Contacts of the helix formed by residues 654 - 671 (chain D) in PDB entry 1XMI
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 SER 654 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577D TYR* 4.4 4.0 + - - -
652D GLN 3.4 3.9 + - - -
653D PHE* 1.3 77.5 - - - +
655D ALA* 1.3 63.8 + - - +
656D GLU* 3.7 12.4 + - - +
657D ARG* 3.4 22.4 + - - +
658D ARG* 3.1 24.3 + - - +
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Residues in contact with ALA 655 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654D SER* 1.3 75.1 - - - +
656D GLU* 1.3 58.4 + - - +
658D ARG* 3.4 28.9 + - - +
659D ASN* 2.9 41.1 + - - +
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Residues in contact with GLU 656 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553D ARG* 4.9 13.4 + - - -
577D TYR* 3.3 29.0 + - + +
654D SER* 3.7 10.7 - - - +
655D ALA* 1.3 76.7 - - - +
657D ARG* 1.3 62.2 + - - +
659D ASN* 4.2 7.0 - - - +
660D SER* 3.0 27.7 + - - -
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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
----------------------------------------------------------
573D SER* 5.2 2.0 + - - -
576D GLY* 3.1 38.3 + - - +
577D TYR* 3.6 38.9 - - + -
648D ASP* 2.9 38.6 + - - -
653D PHE* 3.3 45.8 - - + +
654D SER* 3.4 21.0 + - - +
655D ALA 3.3 0.6 - - - -
656D GLU* 1.3 78.9 - - - +
658D ARG* 1.3 64.0 + - - +
660D SER* 3.3 3.5 + - - -
661D ILE* 3.1 27.8 + - - +
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Residues in contact with ARG 658 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650D PHE* 3.7 38.7 + - + -
651D ASP 5.5 2.6 + - - -
653D PHE* 3.0 33.4 + - + -
654D SER* 3.1 14.4 + - - +
655D ALA* 3.4 34.3 + - - +
657D ARG* 1.3 76.9 - - - +
659D ASN* 1.3 61.1 + - - +
661D ILE* 3.3 12.8 + - - +
662D LEU* 3.1 32.4 + - + +
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Residues in contact with ASN 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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494A PHE* 3.5 46.2 - - + +
655D ALA* 2.9 29.4 + - - +
656D GLU* 4.2 6.4 - - - +
658D ARG* 1.3 76.7 + - - +
660D SER* 1.3 56.0 + - - +
662D LEU* 3.7 12.2 - - - +
663D THR* 2.5 38.8 + - - +
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Residues in contact with SER 660 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549D SER* 6.2 0.2 - - - -
550D GLY* 3.2 13.4 - - - +
551D GLY 3.1 22.2 + - - +
577D TYR* 2.7 36.2 + - - +
656D GLU 3.0 19.8 + - - -
657D ARG 3.3 5.8 + - - -
659D ASN* 1.3 75.4 - - - +
661D ILE* 1.3 62.8 + - - +
663D THR* 3.5 7.8 + - - +
664D GLU* 3.1 25.5 + - - +
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Residues in contact with ILE 661 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ATP 4.6 16.6 - - - +
576D GLY 3.9 9.0 - - - +
577D TYR 4.0 9.4 - - - +
578D LEU 3.6 18.4 - - - +
579D ASP* 3.8 20.4 - - + +
580D VAL 5.4 0.7 - - - +
650D PHE* 4.7 6.3 - - + -
653D PHE* 3.7 35.9 - - + -
657D ARG 3.1 17.7 + - - +
658D ARG* 3.5 9.2 - - - +
659D ASN 3.3 0.2 - - - -
660D SER* 1.3 76.0 - - - +
662D LEU* 1.3 60.4 + - + +
664D GLU* 3.4 4.7 + - - +
665D THR* 3.0 32.2 + - - +
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Residues in contact with LEU 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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465A THR* 4.9 7.6 - - + -
469A MET* 3.6 29.8 - - + -
490A PHE* 4.6 3.2 - - + -
492A SER* 3.7 25.4 - - - +
493A GLN* 5.2 6.1 - - + -
494A PHE* 4.0 22.2 - - + +
572A ASP* 6.0 0.4 - - - +
658D ARG* 3.1 15.3 + - + +
659D ASN* 3.7 19.5 - - - +
660D SER 3.3 0.4 - - - -
661D ILE* 1.3 81.4 - - + +
663D THR* 1.3 57.8 + - - +
665D THR* 3.2 7.0 + - - +
666D LEU* 2.9 29.3 + - - +
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Residues in contact with THR 663 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A PHE* 3.7 19.3 - - + -
496A TRP* 4.0 39.4 + - + -
543A GLU* 5.4 1.1 - - - +
549D SER* 4.1 17.8 + - - -
550D GLY 6.1 0.2 - - - +
659D ASN 2.5 31.2 + - - +
660D SER* 3.9 7.9 + - - +
662D LEU* 1.3 72.3 - - - +
664D GLU* 1.3 63.0 + - - +
666D LEU* 3.6 9.5 - - - +
667D ARG* 2.9 28.2 + - - +
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Residues in contact with GLU 664 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549D SER* 4.4 5.0 + - - -
551D GLY* 3.6 20.4 + - - -
552D GLN 4.3 0.3 + - - -
555D ARG* 2.8 37.2 + - - -
577D TYR 4.0 7.2 - - - +
578D LEU* 3.9 5.7 - - + +
579D ASP* 3.2 21.3 - - - +
582D THR* 3.7 8.5 - - - +
660D SER 3.1 20.3 + - - +
661D ILE 3.5 5.2 - - - +
662D LEU 3.3 0.2 - - - -
663D THR* 1.3 79.7 + - - +
665D THR* 1.3 60.2 + - - +
667D ARG* 2.9 42.9 + - - +
668D ARG* 3.3 21.8 + - - +
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Residues in contact with THR 665 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A MET* 4.1 17.5 - - - +
472A MET* 4.0 17.3 - - - -
474A GLU* 3.3 30.3 + - + +
490A PHE* 4.0 19.7 - - + -
579D ASP* 3.5 5.6 - - - +
661D ILE* 3.0 18.2 + - - +
662D LEU* 3.3 12.1 - - - -
664D GLU* 1.3 74.5 - - - +
666D LEU* 1.3 63.2 + - - +
668D ARG* 3.4 7.2 + - - +
669D PHE* 3.2 28.6 - - + -
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Residues in contact with LEU 666 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490A PHE* 3.3 41.9 - - + +
491A CYS* 4.5 0.7 - - - -
492A SER* 3.8 29.8 - - - +
494A PHE* 3.9 8.3 - - + +
496A TRP* 3.8 40.4 - - + +
557A SER* 5.5 2.9 - - - +
560A ARG* 5.3 7.2 - - - +
662D LEU 2.9 17.5 + - - +
663D THR* 3.6 12.8 - - - +
664D GLU 3.4 0.2 - - - -
665D THR* 1.3 76.4 - - - +
667D ARG* 1.3 62.8 + - - +
669D PHE* 3.1 5.2 + - - +
670D SER* 2.9 31.8 + - - -
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Residues in contact with ARG 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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496A TRP* 4.4 17.2 - - + -
525D GLN* 3.9 16.4 + - - +
528D GLU* 6.2 3.9 - - - +
529D ASP* 4.9 7.4 - - - -
552D GLN* 6.1 0.2 - - - -
555D ARG* 3.8 23.1 - - - +
582D THR* 3.0 29.3 + - - +
663D THR 2.9 21.2 + - - +
664D GLU* 2.9 39.2 + - - +
666D LEU* 1.3 72.0 - - - +
668D ARG* 1.3 76.0 + - - +
671D LEU* 2.9 52.3 + - + +
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Residues in contact with ARG 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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474A GLU* 4.0 7.0 - - - -
512B TYR* 3.6 21.8 - - - -
514B GLU* 3.7 30.0 + - + +
515B TYR* 5.1 1.6 + - - +
525D GLN* 4.8 1.4 + - - -
579D ASP* 3.1 23.8 - - - -
581D LEU* 3.6 26.8 - - - +
582D THR* 3.1 21.7 + - - +
585D GLU* 2.6 43.4 + - - -
664D GLU 3.3 12.6 - - - +
665D THR 3.6 7.2 - - - +
666D LEU 3.2 0.8 - - - -
667D ARG* 1.3 93.2 - - - +
669D PHE* 1.3 74.0 + - + +
671D LEU 3.9 8.7 - - - +
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Residues in contact with PHE 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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472A MET* 3.6 53.4 - - + -
474A GLU* 5.0 2.5 - - - -
488A ILE* 3.7 42.0 - - + +
489A SER* 4.7 1.9 + - - -
490A PHE* 4.5 16.8 + - + +
564A LYS* 2.7 35.8 + - - +
514B GLU* 3.8 35.7 - - + -
581D LEU* 5.3 1.8 - - + -
665D THR* 3.2 28.3 - - + +
666D LEU 3.1 5.5 + - - +
668D ARG* 1.3 93.8 - - + +
670D SER* 1.3 59.3 + - - +
671D LEU 3.9 0.4 - - - -
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Residues in contact with SER 670 (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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490A PHE 5.8 2.5 - - - -
496A TRP* 4.8 3.7 - - - -
508A ALA* 3.2 20.8 - - - +
510A VAL* 5.3 4.5 - - - +
560A ARG* 3.2 33.3 - - - +
564A LYS* 5.2 4.3 - - - +
666D LEU* 2.9 23.8 + - - -
669D PHE* 1.3 81.1 - - - +
671D LEU* 1.3 69.6 + - - +
672D GLU 4.9 2.2 - - - +
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Residues in contact with LEU 671 (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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496A TRP* 4.0 15.0 - - + -
498A MET* 3.7 41.3 - - + -
508A ALA* 4.2 12.3 - - + +
509A GLY* 6.1 0.4 - - - -
515B TYR* 4.9 2.6 - - - +
528D GLU* 4.6 12.6 - - + +
529D ASP* 6.0 1.6 - - - +
532D LYS* 4.7 15.0 - - + -
667D ARG* 2.9 33.7 + - + +
668D ARG* 3.9 10.6 - - - +
669D PHE 5.1 0.3 - - - -
670D SER* 1.3 92.6 + - - +
672D GLU* 1.3 74.0 + - - +
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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