Contacts of the helix formed by residues 649 - 669 (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 TYR 649 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647D CYS* 3.7 20.9 - - + -
648D PRO* 1.3 83.3 - - + +
650D ARG* 1.3 50.9 + - - +
652D ILE* 2.9 49.9 - - + +
653D GLU* 2.4 29.3 + - - +
656D TYR* 4.5 15.2 + + - -
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Residues in contact with ARG 650 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633D LYS* 4.9 8.7 - - - +
641D GLU* 2.8 57.4 + - - +
642D SER* 4.7 2.1 - - - -
645D VAL* 2.7 43.0 - - + +
646D VAL* 3.2 27.3 + - + +
647D CYS* 3.7 3.0 - - + +
649D TYR* 1.3 74.8 - - - +
651D ALA* 1.3 60.2 - - - +
652D ILE 2.8 4.7 - - - -
653D GLU* 3.6 14.2 - - + +
654D SER* 3.4 17.7 + - - -
657D ARG* 4.9 1.9 + - - -
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Residues in contact with ALA 651 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477D GLU* 6.0 8.1 - - + -
644D GLY 5.1 8.1 - - - +
645D VAL* 5.0 2.7 - - - -
646D VAL 3.6 4.4 + - - +
647D CYS 4.1 11.2 - - - +
648D PRO* 3.5 11.9 - - + +
650D ARG* 1.3 78.8 - - - +
652D ILE* 1.3 52.3 + - - +
654D SER* 3.1 11.5 + - - -
655D LEU* 2.7 40.5 + - + +
658D LYS* 4.5 0.7 + - - -
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Residues in contact with ILE 652 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648D PRO* 2.7 34.1 + - + +
649D TYR* 2.9 56.5 - - + -
650D ARG 2.8 0.2 - - - -
651D ALA 1.3 78.1 - - - +
653D GLU* 1.3 59.5 + - - +
654D SER 2.8 1.1 - - - -
655D LEU* 2.4 46.4 + - + +
656D TYR* 2.6 40.1 + - + -
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Residues in contact with GLU 653 (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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630D ASN* 5.2 1.0 + - - -
631D LEU 5.6 3.3 - - - +
632D ALA* 5.1 0.3 - - - -
633D LYS* 6.0 8.0 - - + -
649D TYR 2.4 24.7 + - - +
650D ARG* 3.6 18.1 - - + +
652D ILE* 1.3 72.2 - - - +
654D SER* 1.3 60.7 + - - +
656D TYR* 2.9 45.3 - - + +
657D ARG* 2.8 45.8 + - - +
744D ILE* 4.1 7.3 - - - +
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Residues in contact with SER 654 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642D SER* 5.6 5.8 - - - -
650D ARG 3.4 12.1 + - - -
651D ALA* 3.1 15.0 + - - -
653D GLU* 1.3 77.5 - - - +
655D LEU* 1.3 68.9 + - - +
657D ARG* 2.9 28.3 + - - +
658D LYS* 3.0 39.7 + - - +
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Residues in contact with LEU 655 (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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648D PRO 4.8 1.1 - - - +
651D ALA* 2.7 32.8 + - + +
652D ILE* 2.4 52.0 + - + +
654D SER* 1.3 73.7 - - - +
656D TYR* 1.3 52.1 + - - +
657D ARG 2.5 8.8 + - - -
658D LYS* 3.0 20.4 + - - +
659D HIS* 2.4 34.2 + - + +
713D PRO* 5.8 3.1 - - + -
719D LEU* 3.7 13.5 - - - +
720D THR* 5.7 1.6 - - - +
722D ARG* 3.6 37.2 - - - +
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Residues in contact with TYR 656 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649D TYR* 4.5 13.0 + + - -
652D ILE* 2.6 54.0 + - + -
653D GLU* 2.9 31.0 - - + +
655D LEU* 1.3 73.4 - - - +
657D ARG* 1.3 56.2 + - - +
659D HIS* 2.4 33.9 + - - -
660D CYS* 3.3 4.0 - - - +
719D LEU* 5.4 0.9 - - - -
743D ASP* 2.8 55.1 + - + -
744D ILE* 2.9 37.6 - - + +
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Residues in contact with ARG 657 (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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630D ASN* 4.3 2.2 - - - +
631D LEU 4.5 1.0 + - - -
632D ALA* 2.9 48.3 - - + +
633D LYS* 4.0 10.5 - - - +
638D THR* 5.3 0.8 + - - +
642D SER* 3.7 28.7 + - - -
650D ARG* 4.9 0.4 + - - +
653D GLU* 2.8 54.3 + - - +
654D SER* 3.4 22.6 - - - +
655D LEU 2.5 6.7 + - - -
656D TYR* 1.3 70.9 - - - +
658D LYS* 1.3 61.5 + - + +
660D CYS* 2.6 37.6 - - + +
661D LEU* 3.5 1.4 + - - +
744D ILE* 3.7 11.2 - - + -
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Residues in contact with LYS 658 (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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651D ALA 4.5 4.6 + - - -
654D SER* 3.0 45.9 + - - +
655D LEU* 3.0 11.6 + - - +
657D ARG* 1.3 72.6 - - + +
659D HIS* 1.3 63.7 + - + +
660D CYS 3.1 0.2 + - - -
661D LEU* 3.4 7.4 + - - +
662D GLU* 2.8 26.4 + - + +
713D PRO* 2.9 56.9 - - + +
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Residues in contact with HIS 659 (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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655D LEU* 2.4 33.4 + - - +
656D TYR* 2.4 38.7 + - - -
658D LYS* 1.3 76.6 - - + +
660D CYS* 1.3 72.5 + - - +
662D GLU* 3.1 11.4 + - - -
663D GLN* 2.9 29.0 + - + +
713D PRO* 4.7 7.3 + - + +
714D GLY 5.0 2.2 - - - +
716D PRO* 3.7 19.5 - - + -
719D LEU* 2.8 64.4 - - + +
744D ILE* 4.5 4.7 - - + +
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Residues in contact with CYS 660 (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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630D ASN* 4.0 9.4 - - - -
656D TYR 3.3 5.2 - - - +
657D ARG* 2.6 26.2 - - - +
658D LYS 3.0 0.4 - - - -
659D HIS* 1.3 85.8 + - - +
661D LEU* 1.3 89.7 + - - +
663D GLN* 3.8 9.6 + - - +
664D GLY* 3.9 6.2 + - - -
745D PRO* 2.9 52.3 - - + +
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Residues in contact with LEU 661 (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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657D ARG 4.6 1.1 - - - +
658D LYS 3.4 7.7 + - - +
659D HIS 3.3 0.4 - - - -
660D CYS* 1.3 87.8 - - - +
662D GLU* 1.3 75.8 + - - +
664D GLY* 3.0 17.5 + - - -
665D LYS* 3.8 11.7 + - + -
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Residues in contact with GLU 662 (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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658D LYS* 2.8 24.9 - - - +
659D HIS* 3.1 13.9 + - - +
661D LEU* 1.3 82.1 - - - +
663D GLN* 1.3 64.8 + - - +
665D LYS* 2.9 27.0 + - - +
666D GLN* 3.4 4.2 + - - +
669D MET* 4.9 1.6 - - - +
713D PRO 5.2 1.3 - - - +
714D GLY* 4.2 28.0 - - - +
716D PRO* 4.4 4.5 - - + -
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Residues in contact with GLN 663 (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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612D LEU* 5.2 2.2 - - - +
613D HIS* 3.7 26.0 + - - +
614D TYR 5.0 1.0 - - - +
621D GLY* 2.7 31.0 + - - +
622D TYR 4.9 2.8 + - - -
659D HIS* 2.9 18.5 + - - +
660D CYS* 4.2 5.5 + - - +
662D GLU* 1.3 71.9 - - - +
664D GLY* 1.3 55.6 + - - +
666D GLN* 2.6 37.8 + - + +
667D GLN* 2.9 20.6 + - - +
716D PRO* 3.5 34.7 - - + +
719D LEU* 4.3 13.3 - - - +
746D GLY* 5.8 1.6 - - - -
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Residues in contact with GLY 664 (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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623D LEU* 4.7 6.9 - - - +
660D CYS 3.9 4.3 + - - -
661D LEU 3.0 11.7 + - - -
663D GLN* 1.3 77.7 - - - +
665D LYS* 1.3 58.7 + - - +
667D GLN* 2.9 35.8 + - - +
668D LEU* 3.3 15.1 + - - +
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Residues in contact with LYS 665 (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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661D LEU* 3.8 14.5 + - + +
662D GLU* 2.9 14.1 + - - +
664D GLY* 1.3 71.0 - - - +
666D GLN* 1.3 51.9 + - - +
667D GLN 2.9 5.6 + - - -
668D LEU* 3.1 11.3 + - + +
669D MET* 2.3 71.6 + - + +
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Residues in contact with GLN 666 (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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606D THR 5.9 1.4 + - - -
610D PHE 5.5 0.9 - - - +
611D PRO* 5.3 6.7 - - - +
613D HIS* 4.3 30.5 + - - +
662D GLU 3.4 1.7 + - - +
663D GLN* 2.6 28.5 + - + +
665D LYS* 1.3 70.1 - - - +
667D GLN* 1.3 52.3 + - - +
669D MET* 2.1 50.9 - - + +
670D PRO* 3.0 23.7 - - - +
716D PRO* 5.3 13.4 - - + +
717D LEU* 5.3 0.4 - - - +
783D PRO* 5.2 12.1 - - - +
363F ARG 5.5 1.9 - - - +
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Residues in contact with GLN 667 (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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610D PHE 5.4 0.3 - - - +
611D PRO* 3.9 30.5 - - + +
612D LEU* 4.5 2.6 - - - +
621D GLY 4.8 0.6 + - - -
622D TYR* 3.7 5.6 - - - +
623D LEU* 2.7 66.3 + - + +
663D GLN* 3.1 13.4 + - - +
664D GLY* 2.9 27.2 - - - +
666D GLN* 1.3 76.0 - - - +
668D LEU* 1.3 65.4 + - + +
669D MET 2.9 3.4 - - - +
670D PRO* 4.3 0.2 - - - +
671D GLN* 2.6 44.8 + - + +
673D ALA* 5.4 0.3 - - - +
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Residues in contact with LEU 668 (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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623D LEU* 5.4 8.5 - - + -
664D GLY 3.5 14.8 - - - +
665D LYS* 3.1 13.2 + - + +
667D GLN* 1.3 75.6 - - + +
669D MET* 1.3 53.6 + - + +
670D PRO 2.6 12.6 - - - +
671D GLN* 2.3 36.3 - - + +
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Residues in contact with MET 669 (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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662D GLU 4.9 1.6 - - - +
665D LYS* 2.3 52.4 + - + +
666D GLN* 2.1 74.7 - - + +
667D GLN 3.1 0.2 - - - -
668D LEU* 1.3 72.2 - - + +
670D PRO* 1.3 66.2 - - + -
363F ARG 5.3 8.1 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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