Contacts of the helix formed by residues 1086 - 1100 (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 MET1086 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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869A GLU 3.1 28.3 - - - +
870A SER* 4.7 3.1 - - - +
871A VAL 3.9 11.4 - - - +
872A MET* 3.6 29.8 - - + +
1084A GLY 3.4 1.1 + - - +
1085A GLU* 1.3 71.5 + - - +
1087A VAL* 1.3 51.0 + - - +
1088A GLY 2.8 3.2 + - - -
1089A ALA* 2.7 35.0 + - + -
1090A LEU* 3.0 11.6 + - - -
1454A VAL* 5.1 3.6 - - + -
1466A ALA* 3.4 40.8 - - + +
1095B ILE* 3.3 36.1 - - + +
1096B ALA* 4.6 5.7 + - - +
1098B GLY* 4.9 3.1 - - - -
60F TYR* 4.5 4.4 + - - -
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Residues in contact with VAL1087 (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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871A VAL* 4.0 0.9 - - + +
872A MET* 3.8 22.2 - - - -
873A VAL* 3.6 26.7 - - + +
879A VAL* 4.1 13.7 - - + -
891A TYR* 3.5 44.2 + - + +
1085A GLU* 3.7 14.8 - - + +
1086A MET* 1.3 69.5 - - - +
1088A GLY* 1.3 59.0 + - - +
1089A ALA 3.4 0.2 - - - -
1090A LEU* 3.9 14.3 - - + +
1091A ALA* 2.8 34.3 + - - +
1400A LEU* 3.4 3.3 - - + +
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Residues in contact with GLY1088 (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* 3.2 35.8 - - - +
871A VAL* 3.0 23.4 + - - -
1086A MET 2.8 4.8 + - - -
1087A VAL* 1.3 75.8 - - - +
1089A ALA* 1.3 59.2 + - - +
1091A ALA* 4.0 0.7 - - - +
1092A ALA* 3.2 15.4 + - - +
1400A LEU* 3.8 13.2 - - - -
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Residues in contact with ALA1089 (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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865A ILE* 4.5 7.4 - - + +
868A MET* 4.4 3.2 + - - -
869A GLU* 4.6 14.6 + - + +
871A VAL 4.4 1.6 + - - -
1086A MET* 2.7 15.2 + - + +
1088A GLY* 1.3 68.2 - - - +
1090A LEU* 1.3 63.2 + - - +
1092A ALA* 3.9 5.0 - - - +
1093A GLN* 3.4 29.8 + - - +
1092B ASP* 4.9 2.9 - - + +
1095B ILE* 4.1 27.6 - - + -
1096B ALA* 4.1 16.4 - - + -
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Residues in contact with LEU1090 (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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466A LYS* 3.8 36.8 - - + +
528A PRO* 3.9 29.2 - - + -
891A TYR* 4.9 6.5 - - + +
898A GLY 6.3 0.7 - - - +
1085A GLU* 4.9 11.9 - - - +
1086A MET 3.0 11.1 + - - +
1087A VAL* 3.9 13.9 - - + +
1089A ALA* 1.3 76.1 - - - +
1091A ALA* 1.3 64.7 + - - +
1093A GLN* 3.6 4.7 + - + +
1094A SER* 3.0 34.3 + - - +
1397A HIS* 4.2 14.6 - - + -
1096B ALA* 4.4 15.3 - - + +
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Residues in contact with ALA1091 (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* 4.3 6.3 - - + -
891A TYR* 5.2 0.9 - - - +
1087A VAL 2.8 22.3 + - - +
1088A GLY 4.0 1.8 - - - +
1089A ALA 3.4 0.2 - - - -
1090A LEU* 1.3 74.2 - - - +
1092A ALA* 1.3 62.5 + - - +
1094A SER* 3.1 3.6 + - - -
1095A LEU* 3.1 24.3 + - - +
1397A HIS* 3.6 40.7 + - - +
1400A LEU* 3.8 18.8 - - + -
1401A LEU* 6.2 0.2 - - + -
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Residues in contact with ALA1092 (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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861A GLN* 5.0 2.6 - - - +
864A LEU* 4.0 17.3 - - + +
865A ILE* 3.7 37.2 - - + +
868A MET* 3.9 16.2 - - + +
1088A GLY 3.2 15.5 + - - +
1089A ALA 3.9 1.1 - - - +
1090A LEU 3.4 0.2 - - - -
1091A ALA* 1.3 78.3 - - - +
1093A GLN* 1.3 56.8 + - - +
1095A LEU* 3.8 3.4 + - - +
1096A GLY* 3.0 23.0 + - - -
1401A LEU* 6.4 0.4 - - - -
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Residues in contact with GLN1093 (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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463A THR 5.6 2.0 + - - -
464A LEU 4.6 1.6 - - - +
465A HIS* 4.4 13.0 - - + -
466A LYS* 3.1 34.2 + - - +
861A GLN* 4.0 24.0 - - - +
865A ILE* 4.2 9.8 - - + +
1089A ALA* 3.4 17.2 + - - +
1090A LEU* 4.1 6.7 - - + +
1091A ALA 3.3 0.4 - - - -
1092A ALA* 1.3 76.3 - - - +
1094A SER* 1.3 54.9 + - - +
1096A GLY 4.3 0.2 - - - +
1097A GLU* 2.7 37.7 + - - +
1089B MET 4.9 0.4 + - - -
1092B ASP* 3.1 46.1 + - - +
1093B CYS* 3.7 6.5 - - - +
1096B ALA* 3.9 6.6 - - - +
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Residues in contact with SER1094 (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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465A HIS* 6.1 0.4 - - - -
529A GLN* 3.4 48.8 + - - +
1090A LEU* 3.0 24.0 + - - +
1091A ALA 3.1 6.1 + - - -
1093A GLN* 1.3 76.6 - - - +
1095A LEU* 1.3 57.2 + - - +
1097A GLU* 4.7 1.6 - - - -
1098A PRO* 3.0 22.1 - - - +
1393A VAL* 4.1 6.7 - - - +
1397A HIS* 3.9 20.3 - - - -
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Residues in contact with LEU1095 (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* 4.5 14.1 - - + -
1091A ALA 3.1 15.1 + - - +
1092A ALA* 4.2 3.6 - - - +
1094A SER* 1.3 75.0 - - - +
1096A GLY* 1.3 65.7 + - - +
1097A GLU 3.3 0.7 - - - -
1098A PRO* 3.2 14.4 - - - +
1099A ALA* 3.6 9.7 + - - +
1124A LEU* 5.2 11.9 - - + -
1382A LEU* 4.7 12.3 - - + -
1386A ILE* 4.2 24.1 - - + +
1393A VAL* 5.0 6.7 - - + +
1397A HIS* 5.4 3.6 - - + +
1398A LEU* 3.7 31.0 - - + -
1401A LEU* 3.6 34.8 - - + -
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Residues in contact with GLY1096 (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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857A THR* 5.6 1.0 - - - +
860A ILE* 5.6 2.3 - - - +
861A GLN* 4.4 21.2 - - - +
864A LEU* 4.8 8.7 - - - +
1092A ALA 3.0 15.3 + - - -
1093A GLN* 3.0 7.3 + - - -
1095A LEU* 1.3 77.3 - - - +
1097A GLU* 1.3 60.8 + - - +
1099A ALA* 3.2 22.2 + - - +
1100A THR* 3.4 12.4 - - - +
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Residues in contact with GLU1097 (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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464A LEU* 3.2 34.4 + - - +
465A HIS* 3.5 36.0 + - + +
493A ASN* 5.4 3.3 + - - -
529A GLN* 3.8 24.9 - - - +
861A GLN* 4.8 0.6 + - - -
1093A GLN 2.7 18.8 + - - +
1094A SER* 4.3 2.7 - - - +
1096A GLY* 1.3 70.7 - - - +
1098A PRO* 1.3 68.8 - - + +
1100A THR* 2.6 31.6 + - - -
1101A GLN* 3.4 22.2 + - - +
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Residues in contact with PRO1098 (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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529A GLN* 3.8 7.4 - - - +
1094A SER 3.0 28.5 - - - +
1095A LEU* 3.2 13.9 - - - +
1097A GLU* 1.3 88.2 - - + +
1099A ALA* 1.3 53.6 + - - -
1101A GLN* 3.0 47.3 + - - +
1386A ILE* 4.4 14.3 - - + +
1389A ASP* 4.1 8.1 - - - +
1391A SER* 4.5 13.5 - - - +
1393A VAL* 3.6 24.0 - - + -
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Residues in contact with ALA1099 (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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853A LYS* 5.4 0.7 - - - +
857A THR* 3.5 5.5 - - + +
860A ILE* 4.7 9.4 - - + -
1095A LEU 3.6 8.7 + - - +
1096A GLY* 3.2 16.8 + - - +
1097A GLU 3.2 0.8 - - - -
1098A PRO* 1.3 82.4 - - - +
1100A THR* 1.3 59.9 + - - +
1101A GLN 3.3 3.6 + - - +
1102A MET 5.1 0.2 - - - +
1121A VAL* 3.2 29.0 - - + +
1124A LEU* 3.7 30.7 - - + -
1386A ILE* 5.4 4.0 - - + +
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Residues in contact with THR1100 (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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464A LEU* 3.5 44.5 - - + +
853A LYS* 3.3 24.8 - - - +
857A THR* 3.6 27.4 - - - +
861A GLN* 4.5 2.5 - - - +
1096A GLY 3.4 15.9 - - - +
1097A GLU* 2.6 18.5 + - - +
1099A ALA* 1.3 74.4 - - - +
1101A GLN* 1.3 64.2 + - - +
1102A MET 3.9 0.2 + - - -
277U GLN* 5.6 1.6 + - - -
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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