Contacts of the helix formed by residues 1394 - 1407 (chain A) in PDB entry 5IYB
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 ASN1394 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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528A PRO 4.3 1.8 + - - -
529A GLN 3.3 20.9 + - - +
530A SER* 4.4 2.2 - - - -
531A ASN* 4.6 3.5 - - - +
898A GLY* 3.9 19.0 + - - -
901A VAL* 3.7 18.4 - - - +
978A VAL* 4.4 7.1 - - - +
1392A TYR* 3.1 25.3 + - + +
1393A VAL* 1.3 76.4 - - - +
1395A TYR* 1.3 83.1 + - - +
1396A ARG* 3.0 35.6 + - - +
1397A HIS* 3.2 26.1 + - + +
1398A LEU* 4.0 1.4 + - - +
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Residues in contact with TYR1395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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892A GLY 4.8 4.5 - - - -
893A GLU* 3.6 18.9 + - - -
978A VAL* 5.6 2.7 - - + -
1375A ARG* 3.3 15.9 + - - -
1379A GLU* 3.0 37.2 + - + -
1383A TYR* 6.0 5.4 - + + -
1392A TYR* 3.8 5.2 + - + +
1393A VAL 3.6 4.5 + - - -
1394A ASN* 1.3 81.3 + - - +
1396A ARG* 1.3 64.5 + - - +
1398A LEU* 3.0 16.9 + - + +
1399A ALA* 3.0 39.3 + - + -
197E SER* 5.8 0.7 - - - -
198E GLU* 3.4 49.8 + - + +
199E THR* 4.5 17.5 - - + -
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Residues in contact with ARG1396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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891A TYR* 4.3 22.9 + - - +
892A GLY* 4.3 21.6 - - - +
894A ASP* 2.8 34.1 + - - -
896A LEU* 3.1 29.5 + - - +
898A GLY* 4.7 6.2 - - - +
901A VAL* 3.9 27.9 - - - +
978A VAL* 4.5 10.5 + - - +
979A LEU* 5.9 0.6 - - - +
1394A ASN* 3.0 36.1 + - - +
1395A TYR* 1.3 84.3 - - + +
1397A HIS* 1.3 65.4 + - + +
1399A ALA* 3.4 4.1 + - - +
1400A LEU* 3.1 24.8 + - - +
199E THR* 3.6 19.0 - - + +
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Residues in contact with HIS1397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528A PRO* 2.7 28.3 + - + -
529A GLN* 3.4 20.3 - - - -
891A TYR* 3.8 17.2 + - - -
898A GLY* 5.3 4.7 - - - -
1090A LEU* 4.2 19.5 - - + -
1091A ALA* 3.6 38.8 - - + +
1094A SER* 3.9 20.2 - - - -
1095A LEU* 5.4 4.0 - - + +
1393A VAL* 4.3 10.1 - - + -
1394A ASN* 3.2 24.3 + - + +
1396A ARG* 1.3 78.2 - - + +
1398A LEU* 1.3 62.2 + - + +
1400A LEU* 3.5 2.9 + - - +
1401A LEU* 3.2 20.8 + - - +
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Residues in contact with LEU1398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1095A LEU* 3.7 37.7 - - + -
1379A GLU* 5.0 10.1 - - + +
1382A LEU* 4.6 15.9 - - + +
1383A TYR* 4.3 39.7 - - + +
1386A ILE* 5.2 4.9 - - + -
1393A VAL* 4.3 28.3 - - + +
1394A ASN 4.5 1.3 - - - +
1395A TYR* 3.0 18.5 + - + +
1397A HIS* 1.3 74.1 - - - +
1399A ALA* 1.3 67.8 + - - +
1401A LEU* 3.3 5.2 + - - +
1402A CYS* 3.3 25.6 + - - -
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Residues in contact with ALA1399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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888A GLN* 4.0 8.7 - - - +
892A GLY* 5.3 2.0 - - - -
893A GLU* 4.9 2.5 - - + -
1375A ARG* 3.5 27.1 + - - +
1379A GLU* 4.6 2.5 - - - -
1395A TYR* 3.0 35.9 + - + -
1396A ARG* 3.8 8.5 - - - +
1398A LEU* 1.3 76.5 - - - +
1400A LEU* 1.3 57.8 + - - +
1402A CYS* 3.5 2.0 + - - +
1403A ASP* 2.9 36.0 + - - +
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Residues in contact with LEU1400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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868A MET* 3.6 12.8 - - + -
871A VAL* 4.3 12.3 - - + -
879A VAL* 4.5 5.4 - - + -
887A VAL* 3.7 26.0 - - + -
888A GLN* 4.1 18.5 - - - +
891A TYR* 4.4 13.7 - - + -
1087A VAL* 3.4 34.1 - - + +
1088A GLY* 3.8 4.5 - - - +
1091A ALA* 3.8 9.9 - - + -
1396A ARG 3.1 18.2 + - - +
1397A HIS 3.7 5.4 - - - +
1398A LEU 3.3 0.2 - - - -
1399A ALA* 1.3 76.8 - - - +
1401A LEU* 1.3 57.0 + - - +
1403A ASP* 4.4 0.9 - - - -
1404A THR* 2.9 35.8 + - - +
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Residues in contact with LEU1401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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864A LEU* 3.6 24.5 - - + -
867A SER* 6.2 0.7 - - - -
868A MET* 3.6 26.4 - - + +
1092A ALA* 6.4 0.2 - - - -
1095A LEU* 3.6 30.1 - - + -
1128A ILE* 3.6 28.0 - - + -
1382A LEU* 3.8 14.4 - - + -
1397A HIS 3.2 11.0 + - - +
1398A LEU* 3.3 9.8 + - - +
1400A LEU* 1.3 75.5 - - - +
1402A CYS* 1.3 66.9 + - - +
1404A THR* 3.2 2.5 + - - -
1405A MET* 3.0 32.1 + - + +
1414A ILE* 5.2 3.1 - - + -
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Residues in contact with CYS1402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1375A ARG* 4.3 20.9 - - + +
1378A LEU* 3.7 25.4 - - + -
1379A GLU* 3.5 35.2 - - + -
1382A LEU* 4.0 13.7 - - - -
1398A LEU* 3.3 14.3 + - - +
1399A ALA 4.1 2.7 - - - +
1401A LEU* 1.3 78.8 - - - +
1403A ASP* 1.3 64.4 + - - +
1405A MET* 3.1 8.2 + - - +
1406A THR* 3.1 28.2 + - - +
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Residues in contact with ASP1403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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887A VAL* 4.1 20.9 - - + +
888A GLN* 2.6 31.3 + - - +
1375A ARG* 2.8 43.3 + - - +
1399A ALA 2.9 15.5 + - - +
1400A LEU 3.9 3.1 - - - +
1402A CYS* 1.3 74.1 - - - +
1404A THR* 1.3 65.0 + - - +
1406A THR* 3.7 6.1 + - - -
1407A CYS* 3.1 31.1 + - - -
195E ARG* 3.9 13.4 + - - -
203E TYR* 5.5 0.7 - - - -
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Residues in contact with THR1404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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867A SER* 4.5 17.0 - - - +
868A MET* 3.2 33.8 - - - +
871A VAL* 4.4 14.7 - - + +
887A VAL* 4.4 10.4 - - + +
1400A LEU* 2.9 30.3 + - - +
1401A LEU* 3.2 4.0 + - - -
1403A ASP* 1.3 76.7 - - - +
1405A MET* 1.3 59.7 + - + +
1406A THR 3.6 0.3 + - - -
1407A CYS* 3.7 7.9 + - - +
1412A MET* 3.0 27.6 - - + +
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Residues in contact with MET1405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1127A LEU 4.9 0.7 - - - +
1128A ILE* 3.8 37.0 - - + +
1130A ILE* 3.4 35.2 - - + -
1378A LEU* 3.9 24.9 - - + -
1382A LEU* 5.9 0.4 - - - -
1401A LEU* 3.0 24.8 + - + +
1402A CYS* 3.1 8.5 + - - +
1404A THR* 1.3 78.0 - - + +
1406A THR* 1.3 60.1 + - + +
1407A CYS 3.5 0.2 - - - -
1410A HIS 3.7 1.2 - - - +
1411A LEU* 3.9 3.2 - - + -
1412A MET* 3.0 61.2 + - - +
1414A ILE* 4.4 11.0 - - + -
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Residues in contact with THR1406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1371A ILE* 3.8 28.7 - - + -
1374A VAL* 4.6 2.2 - - + -
1375A ARG* 4.3 29.8 - - - +
1378A LEU* 5.1 4.0 - - + -
1402A CYS 3.1 17.3 + - - +
1403A ASP* 3.7 9.7 + - - -
1405A MET* 1.3 78.2 - - + +
1407A CYS* 1.3 61.5 + - - +
1408A ARG 3.2 2.9 - - - -
1409A GLY* 2.8 26.6 + - - -
1410A HIS 4.6 2.7 - - - -
1411A LEU* 4.1 12.3 - - + -
207E ARG* 4.0 14.8 + - - -
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Residues in contact with CYS1407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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885A GLN* 5.9 3.4 - - + +
886A VAL 4.0 20.9 - - - -
887A VAL* 4.0 23.6 - - - -
1403A ASP* 3.1 22.6 + - - +
1404A THR* 3.7 8.7 + - - +
1405A MET 3.5 2.0 - - - -
1406A THR* 1.3 80.0 + - - +
1408A ARG* 1.3 62.5 + - - +
1409A GLY 3.1 1.2 + - - -
1412A MET* 5.2 1.6 - - + -
171E PRO* 3.9 16.3 - - + +
172E ARG* 3.1 24.6 + - - +
207E ARG* 5.4 2.2 - - - +
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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