Contacts of the helix formed by residues 647 - 666 (chain B) in PDB entry 1M2V
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 ASP 647 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B PRO* 3.0 20.0 - - + +
159B PRO* 4.4 4.9 - - - -
183B ARG* 2.8 42.5 + - - +
184B SER 3.4 23.3 - - - +
185B THR 2.9 9.6 + - - +
187B ASN* 4.8 4.8 + - - +
645B SER 3.9 0.6 + - - -
646B ALA* 1.3 71.1 - - - +
648B GLN* 1.3 50.8 + - - +
649B LEU 3.1 3.3 + - - -
650B ALA* 2.7 35.6 + - + +
651B ILE* 2.8 36.1 + - - +
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Residues in contact with GLN 648 (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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153B ASP* 4.4 16.8 + - - +
156B LEU* 5.8 2.0 - - - +
646B ALA 3.4 5.9 + - - -
647B ASP* 1.3 72.5 - - - +
649B LEU* 1.3 74.3 + - + +
651B ILE* 3.7 5.1 - - - +
652B ALA* 2.8 28.9 + - - +
705B ALA 4.4 2.5 + - - +
706B ASN* 2.9 26.8 - - - +
707B LEU* 3.2 21.9 - - + -
708B ARG 3.3 1.6 + - - -
709B MET* 3.0 49.6 + - + +
710B PHE* 4.3 13.8 - - + +
713B LEU* 4.6 1.7 - - + +
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Residues in contact with LEU 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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153B ASP 5.7 0.4 - - - +
154B LEU* 3.9 35.0 - - + +
156B LEU 5.0 7.2 - - - +
183B ARG* 3.8 22.7 - - - +
647B ASP* 3.0 7.8 + - - +
648B GLN* 1.3 90.1 - - + +
650B ALA* 1.3 61.8 + - - +
652B ALA* 3.1 4.8 + - - +
653B SER* 2.8 29.5 + - - -
713B LEU* 3.7 24.9 - - + -
745B LEU* 3.9 18.7 - - + +
749B ILE* 4.0 20.4 - - + +
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Residues in contact with ALA 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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183B ARG* 4.2 6.1 - - + +
184B SER 3.9 3.4 - - - +
185B THR* 3.7 22.8 - - + +
206B VAL* 3.9 25.3 - - + +
647B ASP* 2.7 35.6 + - + +
649B LEU* 1.3 73.1 - - - +
651B ILE* 1.3 53.0 + - - +
653B SER* 3.2 4.9 + - - -
654B PHE* 2.7 33.1 + - - +
745B LEU* 4.4 3.7 - - - +
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Residues in contact with ILE 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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185B THR* 3.7 23.8 - - - +
186B LEU* 5.0 1.8 - - + -
201B LEU* 3.8 25.4 - - + -
202B PRO* 3.9 10.8 - - + -
646B ALA* 3.8 23.8 - - + -
647B ASP 2.8 15.7 + - - +
648B GLN* 3.7 4.9 - - - +
650B ALA* 1.3 75.1 - - - +
652B ALA* 1.3 65.2 + - - +
654B PHE* 3.0 8.8 + - - +
655B TYR* 3.0 39.5 + - + -
682B ILE* 5.0 2.5 - - + -
707B LEU* 4.2 9.0 - - + -
710B PHE* 3.5 28.5 - - + -
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Residues in contact with ALA 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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648B GLN 2.8 19.8 + - - +
649B LEU* 3.1 6.0 + - - +
651B ILE* 1.3 76.8 - - - +
653B SER* 1.3 57.0 + - - +
655B TYR 3.5 0.2 + - - -
656B ASN* 3.0 27.9 + - - +
710B PHE* 4.3 4.9 - - + -
713B LEU* 3.7 25.4 - - + -
714B MET* 3.6 30.8 - - + +
748B LEU* 5.1 1.1 - - - -
749B ILE* 4.6 6.3 - - + -
752B ILE* 5.4 2.9 - - + -
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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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206B VAL* 4.2 15.0 - - - +
595B LEU* 4.6 3.9 - - - +
649B LEU 2.8 12.4 + - - -
650B ALA* 3.3 11.2 - - - -
651B ILE 3.1 0.2 - - - -
652B ALA* 1.3 75.8 - - - +
654B PHE* 1.3 65.6 + - - +
656B ASN* 3.1 2.0 + - - +
657B SER* 2.9 34.6 + - - -
745B LEU* 3.9 11.2 - - - +
748B LEU* 3.6 29.6 - - - +
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Residues in contact with PHE 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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185B THR* 4.2 5.2 - - + -
202B PRO* 3.3 30.1 - - + -
203B PHE 3.8 20.4 - - - -
204B GLY* 4.0 15.9 - - - -
595B LEU* 3.8 27.0 - - + +
597B GLU* 3.3 40.6 - - + -
650B ALA 2.7 16.7 + - - +
651B ILE* 3.0 13.2 + - - +
653B SER* 1.3 73.8 - - - +
655B TYR* 1.3 69.9 + + - +
657B SER* 3.5 3.1 + - - -
658B LYS* 3.1 54.9 + - + +
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Residues in contact with TYR 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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200B LYS 3.8 12.1 + - - -
201B LEU 4.7 0.3 - - - -
202B PRO* 3.5 29.2 - - + +
651B ILE* 3.0 43.5 + - + +
654B PHE* 1.3 85.9 - + - +
656B ASN* 1.3 66.8 + - - +
658B LYS* 3.2 5.5 + - + +
659B ALA* 2.8 26.3 + - - +
674B LEU* 4.1 21.2 - - + +
675B ILE* 5.1 2.2 - - + +
678B SER* 3.7 31.7 - - - +
682B ILE* 4.8 3.0 - - + +
710B PHE* 3.9 14.8 - + - -
714B MET* 3.8 18.8 - - - -
717B LEU* 4.9 2.5 - - - -
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Residues in contact with ASN 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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652B ALA 3.0 16.1 + - - +
653B SER* 3.2 11.8 + - - +
655B TYR* 1.3 76.6 - - - +
657B SER* 1.3 62.2 + - - +
659B ALA* 3.1 4.0 + - - +
660B VAL* 2.9 34.0 + - - +
717B LEU* 3.8 25.7 - - + +
723B PHE* 4.5 0.7 - - - -
740B LEU* 3.1 56.6 + - - +
741B GLU* 4.4 0.4 - - - +
748B LEU* 3.2 24.8 - - + +
752B ILE* 4.9 2.2 - - + -
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Residues in contact with SER 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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572B TYR* 4.1 22.7 - - - +
595B LEU* 4.0 24.6 - - - +
653B SER* 2.9 21.1 + - - -
654B PHE 3.8 4.5 - - - -
656B ASN* 1.3 83.7 + - - +
658B LYS* 1.3 57.1 + - - +
660B VAL* 3.5 6.8 + - - +
661B GLU* 3.1 27.4 + - - +
740B LEU 5.5 0.2 + - - -
741B GLU* 5.1 11.1 + - - +
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Residues in contact with LYS 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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570B ARG* 3.1 17.6 - - - +
572B TYR* 2.8 35.9 + - + +
595B LEU* 5.8 0.2 - - + -
597B GLU* 3.0 26.3 + - - -
654B PHE* 3.1 53.4 + - + +
655B TYR* 3.6 10.8 - - + +
656B ASN 3.2 0.4 - - - -
657B SER* 1.3 77.8 - - - +
659B ALA* 1.3 61.5 + - - +
661B GLU* 3.7 12.2 - - - +
662B LYS* 3.4 19.6 + - - +
674B LEU* 3.9 20.8 - - + +
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Residues in contact with ALA 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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655B TYR 2.8 17.0 + - - +
656B ASN* 3.6 4.3 - - - +
658B LYS* 1.3 74.7 - - - +
660B VAL* 1.3 59.6 + - - +
661B GLU 3.0 1.8 - - - -
662B LYS* 3.0 6.9 + - - +
663B ALA 2.8 26.7 + - - -
671B ALA* 3.7 4.8 - - + +
674B LEU* 4.4 7.2 - - + +
675B ILE* 3.9 24.7 - - + -
723B PHE* 3.4 26.9 - - + -
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Residues in contact with VAL 660 (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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656B ASN* 2.9 25.0 + - - +
657B SER 3.9 5.2 - - - +
658B LYS 3.5 0.2 - - - -
659B ALA* 1.3 75.3 - - - +
661B GLU* 1.3 61.3 + - - +
663B ALA* 4.2 0.5 - - - +
664B LEU* 3.4 32.4 + - + +
723B PHE* 3.9 17.5 - - + -
737B LEU* 3.2 42.0 - - + +
740B LEU* 4.1 18.4 - - + -
741B GLU* 3.4 24.5 - - + +
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Residues in contact with GLU 661 (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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570B ARG* 5.0 4.0 + - - -
572B TYR* 3.2 37.4 + - + -
657B SER 3.1 17.0 + - - +
658B LYS* 3.7 12.2 - - - +
659B ALA 3.0 0.6 - - - -
660B VAL* 1.3 79.1 - - - +
662B LYS* 1.3 58.8 + - - +
664B LEU* 5.0 0.9 - - - -
665B ASN* 2.8 50.7 + - - +
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Residues in contact with LYS 662 (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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658B LYS 3.4 9.9 + - - +
659B ALA* 3.0 8.4 + - - +
661B GLU* 1.3 78.7 - - - +
663B ALA* 1.3 62.3 + - - +
664B LEU 3.1 1.6 - - - -
666B SER* 2.7 50.7 + - - -
667B SER 3.1 7.9 - - - +
670B ASP* 3.8 33.0 - - + +
671B ALA* 3.8 15.9 - - + +
674B LEU* 4.2 17.0 - - + -
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Residues in contact with ALA 663 (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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472B THR* 2.9 28.9 + - - +
476B LEU* 3.5 8.1 - - - +
659B ALA 2.8 18.4 + - - +
660B VAL 4.2 0.9 - - - +
662B LYS* 1.3 73.8 - - - +
664B LEU* 1.3 57.6 + - - +
667B SER 3.6 10.3 + - - -
668B LEU* 3.6 22.2 - - + -
671B ALA* 4.0 1.5 - - + +
723B PHE* 3.8 6.1 - - + -
737B LEU* 3.5 30.5 - - + -
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Residues in contact with LEU 664 (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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472B THR* 3.9 9.5 - - - +
476B LEU* 4.3 24.8 - - + +
477B SER* 4.8 14.0 + - - -
510B ALA* 5.6 4.0 - - - +
517B ARG* 3.7 41.5 - - - +
660B VAL* 3.4 30.2 + - + +
661B GLU* 4.2 3.6 - - - +
662B LYS 3.1 0.8 - - - -
663B ALA* 1.3 80.8 - - - +
665B ASN* 1.3 68.2 + - - +
734B ALA* 5.5 5.2 - - + +
737B LEU* 4.0 26.2 - - + -
741B GLU* 4.7 2.2 - - - +
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Residues in contact with ASN 665 (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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472B THR* 4.5 2.0 - - - -
484B LYS* 5.6 4.0 + - - -
661B GLU* 2.8 43.0 + - - +
664B LEU* 1.3 88.9 - - - +
666B SER* 1.3 64.3 + - - +
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Residues in contact with SER 666 (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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472B THR* 3.2 20.3 - - - +
473B ALA* 4.8 2.4 + - - +
662B LYS* 2.7 42.6 + - - -
665B ASN* 1.3 75.4 - - - +
667B SER* 1.3 68.3 + - - -
670B ASP* 3.3 18.7 + - - -
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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
------------------------------------------------------------
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