Contacts of the helix formed by residues 643 - 658 (chain D) in PDB entry 3RMD
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 643 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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641D PHE* 4.0 0.7 - - - +
642D ARG* 1.3 108.8 + - + +
644D THR* 1.3 67.4 + - - +
645D ASN* 3.3 26.2 + - - +
646D HIS* 3.2 20.9 + - - +
647D TRP* 3.8 4.0 + - - -
693D LEU* 3.3 20.3 - - - +
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Residues in contact with THR 644 (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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643D ASP* 1.3 70.3 - - - +
645D ASN* 1.3 62.3 + - - +
646D HIS 2.8 10.5 + - - -
647D TRP* 3.1 38.5 + - - +
648D VAL* 3.1 12.9 - - + +
692D PRO* 3.3 7.3 - - - +
693D LEU* 2.6 30.3 + - - +
713D TRP* 3.6 48.9 - - + -
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Residues in contact with ASN 645 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643D ASP* 3.3 16.4 + - - +
644D THR* 1.3 78.2 - - - +
646D HIS* 1.3 60.6 + - - +
648D VAL* 3.6 8.8 + - - +
649D ASP* 3.2 29.1 + - - +
713D TRP* 6.2 0.8 - - - +
719D ARG* 3.3 36.1 + - - +
720D TYR 5.7 0.7 - - - +
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Residues in contact with HIS 646 (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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640D LYS 4.9 3.4 + - - -
641D PHE* 3.9 12.1 - + + +
642D ARG* 2.7 67.0 + - + +
643D ASP* 3.2 25.9 + - - +
644D THR 2.8 2.8 + - - -
645D ASN* 1.3 78.3 - - - +
647D TRP* 1.3 58.9 + - - +
649D ASP* 3.5 13.3 + - + +
650D PHE* 3.2 22.9 + - - +
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Residues in contact with TRP 647 (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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406D TYR* 3.2 49.2 + + - -
633D ILE* 4.0 11.4 - - + -
638D GLU* 6.2 0.4 - - + -
641D PHE* 3.5 31.6 - - + -
643D ASP 3.8 3.8 + - - -
644D THR* 3.1 37.1 + - + +
646D HIS* 1.3 77.0 - - - +
648D VAL* 1.3 78.3 + - + +
650D PHE* 3.7 1.5 - - - +
651D LEU* 3.0 44.6 + - + +
688D ILE* 3.9 13.2 - - + -
689D ALA 3.6 7.0 - - - -
690D GLY* 3.6 18.6 - - - -
691D PRO 3.9 17.4 + - - -
693D LEU* 4.3 13.8 - - + +
713D TRP* 3.9 13.5 - + - -
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Residues in contact with VAL 648 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644D THR* 3.1 27.6 - - + +
645D ASN* 3.9 6.7 - - - +
646D HIS 3.2 0.6 - - - -
647D TRP* 1.3 105.7 - - + +
649D ASP* 1.3 54.8 + - - +
651D LEU* 3.5 0.3 + - - +
652D ASP* 2.9 25.8 + - - +
688D ILE* 3.6 27.3 - - + +
713D TRP* 3.9 26.5 - - + -
714D ASP* 4.1 6.1 - - + -
719D ARG* 2.7 32.2 + - - +
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Residues in contact with ASP 649 (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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645D ASN* 3.2 17.2 + - - +
646D HIS* 3.5 18.5 - - + +
648D VAL* 1.3 74.9 - - - +
650D PHE* 1.3 60.8 + - - +
652D ASP* 3.1 9.9 + - - +
653D LYS* 2.8 32.2 + - - +
719D ARG* 2.6 35.7 + - - +
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Residues in contact with PHE 650 (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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897B LEU* 4.6 24.9 - - + -
898B PHE* 3.5 33.0 - + - -
901B PHE* 3.8 14.6 - + - -
632D ILE* 3.7 42.6 - - + -
633D ILE* 3.8 24.5 - - + -
636D VAL* 4.2 11.4 - - + -
641D PHE* 3.8 23.3 - + + -
646D HIS 3.2 6.9 + - - +
647D TRP 3.7 4.9 - - - +
648D VAL 3.4 0.4 - - - -
649D ASP* 1.3 79.7 - - - +
651D LEU* 1.3 62.2 + - + +
653D LYS* 3.3 5.3 + - - +
654D PHE* 2.8 28.2 + + + +
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Residues in contact with LEU 651 (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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406D TYR* 4.8 1.1 - - + -
407D VAL 5.7 1.1 - - - +
408D MET* 3.8 25.0 - - + +
629D ALA* 3.5 34.8 - - + -
632D ILE* 4.0 25.1 - - + -
633D ILE* 4.0 10.8 - - + -
647D TRP* 3.0 46.5 + - + +
648D VAL 3.9 3.1 - - - +
650D PHE* 1.3 80.9 - - + +
652D ASP* 1.3 60.2 + - - +
654D PHE* 3.8 4.3 - - + +
655D ALA* 2.8 32.7 + - - +
688D ILE* 4.3 13.2 - - + -
689D ALA 5.6 0.4 - - - +
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Residues in contact with ASP 652 (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 VAL 2.9 15.5 + - - +
649D ASP* 3.4 15.5 - - - +
651D LEU* 1.3 77.2 - - - +
653D LYS* 1.3 61.5 + - - +
655D ALA* 3.9 3.2 - - - +
656D ARG* 2.6 63.7 + - - +
685D ARG* 3.2 27.5 + - - +
688D ILE* 3.7 14.1 - - + +
714D ASP* 5.7 2.7 - - - -
717D GLY* 5.1 2.4 - - - -
719D ARG* 4.9 5.6 - - - +
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Residues in contact with LYS 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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898B PHE* 3.7 18.6 - - + -
649D ASP 2.8 15.9 + - - +
650D PHE* 3.6 6.3 - - - +
652D ASP* 1.3 78.6 + - - +
654D PHE* 1.3 57.9 + - - +
656D ARG* 3.4 12.7 + - - +
657D GLU* 2.9 42.1 + - - +
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Residues in contact with PHE 654 (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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898B PHE* 3.4 18.6 - + + -
901B PHE* 3.4 47.8 - + - -
408D MET* 4.9 2.9 - - + -
604D TYR* 4.6 5.6 - + - -
605D LEU* 3.8 17.5 - - + -
608D VAL* 4.6 7.6 - - + -
609D CYS* 5.9 1.1 - - - -
632D ILE* 3.9 25.4 - - + -
650D PHE* 2.8 25.7 + - + +
651D LEU* 3.8 8.1 - - + +
653D LYS* 1.3 74.7 - - - +
655D ALA* 1.3 59.1 + - + +
658D ARG* 3.0 42.2 + - + +
659D MET* 3.2 34.7 + - + -
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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
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408D MET* 3.6 22.4 - - + -
410D PHE* 4.0 11.2 - - + -
651D LEU 2.8 18.3 + - - +
652D ASP 3.9 3.6 - - - +
654D PHE* 1.3 78.2 - - - +
656D ARG* 1.3 58.3 + - - +
659D MET* 3.0 13.8 + - - +
660D GLU* 2.7 33.4 + - - +
685D ARG* 3.8 19.7 - - + -
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Residues in contact with ARG 656 (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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652D ASP* 2.6 49.9 + - - +
653D LYS* 3.4 12.9 - - - +
655D ALA* 1.3 80.0 - - - +
657D GLU* 1.3 79.2 + - + +
660D GLU* 3.2 15.7 - - + +
661D PRO* 3.2 21.5 - - - +
685D ARG* 5.6 1.9 - - - +
717D GLY* 6.3 0.4 - - - -
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Residues in contact with GLU 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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898B PHE* 4.4 16.2 - - + -
653D LYS* 2.9 23.3 + - - +
656D ARG* 1.3 104.1 + - - +
658D ARG* 1.3 72.9 + - - +
661D PRO* 3.4 15.7 - - - +
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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
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898B PHE* 4.1 40.2 + - + +
901B PHE* 5.6 3.8 - - + +
902B ASP* 5.0 9.5 + - - -
604D TYR* 3.1 33.9 + - - +
608D VAL* 5.5 6.9 - - + +
654D PHE* 3.0 41.5 + - + +
657D GLU* 1.3 94.4 - - - +
659D MET* 1.3 61.7 - - - +
661D PRO* 3.5 4.2 - - - +
662D ALA* 3.5 12.6 + - - +
665D ARG* 5.0 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