Contacts of the strand formed by residues 884 - 888 (chain D) in PDB entry 3IKM
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 TYR 884 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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822D PRO* 3.9 1.7 - - - +
825D VAL* 3.1 36.4 - - + +
881D PRO* 2.8 36.0 - - + +
882D PRO* 3.0 9.0 - - - +
883D GLY* 1.3 88.1 + - - +
885D THR* 1.3 63.6 + - - +
886D LEU* 4.0 6.1 - - - +
1126D ASP 5.2 1.1 - - - -
1140D LEU* 4.1 22.2 - - + -
1141D VAL 3.7 3.4 - - - -
1142D ARG* 2.2 65.9 + - + -
1143D GLU* 3.7 0.4 + - - -
1187D ARG* 4.1 14.2 - - - +
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Residues in contact with THR 885 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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884D TYR* 1.3 73.2 - - - +
886D LEU* 1.3 56.9 + - - +
1140D LEU* 2.9 16.3 - - - +
1141D VAL 3.1 7.1 + - - -
1143D GLU* 3.3 31.4 - - - +
1146D ARG* 2.6 42.6 + - - +
1185D ILE* 4.2 5.8 - - + -
1186D ASP* 2.8 44.4 - - - +
1187D ARG* 3.5 11.3 - - + +
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Residues in contact with LEU 886 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436D PRO* 5.0 9.0 - - + -
879D GLN* 4.4 5.2 - - - +
880D ALA* 4.7 2.9 - - + -
881D PRO* 4.4 10.8 - - + -
884D TYR 4.0 5.8 - - - +
885D THR* 1.3 98.1 - - - +
887D VAL* 1.3 60.6 + - - +
888D GLY 3.8 0.5 + - - -
1130D CYS* 5.2 9.4 - - - -
1138D ARG* 4.9 14.0 - - + -
1139D TYR 3.3 6.7 - - - +
1140D LEU* 3.4 25.4 - - + -
1146D ARG* 2.5 9.3 - - - +
1184D ASP 3.1 12.3 - - - +
1186D ASP* 2.4 33.9 + - - +
1187D ARG* 3.5 21.3 - - - +
1188D CYS 3.8 13.2 - - - +
1189D LEU* 3.8 15.7 - - + -
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Residues in contact with VAL 887 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886D LEU* 1.3 66.2 - - - +
888D GLY* 1.3 52.6 + - - +
1138D ARG* 4.0 0.7 - - - -
1139D TYR* 2.1 56.2 + - + +
1141D VAL* 3.4 12.3 - - + -
1146D ARG* 2.4 50.4 - - - +
1149D ALA* 3.9 7.4 - - + -
1150D ALA* 4.0 5.2 - - - -
1153D LEU* 3.3 21.3 - - + -
1183D VAL* 2.9 36.6 - - + -
1184D ASP 3.2 3.8 - - - -
1185D ILE* 3.3 14.1 - - + -
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Residues in contact with GLY 888 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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886D LEU 3.8 0.2 + - - -
887D VAL* 1.3 76.7 - - - +
889D ALA* 1.3 67.8 + - - +
1137D VAL 2.9 16.2 - - - -
1138D ARG* 3.1 20.8 - - - +
1139D TYR* 4.4 2.7 - - - -
1153D LEU* 4.7 2.0 - - - -
1180D PHE* 5.2 0.2 - - - -
1183D VAL* 4.0 3.8 - - - +
1184D ASP* 3.0 28.9 + - - +
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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