Contacts of the helix formed by residues 943 - 954 (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 ARG 943 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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926D SER* 5.4 4.2 - - - -
929D THR* 4.5 7.3 + - - +
930D ASP* 4.2 16.4 + - - +
932D HIS* 3.3 13.1 - - + -
933D SER* 2.5 36.5 + - - -
936D ALA* 3.7 21.8 - - + -
937D THR* 4.9 7.4 + - - +
941D ILE 4.4 2.9 - - - +
942D SER* 1.3 76.0 + - - +
944D GLU* 1.3 59.2 + - + +
945D HIS 3.2 1.6 - - - -
946D ALA* 2.5 34.1 + - - +
947D LYS* 3.0 8.9 + - - +
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Residues in contact with GLU 944 (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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942D SER* 4.1 4.4 + - - +
943D ARG* 1.3 78.3 - - + +
945D HIS* 1.3 65.1 + - - +
946D ALA 2.7 1.4 + - - -
947D LYS* 3.0 30.9 + - - +
948D ILE* 2.7 17.8 - - - +
1068D ASP 4.0 2.1 - - - +
1069D ILE* 3.0 27.6 - - - +
1071D ARG* 2.5 45.2 + - - +
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Residues in contact with HIS 945 (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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942D SER* 4.4 18.8 + - - +
943D ARG 3.2 0.4 - - - -
944D GLU* 1.3 76.8 - - - +
946D ALA* 1.3 55.7 + - - +
948D ILE* 2.8 29.3 - - + +
949D PHE* 3.1 19.4 + + - +
965D LEU* 4.8 3.6 - - + -
966D LEU* 5.4 3.4 - - - +
969D PHE* 2.9 63.0 - + + +
970D ASN* 4.9 9.8 + - - -
1067D SER 5.5 5.4 - - - -
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Residues in contact with ALA 946 (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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932D HIS* 3.0 16.6 - - + +
935D THR* 5.6 0.7 - - + -
936D ALA* 4.1 9.9 - - + -
941D ILE* 6.0 0.9 - - + -
942D SER 3.9 7.4 + - - +
943D ARG* 2.5 31.0 + - - +
945D HIS* 1.3 70.4 - - - +
947D LYS* 1.3 63.2 + - - -
948D ILE 3.0 3.2 + - - -
949D PHE* 2.8 41.7 + - + -
950D ASN* 3.1 11.2 + - - -
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Residues in contact with LYS 947 (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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929D THR* 2.5 36.9 + - - +
932D HIS* 3.0 35.2 + - + +
943D ARG* 3.0 7.7 + - - +
944D GLU* 3.0 43.7 + - - +
946D ALA* 1.3 71.1 - - - +
948D ILE* 1.3 61.0 + - + +
950D ASN* 3.2 6.0 + - - +
951D TYR* 2.8 39.6 + - + -
1071D ARG* 3.6 27.1 - - - +
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Residues in contact with ILE 948 (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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944D GLU 2.7 22.0 - - - +
945D HIS* 2.8 33.2 - - + +
947D LYS* 1.3 73.7 - - + +
949D PHE* 1.3 59.3 + - - +
951D TYR* 2.9 19.4 - - + +
952D GLY* 2.8 21.3 + - - -
1067D SER* 3.8 18.8 - - - +
1071D ARG* 2.6 71.6 - - + +
1072D THR 5.3 0.7 - - - -
1073D PRO* 5.0 2.9 - - + -
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Residues in contact with PHE 949 (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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935D THR* 5.9 1.6 - - + -
936D ALA* 6.4 0.4 - - - -
945D HIS* 3.1 18.6 - + + +
946D ALA* 2.8 36.7 + - + -
948D ILE* 1.3 81.7 - - + +
950D ASN* 1.3 98.4 + - - +
952D GLY* 2.6 8.5 + - - +
953D ARG* 2.3 61.4 + - + +
962D ALA* 6.6 0.4 - - - -
965D LEU* 5.0 19.5 - - + -
966D LEU* 6.4 2.7 - - + -
985D MET* 4.4 18.6 - - + -
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Residues in contact with ASN 950 (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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932D HIS* 3.5 24.6 - - + -
935D THR* 4.4 8.8 - - - +
946D ALA 3.1 16.4 + - - -
947D LYS* 3.4 7.4 - - - +
948D ILE 3.1 0.6 - - - -
949D PHE* 1.3 90.7 - - - +
951D TYR* 1.3 56.8 + - + +
952D GLY 2.8 0.7 - - - -
953D ARG* 2.5 50.1 + - + +
954D ILE* 2.5 40.3 + - - +
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Residues in contact with TYR 951 (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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892D ASP* 3.6 23.7 + - + +
895D GLU* 4.4 4.7 - - - -
896D LEU* 3.5 36.1 - - + +
947D LYS* 2.8 42.5 + - + -
948D ILE* 2.9 19.0 + - + +
950D ASN* 1.3 73.4 - - + +
952D GLY* 1.3 49.0 + - - +
954D ILE* 2.5 40.1 + - - +
955D TYR* 2.6 40.3 - + + -
1071D ARG 5.5 7.9 - - - -
1072D THR* 5.5 4.3 - - - -
1074D VAL* 4.8 11.7 - - + -
1135D ASP* 6.1 0.2 - - - -
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Residues in contact with GLY 952 (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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948D ILE 2.8 8.9 + - - -
949D PHE* 2.6 13.6 + - - -
951D TYR* 1.3 73.2 - - - +
953D ARG* 1.3 55.4 + - - +
954D ILE 2.1 24.9 - - - +
955D TYR* 4.1 4.7 - - - -
956D GLY* 3.2 15.4 + - - +
957D ALA 5.2 1.3 - - - +
1074D VAL* 6.2 0.4 - - - -
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Residues in contact with ARG 953 (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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935D THR* 5.1 13.9 + - - +
939D VAL* 5.9 4.2 - - - +
949D PHE* 2.3 46.2 + - + +
950D ASN* 2.5 45.2 + - + +
952D GLY* 1.3 67.8 - - - +
954D ILE* 1.3 60.4 + - + +
956D GLY 3.1 11.9 - - - +
958D GLY* 5.9 2.7 - - - +
962D ALA* 6.5 0.7 - - + -
985D MET* 3.3 48.1 + - + +
986D TYR* 5.8 1.6 - - - +
988D ALA* 5.3 4.4 - - - +
989D THR* 3.6 28.8 + - - +
990D LYS* 3.3 19.7 + - - +
1000D GLU* 2.8 17.6 - - + +
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Residues in contact with ILE 954 (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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895D GLU* 5.3 0.9 - - - +
896D LEU* 3.6 31.4 - - + -
899D ALA* 4.4 15.3 - - + -
950D ASN 2.5 16.5 + - - +
951D TYR* 2.5 22.1 - - - +
952D GLY 2.1 28.1 - - - +
953D ARG* 1.3 75.6 - - + +
955D TYR* 1.3 95.4 + - + +
1000D GLU* 3.7 10.5 - - + +
1003D TRP* 3.6 19.3 - - + -
1101D VAL* 4.8 1.6 - - + -
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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