Contacts of the helix formed by residues 1002 - 1010 (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 GLU1002 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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899D ALA 2.4 32.4 - - - +
900D ALA* 3.0 9.8 - - - +
902D LEU* 5.9 0.2 - - + -
903D GLY* 2.9 30.4 + - - +
904D ASP* 3.4 13.0 - - - +
907D PHE* 3.1 22.3 - - + -
914D THR* 4.6 5.4 - - - +
915D ALA* 4.1 9.2 + - - +
999D ASP 3.2 15.8 + - - +
1000D GLU* 2.6 7.4 + - + +
1001D GLY* 1.3 70.8 - - - +
1003D TRP* 1.3 80.1 + - + +
1004D LEU 2.7 1.3 - - - -
1005D VAL* 2.4 42.1 + - - +
1006D ARG* 3.0 1.2 + - - +
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Residues in contact with TRP1003 (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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899D ALA* 4.1 25.1 - - + -
902D LEU* 5.4 6.1 - - + -
954D ILE* 3.6 16.2 - - + -
955D TYR* 2.9 38.6 + - - -
1000D GLU* 2.3 65.4 + - + +
1002D GLU* 1.3 84.5 - - + +
1004D LEU* 1.3 51.5 + - + +
1006D ARG* 2.8 17.9 + - + +
1007D GLU* 2.5 46.3 + - + +
1097D VAL* 3.2 26.2 - - + +
1101D VAL* 3.0 37.5 - - + -
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Residues in contact with LEU1004 (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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986D TYR* 5.3 6.7 - - - +
990D LYS* 5.1 8.5 - - + -
995D TYR* 2.6 63.6 - - + +
996D ARG* 3.7 10.3 - - - +
997D LEU 5.0 0.7 - - - +
1000D GLU* 2.5 40.1 + - + +
1001D GLY* 2.6 33.2 - - - +
1003D TRP* 1.3 80.9 - - + +
1005D VAL* 1.3 54.3 + - - -
1007D GLU* 3.5 17.8 - - - +
1008D LEU* 2.7 29.1 + - - +
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Residues in contact with VAL1005 (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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902D LEU* 5.9 2.0 - - + +
903D GLY* 5.1 3.8 - - - -
906D HIS* 4.5 31.4 - - + -
907D PHE* 5.0 5.8 - - + -
995D TYR* 3.9 12.1 - - - +
1001D GLY 3.3 3.5 + - - +
1002D GLU* 2.4 46.1 + - + +
1004D LEU* 1.3 65.9 - - - +
1006D ARG* 1.3 69.7 + - - +
1008D LEU* 2.8 18.2 - - + -
1009D ASN* 2.2 56.4 + - - +
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Residues in contact with ARG1006 (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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902D LEU* 3.9 31.6 - - + +
1002D GLU 4.2 1.1 - - - +
1003D TRP* 2.8 28.5 + - + +
1005D VAL* 1.3 92.2 + - - +
1007D GLU* 1.3 60.0 + - - +
1009D ASN* 2.6 44.4 + - - +
1010D LEU* 2.9 40.7 + - + +
1016D GLU 4.5 2.0 + - - -
1017D GLY* 2.9 38.3 + - - -
1097D VAL* 5.0 9.2 - - + -
1100D VAL* 4.0 25.0 - - + +
1101D VAL* 5.9 0.4 - - + -
1168D LEU* 6.2 1.4 - - - +
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Residues in contact with GLU1007 (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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986D TYR* 5.0 6.6 + - - -
995D TYR* 5.5 6.4 - - + +
1003D TRP* 2.5 27.0 + - + +
1004D LEU* 3.5 20.8 - - - +
1006D ARG* 1.3 74.4 - - - +
1008D LEU* 1.3 53.2 + - + +
1010D LEU* 5.5 0.7 - - - -
1011D PRO* 2.4 31.1 - - + +
1093D MET* 3.6 35.5 - - + +
1097D VAL* 4.3 23.7 - - + +
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Residues in contact with LEU1008 (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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995D TYR* 4.3 14.8 - - + +
1004D LEU 2.7 12.6 + - - +
1005D VAL* 2.8 43.5 - - + +
1007D GLU* 1.3 76.4 - - + +
1009D ASN* 1.3 67.8 + - - +
1011D PRO* 2.8 15.7 - - + +
1012D VAL* 2.6 43.2 - - + +
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Residues in contact with ASN1009 (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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906D HIS* 5.2 12.1 + - - -
1005D VAL* 2.2 47.8 + - - +
1006D ARG* 2.6 32.5 - - - +
1008D LEU* 1.3 92.9 - - - +
1010D LEU* 1.3 65.5 + - - +
1012D VAL* 2.8 19.5 - - - +
1015D THR* 5.0 1.4 + - - +
1017D GLY* 4.8 11.3 + - - -
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Residues in contact with LEU1010 (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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1006D ARG* 2.9 55.6 + - + +
1007D GLU* 5.2 0.7 - - - -
1009D ASN* 1.3 82.7 - - - +
1011D PRO* 1.4 50.1 - - + +
1012D VAL 2.6 13.3 + - - +
1014D ARG* 4.5 3.8 + - - -
1015D THR* 3.0 49.4 + - + +
1016D GLU 4.1 1.6 - - - +
1017D GLY 4.2 0.2 - - - +
1028D VAL* 2.7 28.9 - - - +
1096D ARG* 4.4 12.8 - - + -
1097D VAL* 5.9 4.0 - - + +
1100D VAL* 3.5 29.8 - - + -
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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