Contacts of the helix formed by residues 928 - 938 (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 GLY 928 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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922D GLN* 4.8 2.0 - - - -
923D GLY* 4.2 4.1 - - - -
927D ARG* 1.3 87.4 - - - +
929D THR* 1.3 58.7 + - - +
930D ASP 3.2 0.9 - - - -
931D LEU* 3.2 17.8 + - - +
932D HIS* 3.1 26.9 + - - +
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Residues in contact with THR 929 (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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926D SER* 3.1 15.9 - - - +
927D ARG* 3.1 17.7 - - + +
928D GLY* 1.3 78.9 - - - +
930D ASP* 1.3 60.6 + - - +
931D LEU 3.1 0.4 - - - -
932D HIS* 3.4 7.9 + - - +
933D SER* 2.8 31.7 + - - -
943D ARG* 4.9 8.7 - - - +
947D LYS* 2.5 41.7 + - - +
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Residues in contact with ASP 930 (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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924D ARG* 2.9 23.5 - - - +
925D LYS* 4.6 4.7 - - - +
926D SER* 2.8 44.6 + - - +
927D ARG 3.4 2.0 - - - +
929D THR* 1.3 79.8 - - - +
931D LEU* 1.3 71.1 + - - +
933D SER* 3.0 11.3 + - - -
934D LYS* 2.8 23.7 + - - +
943D ARG* 4.2 7.4 - - - +
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Residues in contact with LEU 931 (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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918D TRP* 3.4 10.0 - - + -
922D GLN* 2.9 43.3 - - + +
923D GLY* 3.0 37.5 - - - +
924D ARG* 4.0 13.7 - - + +
927D ARG 3.2 4.7 - - - +
928D GLY* 3.5 9.9 - - - +
929D THR 3.1 0.6 - - - -
930D ASP* 1.3 93.0 - - - +
932D HIS* 1.3 64.2 + - - +
933D SER 3.1 0.7 - - - -
934D LYS* 2.7 58.3 - - - +
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Residues in contact with HIS 932 (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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918D TRP* 4.3 10.3 - - - +
928D GLY 3.1 15.8 + - - +
929D THR* 3.4 8.9 + - - +
931D LEU* 1.3 75.8 - - - +
933D SER* 1.3 80.0 + - - +
935D THR* 2.5 46.2 + - + +
936D ALA* 4.5 0.8 - - + +
943D ARG* 3.3 27.8 - - + -
946D ALA* 3.0 23.6 - - + +
947D LYS* 3.0 31.3 + - + +
950D ASN* 3.5 25.6 - - - +
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Residues in contact with SER 933 (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 2.8 17.9 + - - -
930D ASP 3.0 7.4 + - - -
932D HIS* 1.3 88.5 + - - +
934D LYS* 1.3 56.7 + - - -
935D THR 2.5 7.5 + - - -
936D ALA* 2.5 25.0 + - - +
937D THR* 3.0 11.8 + - - -
943D ARG* 2.5 55.0 + - - +
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Residues in contact with LYS 934 (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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918D TRP* 3.2 25.1 - - + -
922D GLN* 2.4 42.6 + - - +
924D ARG* 4.7 11.6 - - - +
930D ASP* 2.8 17.2 + - - +
931D LEU* 2.7 37.4 - - - +
933D SER* 1.3 76.4 - - - +
935D THR* 1.3 57.3 + - - +
936D ALA 3.5 0.2 - - - -
937D THR* 3.6 11.1 - - - -
938D THR* 3.5 22.7 + - + +
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Residues in contact with THR 935 (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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918D TRP* 4.7 13.7 - - + -
931D LEU 4.7 2.0 - - - -
932D HIS* 2.5 47.2 + - + +
933D SER 2.5 4.8 + - - -
934D LYS* 1.3 74.4 - - - +
936D ALA* 1.3 54.6 + - - +
937D THR 3.2 0.4 - - - -
938D THR* 2.3 43.1 + - - +
939D VAL* 4.2 3.1 - - - +
946D ALA* 5.6 1.1 - - + -
949D PHE* 5.9 1.1 - - + -
950D ASN* 4.4 11.0 - - - +
953D ARG* 5.1 13.5 + - - +
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Residues in contact with ALA 936 (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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933D SER* 2.5 14.2 + - - +
935D THR* 1.3 74.9 - - - +
937D THR* 1.3 62.6 + - - +
938D THR 2.8 12.7 - - - +
939D VAL* 3.0 20.2 - - - +
940D GLY 3.1 0.3 + - - -
941D ILE* 3.3 14.6 + - + +
942D SER 3.5 24.7 - - - +
943D ARG* 3.7 20.2 - - + -
946D ALA* 4.1 12.1 - - + -
949D PHE* 6.4 0.2 - - - -
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Residues in contact with THR 937 (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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933D SER* 3.0 16.9 + - - -
934D LYS* 3.6 13.5 + - - -
936D ALA* 1.3 74.4 - - - +
938D THR* 1.3 58.1 + - - +
939D VAL 2.8 0.5 + - - -
940D GLY* 2.4 32.8 + - - +
941D ILE 4.6 1.8 + - - +
943D ARG* 4.9 6.4 + - - +
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Residues in contact with THR 938 (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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934D LYS* 3.5 14.9 + - + +
935D THR* 2.3 57.3 + - - +
936D ALA 2.8 2.1 - - - +
937D THR* 1.3 72.7 - - - +
939D VAL* 1.3 73.3 + - - +
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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