Contacts of the helix formed by residues 1133 - 1155 (chain A) in PDB entry 4YKN
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 ASP1133 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1131A VAL* 3.4 8.0 - - + +
1132A LYS* 1.3 75.4 - - - +
1134A PRO* 1.3 73.3 - - - +
1135A GLU* 2.9 28.0 + - - +
1136A VAL* 3.1 33.7 + - + +
1137A GLN* 3.2 12.7 + - - +
1432A TYR* 5.3 0.9 - - - -
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Residues in contact with PRO1134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1132A LYS 3.2 9.6 - - - +
1133A ASP* 1.3 89.8 - - - +
1135A GLU* 1.3 51.2 + - - +
1137A GLN* 3.2 7.2 + - + +
1138A ASP* 2.7 43.8 + - - +
1432A TYR* 3.5 15.0 - - + +
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Residues in contact with GLU1135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1133A ASP* 2.9 19.2 + - - +
1134A PRO* 1.3 78.1 - - - +
1136A VAL* 1.3 57.4 - - + +
1138A ASP* 3.9 0.7 - - - +
1139A PHE* 3.0 30.1 + - + +
1431A ASP* 6.1 0.2 - - - +
1432A TYR* 3.4 59.2 + - + +
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Residues in contact with VAL1136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1128A PHE* 4.7 9.9 - - + +
1131A VAL* 3.9 29.8 - - + -
1133A ASP* 3.1 29.3 + - + +
1135A GLU* 1.3 79.0 - - + +
1137A GLN* 1.3 68.4 + - - +
1139A PHE* 3.3 6.5 + - - +
1140A ARG* 3.1 34.7 + - + +
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Residues in contact with GLN1137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1128A PHE 3.0 23.2 + - - -
1129A ASP* 3.8 9.2 + - - +
1131A VAL* 2.6 34.7 + - - +
1132A LYS 5.2 1.6 - - - +
1133A ASP 3.2 8.9 + - - +
1134A PRO* 3.2 9.0 + - + +
1136A VAL* 1.3 80.7 - - - +
1138A ASP* 1.3 64.2 + - - +
1140A ARG* 3.7 22.5 + - - +
1141A ARG* 3.3 33.1 + - - +
1307A TYR* 5.7 3.5 - - - +
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Residues in contact with ASP1138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1134A PRO* 2.7 27.8 + - - +
1135A GLU* 3.9 4.5 - - - +
1137A GLN* 1.3 73.0 - - - +
1139A PHE* 1.3 59.4 + - - +
1141A ARG* 2.3 36.7 + - - +
1142A ASN* 2.7 48.4 + - - +
1432A TYR* 2.6 37.4 + - + +
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Residues in contact with PHE1139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1135A GLU* 3.0 19.6 + - + +
1136A VAL* 3.3 6.7 + - - +
1138A ASP* 1.3 74.7 - - - +
1140A ARG* 1.3 74.6 + - + +
1142A ASN* 4.8 2.0 - - - +
1143A ILE* 2.8 72.0 + - + +
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Residues in contact with ARG1140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1125A VAL* 4.0 21.6 - - - +
1128A PHE* 3.3 46.9 + - + +
1129A ASP* 3.0 27.1 + - - +
1136A VAL* 3.1 20.0 + - + +
1137A GLN* 3.9 23.0 + - - +
1138A ASP 3.4 0.2 - - - -
1139A PHE* 1.3 87.5 - - + +
1141A ARG* 1.3 62.1 + - - +
1143A ILE* 3.5 8.9 - - - +
1144A LEU* 3.4 11.4 - - - +
1307A TYR* 3.3 65.2 + - + +
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Residues in contact with ARG1141 (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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1137A GLN* 3.3 20.5 + - - +
1138A ASP* 2.3 36.9 + - - +
1139A PHE 3.2 0.4 - - - -
1140A ARG* 1.3 80.2 - - - +
1142A ASN* 1.3 75.3 + - - +
1144A LEU* 3.5 24.6 + - - +
1145A ASN* 4.6 2.6 + - - +
1307A TYR* 3.9 19.4 + - + +
1308A SER* 3.9 24.7 - - - +
1309A ARG 4.4 12.1 + - - -
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Residues in contact with ASN1142 (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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1138A ASP* 2.7 44.0 + - - +
1139A PHE* 4.3 1.8 - - - +
1141A ARG* 1.3 81.8 + - - +
1143A ILE* 1.3 66.0 + - - +
1144A LEU 3.1 3.6 + - - -
1145A ASN* 3.0 35.7 + - - +
1146A VAL* 5.3 1.0 - - - +
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Residues in contact with ILE1143 (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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1139A PHE* 2.8 60.3 + - + +
1140A ARG* 3.5 11.2 - - - +
1142A ASN* 1.3 77.3 - - - +
1144A LEU* 1.3 64.8 + - + +
1146A VAL* 2.9 44.8 + - + +
1147A CYS* 3.4 11.9 + - - -
1307A TYR* 6.0 0.4 - - - +
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Residues in contact with LEU1144 (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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1140A ARG 3.4 9.6 - - - +
1141A ARG 3.5 15.0 - - - +
1142A ASN 3.1 1.0 - - - -
1143A ILE* 1.3 81.6 - - + +
1145A ASN* 1.3 62.4 + - - +
1146A VAL 3.2 0.2 - - - -
1147A CYS* 3.2 20.2 + - - +
1148A LYS* 3.0 23.9 + - - +
1302A PHE* 4.6 8.1 - - + -
1304A MET* 4.0 18.6 - - + +
1305A PRO* 3.9 26.2 - - + -
1307A TYR* 3.7 29.2 - - + +
1308A SER* 3.7 30.1 - - - -
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Residues in contact with ASN1145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1141A ARG 5.0 1.8 + - - +
1142A ASN* 3.0 29.7 + - - +
1143A ILE 3.0 0.4 - - - -
1144A LEU* 1.3 78.9 - - - +
1146A VAL* 1.3 64.0 + - + +
1148A LYS* 3.5 6.2 + - - +
1149A GLU* 3.2 34.8 + - - +
1304A MET* 5.5 4.0 - - - +
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Residues in contact with VAL1146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1142A ASN 5.3 0.4 - - - +
1143A ILE* 2.9 36.0 + - + +
1145A ASN* 1.3 76.6 - - + +
1147A CYS* 1.3 66.0 + - - +
1149A GLU* 3.3 11.2 + - + +
1150A ALA* 3.1 25.2 + - + +
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Residues in contact with CYS1147 (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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1143A ILE* 3.9 18.4 - - - -
1144A LEU* 3.2 23.1 + - - +
1146A VAL* 1.3 79.6 - - - +
1148A LYS* 1.3 62.6 + - - +
1150A ALA* 3.9 4.6 - - - +
1151A VAL* 3.0 31.0 + - + +
1302A PHE* 3.8 25.4 - - + -
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Residues in contact with LYS1148 (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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1144A LEU 3.0 15.2 + - - +
1145A ASN* 3.9 6.1 - - - +
1146A VAL 3.3 0.2 - - - -
1147A CYS* 1.3 76.5 - - - +
1149A GLU* 1.3 59.5 + - + +
1151A VAL* 3.6 3.3 + - - +
1152A ASP* 2.9 51.4 + - - +
1302A PHE* 4.5 11.0 - - + -
1304A MET* 4.2 20.0 - - + -
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Residues in contact with GLU1149 (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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1145A ASN* 3.2 21.8 + - - +
1146A VAL* 3.7 11.2 - - - +
1147A CYS 3.3 0.2 - - - -
1148A LYS* 1.3 77.9 - - + +
1150A ALA* 1.3 57.9 + - - +
1152A ASP* 3.2 6.7 + - - +
1153A LEU* 2.8 32.2 + - - +
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Residues in contact with ALA1150 (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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1146A VAL* 3.1 19.3 + - + +
1147A CYS* 3.9 4.9 - - - +
1149A GLU* 1.3 76.2 - - - +
1151A VAL* 1.3 63.3 + - + +
1153A LEU* 3.2 8.3 + - - +
1154A ARG* 3.1 37.1 + - - +
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Residues in contact with VAL1151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1147A CYS* 3.0 19.4 + - + +
1148A LYS* 4.0 4.0 - - - +
1150A ALA* 1.3 76.1 - - + +
1152A ASP* 1.3 69.7 + - - +
1154A ARG* 3.6 33.5 - - - +
1155A ASP* 3.2 39.7 + - - +
1300A ASP* 5.9 3.1 - - - +
1301A CYS* 6.0 0.4 - - - -
1302A PHE* 3.8 42.6 - - + +
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Residues in contact with ASP1152 (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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1148A LYS* 2.9 41.8 + - - +
1149A GLU* 3.7 6.0 - - - +
1151A VAL* 1.3 82.2 - - - +
1153A LEU* 1.3 61.6 + - - +
1155A ASP* 3.8 4.0 + - - +
1156A LEU* 3.5 24.9 + - - +
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Residues in contact with LEU1153 (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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1149A GLU 2.8 18.2 + - - +
1150A ALA* 3.2 8.2 + - - +
1152A ASP* 1.3 78.2 - - - +
1154A ARG* 1.3 61.2 + - - +
1156A LEU* 3.4 31.5 - - + +
1161A SER* 4.6 4.0 + - - -
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Residues in contact with ARG1154 (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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1150A ALA* 3.1 24.1 + - - +
1151A VAL* 3.6 36.7 - - - +
1153A LEU* 1.3 74.5 - - - +
1155A ASP* 1.3 64.7 + - - +
1161A SER* 2.4 41.5 + - - +
1162A ARG* 3.3 7.6 + - + +
1165A TYR* 3.3 69.1 + - + -
1300A ASP* 4.1 20.2 + - - -
1302A PHE* 5.9 0.4 - - - +
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Residues in contact with ASP1155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1151A VAL* 3.2 35.0 + - - +
1152A ASP* 4.0 5.2 - - - +
1153A LEU 3.3 0.2 - - - -
1154A ARG* 1.3 84.7 + - - +
1156A LEU* 1.3 66.6 + - - +
1157A ASN 3.5 2.7 - - - -
1158A SER* 3.9 12.0 + - - -
1161A SER* 3.7 2.2 - - - -
1162A ARG* 2.7 52.2 + - - +
1300A ASP* 4.5 7.9 - - - +
1301A CYS* 6.0 0.2 - - - -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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