Contacts of the strand formed by residues 1133 - 1143 (chain B) in PDB entry 2IUK
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 PHE1133 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1017B LEU* 4.1 14.6 - - + -
1018B MET 3.6 11.2 - - - +
1019B PRO* 4.4 2.0 - - + -
1020B LYS* 4.3 2.7 - - + +
1061B PHE* 3.9 24.5 - + + -
1066B ILE* 3.4 42.8 - - + -
1125B ILE* 4.0 4.9 - - + -
1127B ASN* 3.2 36.8 - - + -
1131B ASP 4.6 1.8 - - - +
1132B GLU* 1.3 74.6 - - - +
1134B PHE* 1.3 60.0 + - - +
1135B LEU* 3.8 35.9 - - + -
1156B TRP* 3.5 6.7 - - - -
1157B VAL* 3.0 48.2 + - + -
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Residues in contact with PHE1134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017B LEU* 3.2 2.8 - - - +
1018B MET* 2.6 77.7 + - + +
1023B LEU* 3.6 22.0 - - + -
1133B PHE* 1.3 70.8 - - - +
1135B LEU* 1.3 58.1 + - - +
1136B VAL* 3.5 9.0 + - + -
1154B ASN* 3.3 50.0 - - + -
1155B SER 3.9 1.1 - - - -
1156B TRP* 3.5 47.0 - + + -
1269B PHE* 6.2 6.1 - + - -
1794B GLU* 5.8 2.7 - - - -
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Residues in contact with LEU1135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1015B VAL* 4.0 18.4 - - + -
1016B VAL 3.3 20.9 - - - +
1017B LEU* 3.9 10.8 - - + -
1123B PHE* 4.1 13.7 - - + -
1125B ILE* 4.1 9.4 - - + -
1133B PHE* 3.6 23.0 + - + -
1134B PHE* 1.3 71.6 - - - +
1136B VAL* 1.3 58.4 + - - +
1137B SER 4.5 0.4 - - - +
1138B VAL* 4.3 6.5 - - + -
1153B CYS* 3.5 33.5 - - + +
1154B ASN* 3.1 5.5 + - - -
1155B SER 2.8 47.5 + - - +
1157B VAL* 4.1 5.2 - - + -
1169B PHE* 4.1 18.2 - - + -
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Residues in contact with VAL1136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1016B VAL* 2.9 22.0 + - + +
1017B LEU* 3.8 13.2 - - - -
1018B MET* 3.7 41.1 - - + -
1104B GLN* 3.6 23.6 - - + +
1134B PHE* 3.8 6.5 - - + -
1135B LEU* 1.3 73.6 - - - +
1137B SER* 1.3 64.9 + - - +
1152B VAL* 4.7 0.7 - - - +
1153B CYS* 3.3 8.1 + - - -
1154B ASN* 3.2 35.9 + - - +
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Residues in contact with SER1137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1014B THR 3.5 1.8 - - - +
1016B VAL* 2.9 43.3 + - - +
1104B GLN* 5.5 0.3 + - - -
1135B LEU* 3.9 1.6 - - - +
1136B VAL* 1.3 82.5 - - - +
1138B VAL* 1.3 66.6 + - - +
1139B LYS* 3.2 27.7 + - - -
1151B PHE 3.4 14.8 - - - -
1152B VAL* 5.1 1.3 - - - -
1153B CYS* 3.9 4.9 - - - +
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Residues in contact with VAL1138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1013B GLY* 5.2 0.7 - - - -
1014B THR 3.3 7.0 - - - +
1015B VAL* 3.7 25.8 - - + -
1068B MET* 4.0 13.5 - - + -
1111B PHE* 5.8 0.2 - - + -
1123B PHE* 3.5 34.1 - - + -
1135B LEU* 4.3 11.0 - - + -
1137B SER* 1.3 81.9 - - - +
1139B LYS* 1.3 60.2 + - - +
1140B LEU* 3.5 26.5 - - + -
1150B GLU* 3.5 0.2 - - - -
1151B PHE* 2.7 49.9 + - + -
1153B CYS* 4.0 0.8 - - - -
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Residues in contact with LYS1139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1013B GLY* 3.2 0.9 - - - -
1014B THR* 2.9 58.7 + - + +
1016B VAL* 3.1 32.9 - - - +
1137B SER* 3.2 19.1 + - - +
1138B VAL* 1.3 75.1 - - - +
1140B LEU* 1.3 62.5 - - - +
1141B GLU* 2.9 16.5 - - + +
1148B THR* 4.6 6.5 - - - +
1149B ILE 3.3 9.0 - - - +
1150B GLU* 4.2 20.6 - - + +
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Residues in contact with LEU1140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1011B ILE* 4.9 3.6 - - + -
1012B LYS 3.0 12.6 - - - +
1013B GLY* 4.2 1.1 - - - -
1068B MET* 4.9 0.2 - - + -
1070B LEU* 3.7 22.7 - - + -
1111B PHE* 4.1 19.7 - - + -
1120B PRO* 3.7 30.3 - - + -
1138B VAL* 3.5 28.7 - - + -
1139B LYS* 1.3 73.7 - - - +
1141B GLU* 1.3 62.4 + - - +
1143B ILE* 4.1 10.1 - - + +
1148B THR* 3.1 6.4 + - - -
1149B ILE* 2.7 43.2 + - + +
1151B PHE* 3.6 20.2 - - + -
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Residues in contact with GLU1141 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1011B ILE* 3.6 0.3 - - - +
1012B LYS* 2.8 55.9 + - + +
1014B THR* 3.1 23.0 + - - -
1139B LYS* 2.9 30.4 - - + +
1140B LEU* 1.3 74.8 - - - +
1142B ASP* 1.4 77.5 + - + +
1143B ILE* 3.0 14.0 + - - +
1147B GLY 4.0 7.2 - - - +
1148B THR* 4.3 11.4 - - - +
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Residues in contact with ASP1142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009B GLN* 3.7 31.5 - - - +
1010B LYS 3.6 10.8 - - - +
1011B ILE* 3.5 7.6 - - - +
1012B LYS* 2.9 49.3 + - - +
1110B PHE* 5.6 1.9 - - - -
1141B GLU* 1.4 79.6 - - + +
1143B ILE* 1.3 63.0 + - - +
1144B PRO* 3.5 8.2 - - - +
1147B GLY 3.8 7.6 + - - -
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Residues in contact with ILE1143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009B GLN* 5.4 0.4 - - - -
1011B ILE* 3.6 17.7 - - + -
1113B TRP* 3.9 22.2 - - + -
1119B ILE* 4.1 9.9 - - + -
1120B PRO* 4.2 11.9 - - + -
1140B LEU* 4.1 17.0 - - + +
1141B GLU 3.2 14.3 - - - +
1142B ASP* 1.3 78.3 - - - +
1144B PRO* 1.4 73.5 - - + +
1145B ASN 3.2 3.3 + - - -
1146B HIS* 3.2 29.8 + - + +
1147B GLY 3.8 8.4 + - - +
1148B THR* 5.1 1.8 - - - -
1149B ILE* 3.5 37.5 - - + +
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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