Contacts of the helix formed by residues 943 - 956 (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 ARG 943 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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926A SER* 5.7 2.6 + - - -
929A THR* 4.5 5.1 + - - +
930A ASP* 4.1 12.3 - - - +
933A SER* 2.9 54.0 + - - +
936A ALA* 4.1 3.8 - - + -
937A THR* 4.0 11.1 + - - -
941A ILE 4.0 8.1 + - - +
942A SER* 1.3 75.1 - - - +
944A GLU* 1.3 56.7 + - - +
945A HIS 2.8 4.5 - - - -
946A ALA* 2.5 26.6 + - + -
947A LYS* 2.5 35.0 + - + +
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Residues in contact with GLU 944 (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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942A SER* 4.4 1.9 + - - +
943A ARG* 1.3 76.1 - - - +
945A HIS* 1.3 56.3 + - - +
947A LYS* 3.0 33.1 + - - +
948A ILE* 2.9 30.9 + - - +
1068A ASP* 4.5 10.5 - - - +
1069A ILE* 3.5 55.0 + - - +
1070A PRO 5.2 2.5 - - - +
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Residues in contact with HIS 945 (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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941A ILE* 5.6 3.2 - - + +
942A SER* 2.9 23.8 + - - +
943A ARG 2.8 0.6 - - - -
944A GLU* 1.3 77.7 - - - +
946A ALA* 1.3 60.5 + - - +
948A ILE* 3.2 5.6 - - + +
949A PHE* 2.8 53.0 - + - -
965A LEU 4.9 0.4 - - - -
966A LEU* 4.9 5.8 - - - -
969A PHE* 2.9 59.6 - + + +
970A ASN* 5.1 4.6 + - - -
1068A ASP* 3.6 26.2 + - - +
1071A ARG* 6.0 0.7 - - - -
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Residues in contact with ALA 946 (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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932A HIS 4.9 1.3 - - - +
935A THR* 4.3 11.5 - - + +
936A ALA* 3.3 36.6 - - + +
941A ILE* 4.5 4.5 - - + +
942A SER 3.4 5.5 + - - +
943A ARG* 2.5 13.9 + - + +
945A HIS* 1.3 74.0 - - - +
947A LYS* 1.3 65.5 + - - +
949A PHE* 3.3 13.4 + - - +
950A ASN* 3.5 16.6 + - - -
953A ARG* 5.0 1.2 + - - -
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Residues in contact with LYS 947 (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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929A THR* 3.0 37.0 - - + +
932A HIS* 3.3 40.1 - - + +
943A ARG* 2.5 22.7 + - + +
944A GLU* 3.0 51.2 + - - +
946A ALA* 1.3 71.5 - - - +
948A ILE* 1.3 64.1 + - + +
950A ASN* 3.1 16.6 + - - +
951A TYR* 2.8 27.9 + - + +
1069A ILE 5.7 0.2 + - - -
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Residues in contact with ILE 948 (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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944A GLU 2.9 25.1 - - - +
945A HIS* 3.2 25.8 - - + +
947A LYS* 1.3 76.0 - - + +
949A PHE* 1.3 70.5 + - + +
951A TYR* 3.1 17.0 - - + +
952A GLY* 2.8 21.7 + - - -
1068A ASP* 5.1 2.0 - - - +
1070A PRO 3.8 8.7 - - - +
1071A ARG* 3.2 67.1 - - - +
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Residues in contact with PHE 949 (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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945A HIS* 2.8 51.1 - + - -
946A ALA* 3.3 7.3 + - - +
947A LYS 3.3 1.2 - - - -
948A ILE* 1.3 92.5 - - + +
950A ASN* 1.3 54.4 + - - +
952A GLY* 3.1 5.3 - - - +
953A ARG* 2.4 50.3 + - - +
962A ALA* 5.1 10.5 - - + -
965A LEU* 3.3 41.3 - - + -
966A LEU* 3.8 17.3 - - + -
969A PHE* 3.8 13.7 - + - -
1071A ARG* 4.6 5.6 - - - -
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Residues in contact with ASN 950 (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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896A LEU* 6.0 2.5 - - + -
932A HIS* 5.3 8.0 - - + +
935A THR* 3.5 32.6 + - - +
946A ALA 3.5 19.2 + - - -
947A LYS* 3.1 10.7 + - - +
949A PHE* 1.3 73.2 - - - +
951A TYR* 1.3 62.3 + - + +
952A GLY 2.8 0.7 - - - -
953A ARG* 2.4 33.0 + - + +
954A ILE* 2.3 42.2 + - + +
989A THR* 5.2 6.6 + - - +
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Residues in contact with TYR 951 (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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893A SER* 4.8 5.9 + - - -
896A LEU* 3.3 35.8 - - + +
932A HIS* 3.5 32.8 + + - -
947A LYS* 2.8 37.0 + - + +
948A ILE* 3.1 15.9 + - + +
950A ASN* 1.3 85.1 - - + +
952A GLY* 1.3 51.4 + - - +
954A ILE* 2.6 30.0 + - - +
955A TYR* 2.7 45.5 - - + -
1072A THR* 5.9 12.3 - - + -
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Residues in contact with GLY 952 (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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948A ILE 2.8 14.0 + - - -
949A PHE* 3.1 9.6 - - - -
950A ASN 2.8 0.8 - - - -
951A TYR* 1.3 76.0 - - - +
953A ARG* 1.3 61.0 + - - +
955A TYR* 3.1 20.4 + - - +
956A GLY* 3.4 12.1 + - - -
957A ALA 4.6 2.8 + - - -
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Residues in contact with ARG 953 (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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935A THR* 4.9 7.5 - - - +
946A ALA 5.0 1.2 + - - -
949A PHE* 2.4 37.5 + - + +
950A ASN* 2.4 62.8 + - - +
952A GLY* 1.3 71.3 - - - +
954A ILE* 1.3 63.5 + - - +
955A TYR* 3.1 4.9 + - - -
956A GLY 4.1 1.6 + - - -
957A ALA 4.7 2.9 + - - -
958A GLY 5.4 3.6 - - - +
962A ALA* 4.9 3.0 - - - +
985A MET* 3.0 57.4 + - - +
986A TYR* 3.0 44.4 + - + +
989A THR* 5.0 4.2 + - - +
990A LYS* 3.9 26.9 + - - +
1000A GLU* 4.3 5.7 - - - +
1003A TRP* 4.3 2.3 + - - -
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Residues in contact with ILE 954 (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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895A GLU* 5.2 1.3 - - + +
896A LEU* 3.3 37.5 - - + +
899A ALA* 4.0 21.5 - - + -
950A ASN* 2.3 25.7 + - + +
951A TYR* 2.6 14.5 + - - +
953A ARG* 1.3 67.1 - - - +
955A TYR* 1.3 79.8 + - + +
1000A GLU* 4.8 3.6 - - - +
1003A TRP* 2.8 48.8 + - + +
1101A VAL* 4.3 12.3 - - + +
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Residues in contact with TYR 955 (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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895A GLU* 3.3 29.1 + - + +
896A LEU* 5.2 0.5 - - - +
951A TYR* 2.7 67.4 + + + -
952A GLY* 3.3 12.6 - - - +
953A ARG 3.0 2.5 - - - -
954A ILE* 1.3 94.0 - - + +
956A GLY* 1.3 59.9 + - - +
1003A TRP* 4.5 0.6 + - - -
1056A GLU* 5.8 0.4 - - - +
1072A THR* 5.3 7.4 + - - +
1074A VAL* 3.8 20.0 - - + -
1097A VAL* 3.4 7.8 - - - +
1098A ASN* 2.4 69.7 + - - +
1101A VAL* 4.8 2.0 - - + -
1102A GLN* 2.6 23.1 - - - -
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Residues in contact with GLY 956 (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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952A GLY 3.4 5.7 + - - -
953A ARG 4.1 1.8 + - - -
955A TYR* 1.3 82.2 - - - +
957A ALA* 1.3 62.4 + - - +
1056A GLU* 5.3 3.8 + - - -
1093A MET* 4.5 1.7 - - - +
1094A THR* 3.0 46.1 + - - -
1097A VAL* 4.8 5.1 - - - +
1098A ASN* 4.0 4.4 - - - +
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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