Contacts of the helix formed by residues 1109 - 1123 (chain C) in PDB entry 3IYD
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 ILE1109 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673C HIS* 2.7 26.9 + - - +
1107C MET* 3.6 0.6 - - - +
1108C ASN* 1.3 73.4 - - - +
1110C GLY* 1.3 57.7 + - - +
1112C ILE* 4.4 11.9 - - + -
644D MET* 3.6 39.3 - - + -
711D GLY 4.8 5.6 - - - +
712D GLN* 3.5 36.1 - - + +
739D GLN 5.2 0.2 - - - +
740D LEU* 4.1 27.3 - - + +
763D PHE* 3.7 29.5 - - + +
764D ARG* 5.4 1.3 - - - +
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Residues in contact with GLY1110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669C PRO 5.1 1.2 - - - +
670C PHE* 4.3 14.6 - - - +
673C HIS* 3.5 21.1 - - - -
674C ASP* 3.9 10.1 - - - -
1070C HIS* 4.7 2.9 + - - -
1108C ASN 3.1 4.8 + - - -
1109C ILE* 1.3 77.0 - - - +
1111C GLN* 1.3 61.1 + - - +
1112C ILE* 3.1 10.7 + - - +
1113C LEU* 3.6 19.3 + - - +
1114C GLU* 4.6 0.7 + - - +
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Residues in contact with GLN1111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1070C HIS* 3.3 54.0 + - + +
1072C ASN* 4.6 5.0 + - - +
1108C ASN* 5.0 4.1 + - - +
1110C GLY* 1.3 75.6 - - - +
1112C ILE* 1.3 61.5 + - - +
1113C LEU 3.3 1.1 - - - -
1114C GLU* 3.3 19.5 + - - +
1115C THR* 3.3 18.7 + - - +
1230C MET* 3.6 27.7 - - + +
712D GLN* 2.9 29.7 + - - +
713D GLU* 2.8 28.0 + - + +
714D GLU* 4.4 10.9 + - - +
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Residues in contact with ILE1112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1109C ILE* 4.4 13.7 - - + -
1110C GLY* 3.1 2.4 - - - -
1111C GLN* 1.3 75.0 - - - +
1113C LEU* 1.3 60.2 + - + +
1114C GLU 3.0 9.4 + - - -
1115C THR* 3.3 2.6 + - - +
1116C HIS* 3.2 54.9 + - + +
639D VAL* 4.4 21.3 - - + -
640D GLY 4.9 3.8 - - - +
641D ILE* 3.7 31.9 - - + -
644D MET* 6.2 1.3 - - + -
712D GLN* 3.2 35.6 - - + +
713D GLU* 4.4 9.9 - - - +
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Residues in contact with LEU1113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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670C PHE* 3.5 48.4 - - + -
673C HIS* 3.6 30.5 - - + +
700C VAL* 5.3 1.0 - - - +
1110C GLY* 3.6 7.5 + - - +
1111C GLN 3.3 0.6 - - - -
1112C ILE* 1.3 77.3 - - + +
1114C GLU* 1.3 57.7 + - - +
1116C HIS* 5.7 0.4 - - - -
1117C LEU* 3.2 30.9 - - - +
1190C ALA* 5.8 3.4 - - + +
1191C LYS* 6.2 1.8 - - - -
1192C GLU* 5.4 12.6 - - + +
1195C ILE* 3.6 26.5 - - + -
641D ILE* 4.1 24.7 - - + -
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Residues in contact with GLU1114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669C PRO* 4.2 9.0 - - + +
670C PHE* 5.5 2.2 - - + -
698C PRO* 5.3 1.9 - - - +
699C LEU* 5.7 2.6 + - + +
700C VAL* 3.7 33.0 - - + +
799C ASN* 5.9 0.5 + - - -
1069C ARG* 3.3 23.4 + - - -
1070C HIS* 3.6 27.5 + - - -
1110C GLY 4.6 0.9 + - - +
1111C GLN* 3.6 14.1 - - + +
1112C ILE 3.0 0.4 - - - -
1113C LEU* 1.3 80.6 - - - +
1115C THR* 1.3 58.3 + - - +
1118C GLY* 3.3 23.1 + - - +
1229C TYR* 4.0 10.8 - - - +
1230C MET* 5.8 0.9 - - - -
1231C TYR* 3.7 20.8 + - - +
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Residues in contact with THR1115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802C VAL* 6.1 0.7 - - + -
1111C GLN* 3.3 15.3 + - - +
1112C ILE* 3.3 4.0 + - - -
1114C GLU* 1.3 77.8 - - - +
1116C HIS* 1.3 73.4 + - + +
1118C GLY* 3.3 1.7 + - - -
1119C MET* 3.1 22.5 + - - +
1226C THR* 4.4 14.1 - - + +
1227C VAL 4.6 1.1 - - - +
1228C GLY* 3.6 34.5 - - - +
1229C TYR 3.8 13.9 + - - -
1230C MET* 4.9 6.4 - - - +
713D GLU* 3.8 24.5 + - - +
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Residues in contact with HIS1116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1112C ILE* 3.2 53.1 + - + +
1113C LEU* 5.7 0.2 - - - -
1115C THR* 1.3 83.9 - - + +
1117C LEU* 1.3 62.0 + - - +
1119C MET* 3.1 22.4 + - + +
1120C ALA 3.2 9.5 + - - -
1195C ILE* 5.4 2.7 - - + -
1199C LEU* 3.4 28.7 - - + +
1207C SER 3.5 27.2 + - - -
1208C GLY* 3.9 12.5 - - - -
1209C GLN* 4.9 0.2 + - - -
1226C THR* 3.9 20.9 + - + -
639D VAL 4.6 1.5 + - - -
640D GLY* 4.2 7.5 - - - -
641D ILE* 4.1 20.5 + - + +
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Residues in contact with LEU1117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C PHE* 6.4 0.4 - - + -
670C PHE* 5.1 4.7 - - + -
700C VAL* 4.9 9.4 - - + -
1112C ILE 4.4 0.8 + - - -
1113C LEU* 3.2 27.6 + - - +
1114C GLU* 4.8 0.4 - - - -
1115C THR 3.4 0.4 - - - -
1116C HIS* 1.3 79.3 - - - +
1118C GLY* 1.3 55.4 + - - +
1120C ALA* 3.5 1.0 + - + -
1121C ALA* 3.0 29.8 + - + +
1182C ILE* 4.1 43.1 - - + -
1190C ALA* 5.0 5.6 - - + -
1195C ILE* 4.0 40.7 - - + +
1198C LEU* 4.5 22.9 - - + -
1199C LEU* 4.5 2.2 - - - -
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Residues in contact with GLY1118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699C LEU* 3.3 34.6 - - - +
700C VAL* 5.7 3.8 - - - +
1114C GLU* 3.3 22.3 + - - +
1115C THR 3.7 1.3 - - - -
1116C HIS 3.2 0.8 - - - -
1117C LEU* 1.3 79.3 - - - +
1119C MET* 1.3 60.7 + - - +
1121C ALA 3.7 0.2 + - - -
1122C LYS* 3.6 14.6 + - - +
1229C TYR* 4.5 12.1 - - - -
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Residues in contact with MET1119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1115C THR 3.1 11.8 + - - +
1116C HIS* 3.1 18.6 + - + +
1118C GLY* 1.3 76.5 - - - +
1120C ALA* 1.3 63.4 + - + +
1122C LYS* 3.4 22.5 + - - +
1123C GLY* 3.5 9.0 + - - -
1199C LEU* 5.4 6.1 - - + -
1202C GLY* 5.3 1.2 - - - -
1203C ASP* 5.6 4.9 - - - +
1205C PRO* 5.0 16.2 - - + +
1206C THR* 6.1 2.0 - - - -
1208C GLY* 4.2 27.4 - - - +
1210C ILE* 5.5 9.6 - - - -
1227C VAL 3.6 24.2 - - - +
1228C GLY* 5.1 4.3 - - - -
1229C TYR* 5.0 8.9 - - + -
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Residues in contact with ALA1120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116C HIS 3.2 3.5 + - - +
1117C LEU* 4.1 2.7 - - - +
1119C MET* 1.3 77.0 - - + +
1121C ALA* 1.3 65.6 + - - +
1122C LYS 3.1 2.0 - - - -
1123C GLY* 3.4 1.6 + - - +
1124C ILE* 3.2 28.8 + - - +
1198C LEU* 3.6 29.6 - - + +
1199C LEU* 3.6 28.7 - - + -
1202C GLY* 4.4 12.4 - - - -
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Residues in contact with ALA1121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ARG* 4.5 3.5 + - - -
699C LEU* 4.3 18.8 - - + +
700C VAL* 6.5 0.7 - - + -
1117C LEU* 3.0 20.1 + - + +
1118C GLY* 4.0 6.3 - - - +
1119C MET 3.3 0.4 - - - -
1120C ALA* 1.3 77.7 - - - +
1122C LYS* 1.3 61.0 + - - +
1124C ILE* 3.4 15.6 - - + +
1125C GLY* 3.3 15.9 + - - -
1180C MET 3.5 26.0 + - - +
1182C ILE* 5.1 8.1 - - + -
1198C LEU* 4.6 1.0 - - - +
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Residues in contact with LYS1122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699C LEU* 5.7 2.9 - - + -
801C ARG* 5.3 2.0 - - - +
1118C GLY 3.6 10.6 + - - +
1119C MET* 3.4 16.6 + - - +
1120C ALA 3.1 0.4 - - - -
1121C ALA* 1.3 79.2 - - - +
1123C GLY* 1.3 69.9 + - - +
1124C ILE 3.3 0.2 - - - -
1125C GLY* 3.2 12.6 + - - -
1203C ASP* 4.6 15.3 + - - -
1229C TYR* 3.9 31.5 + - + +
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Residues in contact with GLY1123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1119C MET 3.5 5.6 + - - -
1120C ALA 3.4 5.8 + - - -
1122C LYS* 1.3 83.6 - - - +
1124C ILE* 1.3 61.6 + - - +
1125C GLY* 3.5 0.5 + - - -
1202C GLY* 4.1 16.3 - - - +
1203C ASP* 3.8 21.8 - - - -
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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