Contacts of the helix formed by residues 1357 - 1376 (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 ASN1357 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1181U ASN 5.6 4.5 - - - -
1355U ILE* 3.4 5.3 + - - +
1356U LYS* 1.3 83.0 + - + +
1358U MET* 1.3 65.5 + - - +
1359U PRO* 3.5 7.0 - - + -
1360U GLN* 3.5 11.0 + - + +
1361U MET* 3.2 20.5 + - - +
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Residues in contact with MET1358 (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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1182U VAL* 6.2 3.1 - - + -
1202U GLY* 3.8 25.8 - - - +
1205U GLU* 5.4 4.0 - - + -
1206U TYR* 3.8 20.7 - - + +
1209U ALA* 5.6 0.2 - - - +
1357U ASN* 1.3 73.9 - - - +
1359U PRO* 1.4 60.7 - - - +
1361U MET* 2.9 9.8 + - - +
1362U ALA* 2.8 30.1 + - - +
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Residues in contact with PRO1359 (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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1357U ASN* 3.5 5.0 - - + -
1358U MET* 1.4 77.0 - - - +
1360U GLN* 1.3 56.9 + - - +
1362U ALA* 3.8 6.6 - - + +
1363U ASN* 2.9 30.0 + - - +
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Residues in contact with GLN1360 (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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1355U ILE* 5.3 5.6 - - - -
1356U LYS* 4.8 7.6 - - + +
1357U ASN* 3.5 21.3 + - + +
1358U MET 3.2 0.6 - - - -
1359U PRO* 1.3 78.9 - - - +
1361U MET* 1.3 56.7 + - - +
1363U ASN* 3.4 7.0 - - - +
1364U PHE* 3.0 27.2 + - - +
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Residues in contact with MET1361 (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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1206U TYR* 5.7 4.3 - - + +
1209U ALA* 4.7 12.3 - - + -
1355U ILE* 4.8 13.2 - - + +
1357U ASN 3.2 10.8 + - - +
1358U MET* 2.9 12.3 + - - +
1360U GLN* 1.3 77.8 - - - +
1362U ALA* 1.3 59.4 + - - +
1364U PHE* 3.1 8.1 + - - +
1365U VAL* 2.8 31.9 + - - +
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Residues in contact with ALA1362 (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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1205U GLU* 5.7 7.0 - - + +
1209U ALA* 4.5 15.4 - - + +
1358U MET 2.8 17.9 + - - +
1359U PRO* 3.9 7.9 - - + +
1361U MET* 1.3 72.6 - - - +
1363U ASN* 1.3 62.5 + - - +
1365U VAL* 4.2 3.1 - - - +
1366U TYR* 3.2 22.5 + - - +
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Residues in contact with ASN1363 (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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1359U PRO 2.9 18.3 + - - +
1360U GLN* 3.4 9.6 - - - +
1362U ALA* 1.3 74.3 - - - +
1364U PHE* 1.3 65.1 + - - +
1366U TYR* 3.1 7.7 + - - +
1367U ASN* 3.0 23.7 + - - +
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Residues in contact with PHE1364 (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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1360U GLN 3.0 11.4 + - - +
1361U MET* 3.1 11.0 + - - +
1363U ASN* 1.3 78.4 - - - +
1365U VAL* 1.3 57.8 + - - +
1367U ASN* 3.4 5.8 + - - +
1368U MET* 2.8 31.3 + - - +
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Residues in contact with VAL1365 (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* 4.3 22.0 - - + +
1212U MET* 5.0 7.2 - - + -
1213U TYR* 5.0 12.1 - - + +
1361U MET 2.8 20.3 + - - +
1362U ALA* 4.3 6.1 - - - +
1364U PHE* 1.3 70.2 - - - +
1366U TYR* 1.3 61.5 + - - +
1368U MET* 3.8 6.5 - - - +
1369U TYR* 2.9 31.2 + - - +
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Residues in contact with TYR1366 (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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1362U ALA 3.2 13.3 + - - +
1363U ASN* 3.1 11.3 + - - +
1365U VAL* 1.3 78.5 - - - +
1367U ASN* 1.3 57.4 + - - +
1369U TYR* 3.3 5.3 + - - +
1370U MET* 2.9 31.1 + - - +
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Residues in contact with ASN1367 (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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1363U ASN 3.0 15.4 + - - +
1364U PHE* 3.8 6.1 - - - +
1366U TYR* 1.3 76.4 - - - +
1368U MET* 1.3 62.4 + - - +
1370U MET* 3.4 6.4 + - - +
1371U HIS* 3.0 24.4 + - - +
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Residues in contact with MET1368 (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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1216U LEU* 5.6 9.8 - - + +
1364U PHE 2.8 21.7 + - - +
1365U VAL* 3.8 8.5 - - - +
1367U ASN* 1.3 73.4 - - - +
1369U TYR* 1.3 56.6 + - - +
1371U HIS* 3.4 7.5 + - - +
1372U LEU* 3.1 25.3 + - - +
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Residues in contact with TYR1369 (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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1216U LEU* 5.8 7.4 - - + +
1365U VAL 2.9 19.7 + - - +
1366U TYR* 3.7 4.9 - - - +
1368U MET* 1.3 72.8 - - - +
1370U MET* 1.3 60.3 + - - +
1371U HIS 3.1 1.3 - - - -
1372U LEU* 3.0 7.7 + - - +
1373U ILE* 2.8 31.4 + - - +
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Residues in contact with MET1370 (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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1366U TYR 2.9 18.3 + - - +
1367U ASN* 3.4 6.3 + - - +
1369U TYR* 1.3 76.1 - - - +
1371U HIS* 1.3 59.3 + - - +
1373U ILE* 4.0 7.9 - - - +
1374U GLN* 3.6 19.9 + - - +
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Residues in contact with HIS1371 (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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1367U ASN 3.0 16.9 + - - +
1368U MET* 3.6 8.5 - - - +
1370U MET* 1.3 79.5 - - - +
1372U LEU* 1.3 57.3 + - - +
1373U ILE 3.4 0.2 - - - -
1374U GLN* 3.7 5.2 + - - +
1375U THR* 3.3 27.9 + - - -
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Residues in contact with LEU1372 (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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1216U LEU* 5.8 8.1 - - + +
1250U LEU* 6.0 6.3 - - + -
1368U MET 3.1 15.1 + - - +
1369U TYR* 3.0 9.3 + - - +
1371U HIS* 1.3 77.4 - - - +
1373U ILE* 1.3 60.2 + - - +
1374U GLN 3.3 0.4 - - - -
1375U THR* 3.8 4.3 - - - +
1376U THR* 2.9 33.0 + - - +
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Residues in contact with ILE1373 (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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1369U TYR 2.8 14.4 + - - +
1370U MET* 4.3 8.5 - - - +
1371U HIS 3.4 0.2 - - - -
1372U LEU* 1.3 78.4 - - - +
1374U GLN* 1.3 59.3 + - - +
1376U THR 3.0 17.3 - - - +
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Residues in contact with GLN1374 (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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1370U MET 3.6 16.7 + - - +
1371U HIS* 4.0 5.6 - - - +
1372U LEU 3.3 0.2 - - - -
1373U ILE* 1.3 81.0 - - - +
1375U THR* 1.3 58.9 + - - +
1376U THR 3.6 0.6 + - - -
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Residues in contact with THR1375 (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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1371U HIS 3.3 17.4 + - - -
1372U LEU* 4.6 2.9 - - - -
1374U GLN* 1.3 80.4 - - - +
1376U THR* 1.3 58.5 + - - +
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Residues in contact with THR1376 (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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1372U LEU* 2.9 19.3 + - - +
1373U ILE* 3.0 21.1 - - - +
1374U GLN 4.6 0.7 - - - +
1375U THR* 1.3 79.2 - - - +
1377U HIS* 1.3 66.4 + - - +
1378U HIS 5.4 0.4 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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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