Contacts of the helix formed by residues 1117 - 1135 (chain H) in PDB entry 5YWB
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 PRO1117 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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825H GLU* 3.8 27.4 - - - +
828H ILE* 5.2 4.0 - - + -
1115H THR 3.6 6.3 - - - +
1116H THR* 1.3 93.5 - - + +
1118H LEU* 1.3 62.1 + - - +
1119H GLY 3.3 0.4 - - - +
1120H SER* 2.5 38.7 + - - +
1121H ILE* 3.4 3.3 + - - +
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Residues in contact with LEU1118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503H LEU* 4.2 31.9 - - + +
504H ARG* 4.6 9.9 - - + +
825H GLU* 5.3 2.7 + - + +
826H ARG* 3.4 29.6 - - - +
828H ILE* 3.7 22.2 - - + +
1113H PHE* 3.9 30.3 - - + +
1116H THR 3.3 2.9 + - - +
1117H PRO* 1.3 69.6 - - - +
1119H GLY* 1.3 66.2 + - - +
1121H ILE* 3.1 21.3 + - + +
1122H LEU* 2.9 24.8 + - - +
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Residues in contact with GLY1119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825H GLU* 5.2 14.4 - - - +
1117H PRO* 3.3 2.2 - - - +
1118H LEU* 1.3 78.3 - - - +
1120H SER* 1.3 55.7 + - - +
1122H LEU* 3.4 6.6 + - - +
1123H ASN* 2.9 33.1 + - - +
1198H LEU* 6.0 3.6 - - - -
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Residues in contact with SER1120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1116H THR* 4.1 9.2 - - - +
1117H PRO* 2.5 37.4 + - - +
1119H GLY* 1.3 76.2 - - - +
1121H ILE* 1.3 61.5 + - - +
1123H ASN* 4.8 3.1 - - - -
1124H ARG* 2.9 53.4 + - - +
1198H LEU* 5.6 12.0 - - - +
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Residues in contact with ILE1121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503H LEU* 3.7 23.3 - - + -
1105H ILE* 5.1 15.7 - - + -
1112H PHE* 4.8 15.7 - - + -
1113H PHE* 5.0 11.2 - - + -
1116H THR* 3.7 37.5 - - + -
1117H PRO 3.7 2.7 - - - +
1118H LEU* 3.1 26.8 + - + +
1120H SER* 1.3 82.6 + - - +
1122H LEU* 1.3 59.4 + - - +
1124H ARG* 3.7 4.4 - - - +
1125H PHE* 2.9 37.7 + - + +
1318H LEU* 4.8 18.5 - - + +
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Residues in contact with LEU1122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415H GLY* 6.2 0.4 - - - -
419H ASN* 5.1 10.3 - - - +
496H LEU* 4.7 15.7 - - + +
499H THR* 3.9 23.8 - - + -
500H ASN* 3.1 37.9 - - - +
503H LEU* 4.9 8.1 - - + -
1118H LEU 2.9 16.1 + - - +
1119H GLY* 4.0 5.6 - - - +
1121H ILE* 1.3 79.1 - - - +
1123H ASN* 1.3 61.7 + - + +
1125H PHE* 3.2 7.9 - - + +
1126H SER* 2.9 28.9 + - - -
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Residues in contact with ASN1123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422H ALA* 5.4 8.0 - - - +
1119H GLY 2.9 18.6 + - - +
1120H SER* 4.2 2.7 - - - +
1122H LEU* 1.3 75.7 - - + +
1124H ARG* 1.3 60.7 + - - +
1126H SER* 4.5 4.1 - - - +
1127H SER* 2.9 46.3 + - - -
1198H LEU* 4.9 15.1 - - + +
1201H LEU* 4.6 18.4 - - - +
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Residues in contact with ARG1124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1120H SER* 2.9 44.6 + - - +
1121H ILE 3.7 2.9 - - - +
1123H ASN* 1.3 76.1 - - - +
1125H PHE* 1.3 66.9 + - - +
1127H SER* 5.0 1.1 - - - -
1128H ASP* 2.9 51.9 + - - +
1314H ARG* 3.2 53.9 - - - +
1315H ILE* 4.8 5.4 - - + +
1318H LEU* 3.6 29.6 - - + +
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Residues in contact with PHE1125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495H ARG* 3.5 29.8 - - - -
496H LEU* 5.4 2.9 - - + -
499H THR* 4.8 23.6 - - + -
503H LEU* 5.7 2.0 - - + -
522H VAL* 6.2 0.2 - - + -
1098H HIS* 3.9 15.9 - + - -
1101H LEU* 3.5 35.4 - - + -
1102H LEU* 3.6 38.1 - - + -
1105H ILE* 5.2 6.3 - - + -
1121H ILE* 2.9 23.5 + - + +
1122H LEU* 3.2 16.2 - - + +
1124H ARG* 1.3 78.7 - - - +
1126H SER* 1.3 63.3 + - - +
1128H ASP* 4.1 0.2 - - - +
1129H CYS* 3.0 32.0 + - - -
1315H ILE* 5.3 1.7 - - - +
1318H LEU* 6.0 0.2 - - - +
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Residues in contact with SER1126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419H ASN* 5.9 1.1 - - - -
423H ILE* 5.3 5.9 - - - +
495H ARG* 5.5 1.3 - - - +
496H LEU* 3.2 42.2 - - - +
1122H LEU* 2.9 22.1 + - - -
1123H ASN* 4.2 5.4 - - - -
1125H PHE* 1.3 74.0 - - - +
1127H SER* 1.3 64.1 + - - +
1129H CYS* 3.9 2.1 - - - +
1130H ASN* 2.9 41.1 + - - +
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Residues in contact with SER1127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1123H ASN* 2.9 32.7 + - - -
1124H ARG* 4.4 1.3 - - - -
1126H SER* 1.3 73.9 - - - +
1128H ASP* 1.3 62.1 + - - +
1130H ASN* 3.8 5.1 - - - +
1131H THR* 2.9 37.1 + - - -
1314H ARG* 5.8 2.5 + - - -
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Residues in contact with ASP1128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124H ARG* 2.9 45.2 + - - +
1125H PHE 4.1 0.2 - - - +
1127H SER* 1.3 79.0 + - - +
1129H CYS* 1.3 58.6 + - - +
1131H THR* 3.3 4.7 + - - -
1132H ILE* 2.9 39.7 + - + +
1311H ALA* 3.0 39.1 - - + +
1314H ARG* 3.2 18.5 + - - +
1315H ILE* 3.4 21.0 - - + +
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Residues in contact with CYS1129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495H ARG* 4.4 16.4 - - - +
526H ARG* 4.6 9.9 - - - +
1097H LEU 6.4 0.2 - - - -
1098H HIS* 4.5 17.7 - - - -
1101H LEU* 4.5 11.7 - - - -
1125H PHE* 3.0 47.2 + - - +
1126H SER 4.0 1.8 - - - +
1128H ASP* 1.3 78.2 - - - +
1130H ASN* 1.3 59.2 + - - +
1132H ILE* 3.4 6.8 + - - +
1133H ASP* 2.9 36.8 + - - +
1315H ILE* 5.4 2.9 - - - -
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Residues in contact with ASN1130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423H ILE* 5.4 9.7 - - - +
427H GLN* 5.8 2.4 - - - +
492H SER* 4.1 17.5 + - - -
495H ARG* 4.1 9.7 + - - -
496H LEU* 5.7 2.1 - - - +
602H LYS* 4.9 14.8 - - - +
1126H SER* 2.9 32.0 + - - +
1127H SER* 3.8 5.1 - - - +
1129H CYS* 1.3 77.0 - - - +
1131H THR* 1.3 62.8 + - - +
1133H ASP* 3.3 5.1 + - - +
1134H GLN* 2.9 34.3 + - - +
1135H HIS* 4.1 4.9 + - + -
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Residues in contact with THR1131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1127H SER* 2.9 23.3 + - - -
1128H ASP* 3.7 6.9 - - - -
1130H ASN* 1.3 76.0 - - - +
1132H ILE* 1.3 61.0 + - + +
1135H HIS* 2.7 47.9 + - + +
1136H ILE* 3.0 9.6 + - + -
1308H GLN* 3.8 37.0 - - + +
1311H ALA* 5.1 7.9 - - + -
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Residues in contact with ILE1132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004H TYR* 6.1 0.9 - - + -
1090H GLY 5.3 2.2 - - - +
1093H VAL* 4.4 14.8 - - + -
1094H ALA* 4.2 25.5 - - + +
1097H LEU* 3.6 26.5 - - + -
1128H ASP* 2.9 29.3 + - + +
1129H CYS* 3.9 6.5 - - - +
1131H THR* 1.3 78.1 - - + +
1133H ASP* 1.3 64.6 + - - +
1134H GLN 3.5 0.2 + - - -
1136H ILE* 3.2 35.1 - - + +
1137H PRO* 3.8 2.6 - - - +
1311H ALA* 6.0 1.8 - - + -
1312H VAL* 4.1 30.3 - - + +
1315H ILE* 5.1 6.3 - - + -
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Residues in contact with ASP1133 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495H ARG* 5.1 2.4 + - - -
526H ARG* 3.0 30.1 + - - -
529H GLU* 4.2 3.8 - - - +
533H LEU* 3.7 33.6 - - + +
536H PHE* 5.9 2.4 - - - -
1091H LEU* 6.1 0.7 - - - +
1094H ALA* 3.1 27.4 - - - +
1129H CYS* 2.9 26.4 + - - +
1130H ASN* 3.9 6.1 - - - +
1131H THR 3.3 0.2 - - - -
1132H ILE* 1.3 79.9 - - - +
1134H GLN* 1.3 69.7 + - + +
1137H PRO* 4.0 11.3 - - - +
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Residues in contact with GLN1134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485H GLN* 5.0 4.8 - - - +
488H THR* 4.7 14.1 - - - +
489H LEU* 4.3 11.9 - - - +
529H GLU* 5.4 1.6 + - - -
533H LEU* 4.8 8.7 - - + +
536H PHE* 6.0 3.8 - - + -
598H ARG* 3.2 47.7 + - - +
602H LYS* 2.4 44.2 + - - +
1130H ASN* 2.9 20.7 + - - +
1133H ASP* 1.3 90.5 - - + +
1135H HIS* 1.3 63.2 + - + +
1136H ILE 3.8 0.2 - - - -
1137H PRO* 3.9 5.3 - - - +
1138H SER* 4.0 6.2 + - - -
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Residues in contact with HIS1135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427H GLN* 5.5 5.6 - - - -
430H TRP* 4.9 21.3 + + - -
598H ARG* 3.6 31.4 + - - -
599H SER* 5.9 0.8 + - - -
602H LYS* 5.3 5.2 - - - -
1130H ASN* 4.1 4.7 + - + -
1131H THR* 2.7 43.4 + - + +
1134H GLN* 1.3 79.4 - - + +
1136H ILE* 1.3 61.9 + - - +
1137H PRO* 3.4 1.3 - - - -
1138H SER* 3.5 3.6 + - - -
1139H THR* 3.2 30.7 + - - +
1304H ASP* 5.8 1.8 - - - -
1308H GLN* 3.4 18.6 - - - +
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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
------------------------------------------------------------
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