Contacts of the helix formed by residues 598 - 603 (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 VAL 598 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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471D CYS* 6.1 0.7 - - - -
486D TRP* 3.0 57.4 - - + +
490D TRP* 2.8 23.3 - - + +
596D MET 3.4 0.4 + - - -
597D ARG* 1.3 67.2 - - + +
599D THR* 1.3 49.1 + - - -
600D PRO* 2.3 20.4 - - - +
601D LYS* 2.5 44.9 + - + +
602D LEU* 3.2 31.1 - - + +
616D GLU* 2.5 8.3 + - - -
721D ALA* 5.4 0.4 - - + -
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Residues in contact with THR 599 (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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463D LEU* 4.1 11.8 - - + +
490D TRP* 3.2 7.2 - - - -
593D SER 2.5 16.5 + - - -
594D LEU* 3.4 18.2 - - + +
596D MET 2.4 21.7 + - - -
597D ARG 2.2 19.3 + - - -
598D VAL* 1.3 67.2 - - - +
600D PRO* 1.3 54.1 - - - +
602D LEU* 3.2 13.8 - - - +
603D MET* 2.6 44.9 + - - +
766D PHE* 3.6 31.6 - - + -
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Residues in contact with PRO 600 (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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597D ARG 2.7 24.0 - - - +
598D VAL 2.3 8.2 - - - +
599D THR* 1.3 80.9 - - + +
601D LYS* 1.3 59.3 + - - -
602D LEU 3.1 1.1 - - - -
603D MET* 2.9 24.0 - - + +
605D LEU* 3.4 27.5 - - + +
613D HIS* 3.4 12.5 + - - -
614D TYR* 5.3 6.7 - - + +
616D GLU* 3.1 36.8 - - + +
617D ARG* 4.5 3.4 - - + +
765D PRO* 4.8 11.2 - - + -
766D PHE* 4.9 2.2 - - + -
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Residues in contact with LYS 601 (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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486D TRP* 3.7 6.2 - - - -
598D VAL* 2.5 55.4 + - + +
600D PRO* 1.3 74.3 - - - +
602D LEU* 1.3 56.5 + - - +
613D HIS* 5.3 0.4 - - - -
615D SER* 4.7 5.2 - - - -
616D GLU* 2.4 54.3 + - + +
715D GLN* 3.5 6.2 - - - +
717D LEU* 2.8 47.2 - - + +
718D ALA* 5.5 0.2 - - - -
721D ALA* 2.9 39.2 - - + +
722D ARG 2.8 27.2 - - - +
723D GLY 3.5 7.7 - - - +
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Residues in contact with LEU 602 (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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463D LEU* 4.6 13.7 - - + -
466D LEU* 4.6 27.6 - - + +
467D ALA* 4.3 22.9 - - + -
470D ALA* 5.7 4.0 - - + -
471D CYS* 4.7 17.0 - - - -
490D TRP* 4.5 7.9 - - + -
598D VAL* 3.2 27.4 - - + +
599D THR* 3.2 41.1 - - - +
601D LYS* 1.3 79.2 - - - +
603D MET* 1.3 53.4 - - + +
604D ALA* 2.5 20.7 + - - +
715D GLN* 4.6 14.5 + - - +
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Residues in contact with MET 603 (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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459D MET* 6.2 0.2 - - + -
463D LEU* 4.3 20.2 - - + -
466D LEU* 5.0 11.4 - - + -
594D LEU* 5.2 2.9 - - + -
599D THR* 2.6 29.1 + - + +
600D PRO* 2.9 8.8 - - + +
602D LEU* 1.3 77.4 - - + +
604D ALA* 1.3 53.5 + - - +
605D LEU* 2.3 45.6 + - + +
766D PHE* 3.7 30.7 - - + -
788D GLY* 4.9 3.6 - - - -
791D ALA* 3.9 22.2 - - + +
792D LEU* 3.7 30.5 - - + -
795D ASN* 4.9 0.7 - - - +
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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