Contacts of the helix formed by residues 874 - 879 (chain A) 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 LEU 874 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441A TRP* 3.0 26.9 - - + -
444A TYR* 2.8 41.1 - - + +
445A LEU* 3.8 28.0 - - + +
448A ALA* 4.8 0.9 - - + -
801A TRP* 3.9 6.7 - - + -
808A ILE* 3.5 36.1 - - + -
871A GLY* 3.6 25.8 - - - +
873A GLU* 1.3 71.8 - - - +
875A LYS* 1.3 64.8 + - - +
876A ALA 3.0 4.3 + - - -
877A MET* 3.0 13.4 + - - +
878A VAL* 3.1 12.1 + - - +
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Residues in contact with LYS 875 (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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862A ALA* 3.4 26.0 - - + +
863A SER* 2.9 25.0 + - - +
864A ASN* 4.5 2.8 - - - +
873A GLU* 2.4 38.7 + - + +
874A LEU* 1.3 76.6 - - - +
876A ALA* 1.3 63.7 + - - +
878A VAL* 2.4 30.4 - - + +
1136A GLU* 4.7 9.3 + - - -
1138A ARG* 5.5 5.6 - - - +
1189A LEU* 2.9 39.0 + - + +
1190A ARG* 4.6 13.1 - - + +
1191A LYS* 4.7 16.6 - - - +
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Residues in contact with ALA 876 (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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873A GLU 4.7 0.2 + - - -
874A LEU 3.1 0.6 - - - -
875A LYS* 1.3 80.4 - - - +
877A MET* 1.3 70.5 + - - +
878A VAL 2.5 2.8 + - - -
879A GLN 3.1 15.9 + - - +
1188A CYS* 3.6 24.1 - - + -
1189A LEU* 3.7 16.0 + - - +
1190A ARG* 3.8 19.1 - - - +
1206A MET* 3.9 19.1 - - + -
1207A GLU* 5.2 1.1 - - + +
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Residues in contact with MET 877 (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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437A VAL* 4.1 0.9 - - - -
438A ASN* 4.1 10.8 - - + +
440A ASN* 2.9 41.1 - - + +
441A TRP* 2.9 36.5 - - + +
444A TYR* 3.3 43.9 - - + -
874A LEU 3.0 6.3 + - - +
876A ALA* 1.3 78.5 - - - +
878A VAL* 1.3 67.6 + - - +
879A GLN* 2.9 3.3 + - - -
880A ALA* 4.0 21.5 - - + -
1206A MET* 5.2 1.4 - - - +
1212A ILE* 5.6 4.9 - - + -
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Residues in contact with VAL 878 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A LEU* 3.6 10.8 - - + -
437A VAL* 2.4 38.9 + - + +
441A TRP* 2.9 13.9 - - + +
859A TRP* 3.3 35.9 - - + -
874A LEU 3.1 4.7 + - - +
875A LYS* 2.4 44.9 - - + +
876A ALA 2.5 6.5 + - - -
877A MET* 1.3 73.5 - - - +
879A GLN* 1.3 86.9 + - + +
1189A LEU* 4.3 3.1 - - + -
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Residues in contact with GLN 879 (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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434A TYR 4.6 0.2 - - - +
435A LEU* 2.7 29.6 - - - +
436A PRO* 2.6 41.5 - - + +
876A ALA 3.1 10.1 + - - +
877A MET* 2.9 3.2 + - - +
878A VAL* 1.3 120.0 + - - +
880A ALA* 1.3 62.4 + - - +
886A LEU* 2.9 28.3 - - + -
1129A PHE* 5.3 2.8 - - - -
1187A ARG 2.3 26.8 - - - +
1189A LEU* 2.8 30.1 - - + +
1212A ILE* 5.2 0.3 - - - +
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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