Contacts of the helix formed by residues 648 - 659 (chain B) in PDB entry 2IJM
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 PRO 648 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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520B LEU* 3.8 21.5 - - + -
524B ILE* 4.2 15.9 - - + -
646B ASN 3.3 8.9 - - - +
647B CYS* 1.3 89.3 - - - +
649B PRO* 1.4 66.9 - - + +
650B THR* 3.8 10.5 - - - +
651B LEU* 2.8 40.8 + - + +
652B TYR 3.1 9.2 + - - -
679B ILE* 4.3 7.4 - - + -
683B GLU* 5.6 2.2 - - + +
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Residues in contact with PRO 649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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643B MET* 4.2 24.2 - - + -
647B CYS 3.6 3.5 - - - +
648B PRO* 1.4 84.8 - - + +
650B THR* 1.3 54.4 + - + +
652B TYR* 3.2 2.3 + - - +
653B SER* 2.8 36.1 + - - -
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Residues in contact with THR 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648B PRO* 3.8 14.2 - - - +
649B PRO* 1.3 77.5 - - + +
651B LEU* 1.3 60.2 + - - -
653B SER* 3.6 8.7 + - - -
654B LEU* 3.3 19.8 + - - +
679B ILE* 3.7 26.3 - - - +
682B GLU* 5.5 8.6 - - - +
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Residues in contact with LEU 651 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524B ILE* 4.1 20.2 - - + -
527B ALA* 5.7 2.7 - - + -
612B MET* 4.0 13.7 - - + -
616B LEU* 3.4 37.9 - - + -
647B CYS* 3.8 4.5 - - - -
648B PRO* 2.8 27.5 + - + +
650B THR* 1.3 73.4 + - - +
652B TYR* 1.3 59.1 + - - +
653B SER 3.2 0.2 - - - -
654B LEU* 3.1 11.2 + - + +
655B MET* 3.0 33.3 + - + +
676B LEU* 3.7 27.8 - - + -
679B ILE* 3.7 18.1 - - + +
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Residues in contact with TYR 652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640B ARG* 4.5 6.9 + - - +
641B LEU 2.7 26.4 + - - -
642B PRO* 3.6 5.0 - - - +
643B MET* 3.4 66.1 + - + -
644B PRO* 4.1 2.5 - - + -
647B CYS* 3.7 5.5 - - - -
648B PRO 3.1 6.2 + - - +
649B PRO 3.2 4.2 + - - +
651B LEU* 1.3 73.4 - - - +
653B SER* 1.3 61.5 + - - +
655B MET* 3.3 20.8 + - - +
656B THR* 2.9 46.2 + - - -
659B TRP* 3.9 16.0 - + - -
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Residues in contact with SER 653 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649B PRO 2.8 17.3 + - - -
650B THR* 3.6 11.6 + - - -
651B LEU 3.2 0.2 - - - -
652B TYR* 1.3 78.2 - - - +
654B LEU* 1.3 56.4 + - - +
656B THR* 3.5 9.5 - - - +
657B LYS* 3.2 40.1 + - - +
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Residues in contact with LEU 654 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612B MET* 4.7 3.4 - - + -
650B THR 3.3 8.5 + - - +
651B LEU* 3.1 13.4 + - + +
653B SER* 1.3 77.7 - - - +
655B MET* 1.3 64.2 + - - +
656B THR 3.2 0.4 - - - -
657B LYS* 3.1 23.5 + - + +
658B CYS* 3.1 25.1 + - - -
667B PRO* 5.1 1.8 - - + -
672B LEU* 3.7 27.4 - - + +
675B GLN* 3.9 46.0 - - + +
676B LEU* 3.9 28.7 - - + -
679B ILE* 4.0 13.9 - - + -
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Residues in contact with MET 655 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609B GLY* 3.7 17.7 - - - +
612B MET* 3.8 21.0 - - + +
613B TRP* 4.0 28.0 - - - -
616B LEU* 3.1 32.3 - - + -
644B PRO* 4.7 0.7 - - - -
647B CYS* 3.5 13.2 - - - -
651B LEU* 3.0 33.3 + - + +
652B TYR* 3.4 22.2 - - + +
654B LEU* 1.3 77.0 - - - +
656B THR* 1.3 59.5 + - - +
658B CYS* 3.2 6.7 + - - +
659B TRP* 3.2 44.5 + - + -
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Residues in contact with THR 656 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640B ARG* 5.8 7.0 - - + +
652B TYR* 2.9 39.1 + - - -
653B SER* 3.5 10.5 - - - +
654B LEU 3.2 0.2 - - - -
655B MET* 1.3 75.4 - - - +
657B LYS* 1.3 64.5 + - + +
659B TRP* 3.1 29.3 + - + +
660B ALA* 3.5 2.3 + - - -
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Residues in contact with LYS 657 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653B SER* 3.2 31.1 + - - +
654B LEU* 3.1 24.4 + - + +
656B THR* 1.3 75.0 - - + +
658B CYS* 1.3 62.6 + - - +
660B ALA* 3.2 21.7 + - - +
665B ARG 4.6 1.9 - - - +
666B ARG* 3.6 1.4 - - - +
667B PRO* 3.6 31.2 - - + +
671B GLU* 4.2 7.1 + - - +
675B GLN* 3.1 29.9 - - - +
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Residues in contact with CYS 658 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605B VAL* 3.4 37.0 - - - +
606B TRP* 3.3 13.2 - - - +
608B PHE* 4.4 0.7 - - - -
609B GLY* 3.9 10.5 - - - -
612B MET* 3.9 17.5 - - - -
654B LEU 3.1 19.0 + - - -
655B MET 3.2 9.2 + - - +
657B LYS* 1.3 75.8 - - - +
659B TRP* 1.3 58.1 + - + +
660B ALA 3.3 1.1 - - - -
666B ARG* 3.2 21.6 - - - -
667B PRO* 4.4 0.4 - - - -
672B LEU* 3.5 29.6 - - - -
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Residues in contact with TRP 659 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606B TRP* 3.3 38.8 - + + -
609B GLY* 3.4 22.6 - - - -
610B VAL* 3.4 26.7 - - + +
613B TRP* 4.1 12.1 - + + -
640B ARG* 3.0 59.8 + - + +
641B LEU* 3.7 49.1 - - + -
652B TYR* 3.9 14.1 - + - -
655B MET* 3.2 34.5 + - + -
656B THR* 3.1 16.7 + - - +
657B LYS 3.1 1.2 - - - -
658B CYS* 1.3 78.8 - - + +
660B ALA* 1.3 60.2 + - - +
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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