Contacts of the helix formed by residues 869 - 879 (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 869 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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448D ALA* 6.1 0.4 - - - -
452D TYR* 3.0 35.0 - - - +
455D LEU* 2.4 31.3 - - + +
794D ILE 2.9 2.0 + - - -
797D MET* 2.6 43.6 + - + +
798D ILE* 2.4 65.1 - - - +
801D TRP* 3.0 14.1 - - + -
868D ASP* 1.3 74.7 - - + +
870D VAL* 1.3 64.2 + - - +
871D GLY 3.5 1.8 - - - -
872D SER* 3.9 0.2 + - - -
873D GLU* 3.8 0.7 - - - -
1200D PRO* 2.3 59.4 - - - +
1201D SER* 5.2 3.6 - - - -
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Residues in contact with VAL 870 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444D TYR 5.1 0.2 - - - +
445D LEU 5.7 0.2 - - - +
448D ALA* 3.1 34.0 + - + +
801D TRP* 2.5 55.5 - - + +
804D ALA* 4.5 1.6 - - + -
805D HIS* 5.2 1.3 - - + +
808D ILE* 4.2 0.7 - - + -
869D ARG* 1.3 80.1 - - - +
871D GLY* 1.3 60.9 + - - +
873D GLU* 2.5 33.6 - - - +
874D LEU* 3.0 32.0 + - + -
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Residues in contact with GLY 871 (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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801D TRP* 5.3 2.8 - - - +
804D ALA* 4.9 11.6 - - - +
808D ILE* 5.1 1.8 - - - -
863D SER* 4.5 5.4 + - - +
864D ASN 3.8 4.9 - - - +
868D ASP 5.4 0.2 + - - -
869D ARG* 3.5 0.4 - - - +
870D VAL* 1.3 82.2 - - - +
872D SER* 1.3 70.5 + - - +
873D GLU 2.8 2.5 + - - -
874D LEU* 3.3 15.5 + - - +
875D LYS 4.6 1.6 + - - -
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Residues in contact with SER 872 (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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863D SER 4.3 1.7 - - - +
864D ASN 2.9 8.5 - - - +
865D ALA* 2.6 56.7 + - - +
866D ARG 4.4 0.4 - - - +
867D PRO* 5.0 2.5 - - - -
868D ASP* 3.4 27.2 + - - -
869D ARG 4.3 0.8 - - - -
870D VAL 3.3 0.2 - - - -
871D GLY* 1.3 76.5 - - - +
873D GLU* 1.3 54.4 + - - +
875D LYS* 5.7 0.7 - - - +
1197D CYS* 3.9 2.4 - - - -
1200D PRO* 2.3 43.6 - - - +
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Residues in contact with GLU 873 (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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444D TYR* 3.9 24.3 - - - +
447D GLU* 4.7 2.3 - - - +
448D ALA* 4.0 7.4 - - - +
865D ALA* 4.4 1.3 - - - -
869D ARG 2.9 5.2 - - - +
870D VAL* 2.5 26.9 - - - +
871D GLY 2.8 0.8 - - - -
872D SER* 1.3 81.1 + - - +
874D LEU* 1.3 81.4 + - + +
875D LYS 3.5 1.2 + - - -
876D ALA* 3.7 6.3 + - - +
877D MET* 3.2 23.5 + - - +
1197D CYS* 5.1 6.2 - - + +
1199D THR 4.8 0.4 - - - -
1200D PRO* 2.7 29.1 - - + +
1203D PRO* 2.5 40.8 - - + +
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Residues in contact with LEU 874 (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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444D TYR* 4.7 12.3 - - + +
445D LEU* 4.8 7.9 - - + +
808D ILE* 3.3 40.8 - - + -
870D VAL* 3.0 26.2 + - + +
871D GLY* 3.3 9.8 + - - -
873D GLU* 1.3 109.9 - - + +
875D LYS* 1.3 60.5 + - - +
877D MET* 4.3 8.7 - - + -
878D VAL* 2.4 54.2 + - + +
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Residues in contact with LYS 875 (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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859D TRP* 5.8 2.7 - - + -
862D ALA* 4.3 18.4 - - + +
863D SER* 3.0 42.9 + - - +
864D ASN* 3.8 9.4 - - - +
871D GLY 4.6 3.8 + - - -
872D SER 5.7 0.7 - - - +
873D GLU 3.5 1.7 + - - -
874D LEU* 1.3 74.9 - - - +
876D ALA* 1.3 71.3 + - + +
878D VAL* 3.8 4.5 - - - -
879D GLN* 2.9 22.1 + - - +
1133D ILE* 6.2 3.8 - - + +
1136D GLU* 5.4 7.1 - - - +
1138D ARG* 5.4 3.0 - - - +
1189D LEU* 2.8 33.9 + - + +
1190D ARG* 4.0 8.7 - - + +
1191D LYS* 3.7 28.2 - - - +
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Residues in contact with ALA 876 (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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441D TRP* 5.0 0.3 - - - -
873D GLU 3.7 6.0 + - - +
874D LEU 3.2 0.2 - - - -
875D LYS* 1.3 87.4 - - + +
877D MET* 1.3 54.1 + - - +
878D VAL 2.5 15.8 + - - -
879D GLN 2.7 14.4 + - - -
1188D CYS* 3.1 26.2 - - - -
1189D LEU* 3.1 32.3 - - - +
1190D ARG* 4.1 10.8 - - + +
1197D CYS* 5.5 6.5 - - + -
1207D GLU* 4.9 7.0 - - - +
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Residues in contact with MET 877 (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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441D TRP* 3.1 34.1 - - + +
444D TYR* 3.0 53.7 - - + +
873D GLU* 3.2 21.0 + - - +
874D LEU* 4.2 8.1 - - + +
876D ALA* 1.3 77.5 - - - +
878D VAL* 1.3 62.6 + - - +
879D GLN 3.2 0.4 - - - -
1188D CYS* 4.0 2.0 - - - -
1203D PRO* 2.8 55.2 - - + +
1204D THR 3.5 0.2 - - - +
1207D GLU* 3.2 25.8 - - + +
1210D TYR* 4.3 1.1 - - + -
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Residues in contact with VAL 878 (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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437D VAL* 4.0 6.2 - - + +
441D TRP* 2.6 29.6 - - + +
444D TYR* 6.5 0.2 - - + -
445D LEU* 5.1 6.5 - - + +
808D ILE* 5.5 0.2 - - + -
811D GLN* 3.6 26.2 - - - +
840D ILE* 5.5 0.7 - - + -
859D TRP* 3.8 15.3 - - + -
874D LEU* 2.4 59.5 + - + +
875D LYS* 3.1 14.6 - - - +
876D ALA 2.5 7.5 + - - -
877D MET* 1.3 74.0 - - - +
879D GLN* 1.3 80.3 + - + +
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Residues in contact with GLN 879 (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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435D LEU* 3.7 24.6 - - + +
436D PRO* 2.2 47.3 - - + +
437D VAL* 4.7 4.0 - - + +
441D TRP* 2.5 14.5 - - - +
859D TRP* 3.8 8.7 - - + -
875D LYS* 2.9 22.2 + - - +
876D ALA 2.7 17.6 + - - -
877D MET 3.2 1.8 - - - -
878D VAL* 1.3 91.6 - - + +
880D ALA* 1.3 63.2 + - - +
886D LEU* 4.4 0.7 - - - +
1187D ARG 2.9 1.0 - - - +
1188D CYS* 3.8 0.2 - - - -
1189D LEU* 2.3 67.4 - - - +
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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