - +
1215U CYS* 3.0 27.5 + - - +
1224U ILE* 6.1 4.5 - - + -
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Residues in contact with MET1212 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1208U VAL 2.9 15.9 + - - +
1209U ALA* 3.6 8.5 - - - +
1211U PHE* 1.3 74.8 - - - +
1213U TYR* 1.3 58.9 + - - +
1215U CYS* 3.2 7.7 + - - +
1216U LEU* 2.9 32.0 + - - +
1251U ILE* 5.5 8.5 - - + +
1365U VAL* 5.0 8.5 - - + -
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Residues in contact with TYR1213 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1209U ALA 2.9 15.3 + - - +
1210U LEU* 3.3 13.2 - - - +
1212U MET* 1.3 76.4 - - - +
1214U MET* 1.3 56.7 + - - +
1216U LEU* 3.3 7.5 + - - +
1217U LEU* 3.0 27.3 + - - +
1365U VAL* 5.0 10.7 - - + +
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Residues in contact with MET1214 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1210U LEU 2.9 16.5 + - - +
1211U PHE* 3.7 7.4 - - - +
1213U TYR* 1.3 73.5 - - - +
1215U CYS* 1.3 65.1 + - - +
1217U LEU* 3.0 15.3 + - - +
1218U GLY 3.1 0.3 + - - -
1219U TYR* 3.0 37.2 + - + +
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Residues in contact with CYS1215 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1211U PHE 3.0 15.2 + - - +
1212U MET* 3.2 9.8 + - - +
1214U MET* 1.3 75.4 - - - +
1216U LEU* 1.3 58.8 + - - +
1218U GLY* 3.0 18.9 + - - -
1219U TYR* 4.1 13.3 + - - +
1221U ALA* 5.2 8.7 - - + +
1250U LEU 3.8 22.0 - - - +
1251U ILE* 4.1 15.5 - - + -
1252U GLY 4.6 4.7 - - - +
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Residues in contact with LEU1216 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1212U MET 2.9 17.3 + - - +
1213U TYR* 3.7 7.0 - - - +
1215U CYS* 1.3 77.3 - - - +
1217U LEU* 1.3 58.5 + - - +
1218U GLY 3.3 0.4 + - - -
1250U LEU* 4.6 9.6 + - + -
1368U MET* 5.6 11.0 - - + +
1369U TYR* 5.8 9.2 - - + -
1372U LEU* 5.8 6.5 - - + -
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Residues in contact with LEU1217 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1171U ALA 5.2 8.1 - - - +
1172U GLY* 5.8 2.5 - - - -
1213U TYR 3.0 12.6 + - - +
1214U MET* 3.0 14.6 + - - +
1216U LEU* 1.3 78.4 - - - +
1218U GLY* 1.3 58.4 + - - +
1219U TYR 3.6 1.1 - - - +
1336U GLU 4.6 9.6 - - - +
1337U PRO* 3.6 12.2 - - + +
1338U PHE* 2.8 33.7 + - + +
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Residues in contact with GLY1218 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1215U CYS 3.0 12.1 + - - -
1216U LEU 3.3 0.6 - - - -
1217U LEU* 1.3 80.1 - - - +
1219U TYR* 1.3 68.0 + - - +
1220U PRO* 3.6 1.0 - - - +
1338U PHE* 3.5 18.1 - - - +
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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) + - + + + + + -
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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