Contacts of the helix formed by residues 643 - 658 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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641B PHE* 4.1 1.0 - - - +
642B ARG* 1.3 105.1 + - - +
644B THR* 1.3 69.7 + - + +
645B ASN* 3.2 12.4 + - - +
646B HIS* 3.0 34.4 + - - +
647B TRP* 3.7 4.2 + - - -
693B LEU* 3.4 18.3 - - - +
73C LYS* 5.5 12.1 - - + -
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Residues in contact with THR 644 (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 ASP* 1.3 72.2 - - + +
645B ASN* 1.3 67.5 + - + +
646B HIS 2.8 10.6 + - - -
647B TRP* 3.0 37.6 + - - +
648B VAL* 3.3 7.0 + - - +
692B PRO* 4.5 0.4 - - - -
693B LEU* 3.5 21.4 + - - +
713B TRP* 3.7 31.0 - - + -
73C LYS* 5.5 3.1 - - - -
77C ASP* 2.9 42.6 - - - +
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Residues in contact with ASN 645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642B ARG* 5.3 1.3 - - - +
643B ASP* 3.2 10.2 + - - +
644B THR* 1.3 83.9 + - + +
646B HIS* 1.3 50.4 + - - +
647B TRP 3.5 0.2 - - - -
648B VAL* 3.6 9.3 + - - +
649B ASP* 2.3 44.7 + - - +
713B TRP* 5.6 4.8 - - - -
719B ARG* 2.8 47.8 + - - +
720B TYR 5.2 1.7 - - - +
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Residues in contact with HIS 646 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640B LYS 4.1 5.6 + - - -
641B PHE* 3.5 25.3 - + + -
642B ARG* 2.4 69.8 + - - +
643B ASP* 3.0 25.4 + - - +
644B THR 2.8 1.6 + - - -
645B ASN* 1.3 73.9 - - - +
647B TRP* 1.3 57.1 + - - +
649B ASP* 2.6 20.8 + - - +
650B PHE* 3.2 12.8 + - - +
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Residues in contact with TRP 647 (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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406B TYR* 3.7 27.9 + + - -
633B ILE* 4.1 12.8 - - + -
641B PHE* 4.0 25.5 - + + -
643B ASP 3.9 3.8 - - - -
644B THR* 3.0 42.4 + - - +
646B HIS* 1.3 76.5 - - - +
648B VAL* 1.3 72.1 + - + +
650B PHE* 3.5 7.7 - - - +
651B LEU* 2.9 54.4 + - + +
688B ILE* 3.7 15.0 - - + -
689B ALA 3.8 2.7 - - - -
690B GLY* 3.5 27.6 - - - -
691B PRO 3.6 23.4 + - - -
693B LEU* 4.2 17.2 - - + +
713B TRP* 3.7 22.7 - + - -
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Residues in contact with VAL 648 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644B THR* 3.3 17.2 + - - +
645B ASN* 3.6 13.9 - - - +
646B HIS 3.2 0.2 - - - -
647B TRP* 1.3 98.8 - - + +
649B ASP* 1.3 57.6 + - - +
651B LEU* 3.3 0.5 + - - +
652B ASP* 2.9 24.4 + - - +
688B ILE* 3.6 11.0 - - + +
713B TRP* 3.8 30.5 - - + -
714B ASP* 4.0 12.8 - - + -
719B ARG* 3.2 38.4 - - - +
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Residues in contact with ASP 649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642B ARG* 5.9 0.2 + - - -
645B ASN* 2.3 39.6 + - - +
646B HIS* 2.6 20.6 + - - +
648B VAL* 1.3 72.1 - - - +
650B PHE* 1.3 59.0 + - - +
652B ASP* 3.4 9.9 - - + +
653B LYS* 2.8 32.6 + - - +
719B ARG* 3.7 13.2 + - - +
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Residues in contact with PHE 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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632B ILE* 3.6 36.3 - - + -
633B ILE* 4.4 3.8 - - + -
635B LYS* 6.1 0.7 - - + -
636B VAL* 3.7 24.0 - - + -
641B PHE* 3.8 30.5 - + + -
646B HIS 3.2 15.2 + - - +
647B TRP* 3.3 12.1 + - - +
649B ASP* 1.3 75.1 + - - +
651B LEU* 1.3 67.0 + - + +
653B LYS* 3.8 7.2 - - + +
654B PHE* 2.9 41.1 + + + +
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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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406B TYR* 4.9 2.0 - - + -
407B VAL 5.6 0.4 - - - +
408B MET* 3.9 21.5 - - + +
629B ALA* 3.9 24.0 - - + -
632B ILE* 3.4 33.4 - - + -
633B ILE* 3.8 14.1 - - + -
647B TRP* 2.9 48.3 + - + +
648B VAL 3.6 3.4 - - - +
650B PHE* 1.3 78.6 - - + +
652B ASP* 1.3 59.7 + - - +
654B PHE* 3.1 7.1 + - + +
655B ALA* 2.8 33.8 + - - +
688B ILE* 4.0 12.6 - - + -
689B ALA 5.5 0.7 - - - +
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Residues in contact with ASP 652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B VAL 2.9 15.4 + - - +
649B ASP* 3.1 14.4 + - + +
651B LEU* 1.3 76.8 - - - +
653B LYS* 1.3 61.1 + - - +
655B ALA* 3.8 3.5 - - - +
656B ARG* 3.1 42.0 + - - +
685B ARG* 3.1 22.7 + - - +
688B ILE* 3.9 12.7 - - + +
714B ASP* 3.7 6.1 - - - +
717B GLY* 5.0 5.4 - - - +
719B ARG* 3.6 17.0 + - - +
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Residues in contact with LYS 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 ASP 2.8 19.5 + - - +
650B PHE* 3.8 7.0 - - + +
652B ASP* 1.3 71.3 - - - +
654B PHE* 1.3 61.9 + - - +
656B ARG* 3.8 16.8 - - - +
657B GLU* 2.5 78.1 + - - +
658B ARG* 5.9 2.4 - - - +
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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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604B TYR* 4.4 6.5 - + - -
605B LEU* 3.9 17.5 - - + -
608B VAL* 4.6 13.5 - - + -
632B ILE* 3.7 42.8 - - + -
650B PHE* 2.9 32.9 + + + +
651B LEU* 3.6 11.7 - - + +
653B LYS* 1.3 78.7 - - - +
655B ALA* 1.3 57.9 + - - +
657B GLU* 5.3 0.4 - - - -
658B ARG* 2.9 63.0 + - + +
659B MET* 3.1 33.4 + - + -
897D LEU* 4.6 6.3 - - + -
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Residues in contact with ALA 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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408B MET* 3.2 37.2 - - + -
410B PHE* 4.1 6.7 - - + -
651B LEU 2.8 12.9 + - - +
652B ASP 3.8 4.0 - - - +
654B PHE* 1.3 73.8 - - - +
656B ARG* 1.3 53.1 + - - +
659B MET* 3.0 18.7 + - - +
660B GLU* 2.7 36.1 + - - +
685B ARG* 4.1 15.5 - - + -
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Residues in contact with ARG 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 ASP* 3.1 34.4 + - - +
653B LYS* 3.7 19.2 - - - +
655B ALA* 1.3 79.0 - - - +
657B GLU* 1.3 86.7 + - + +
660B GLU* 3.3 24.3 - - + +
661B PRO* 3.2 22.2 - - - +
685B ARG* 5.6 1.1 - - + +
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Residues in contact with GLU 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 LYS* 2.5 59.2 + - - +
654B PHE* 5.3 0.2 - - - -
656B ARG* 1.3 107.1 + - + +
658B ARG* 1.3 72.1 + - - +
661B PRO* 3.4 15.7 - - - +
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Residues in contact with ARG 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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604B TYR* 3.3 36.9 + - - +
653B LYS* 5.9 2.5 - - - +
654B PHE* 2.9 46.4 + - + +
657B GLU* 1.3 92.8 + - - +
659B MET* 1.3 64.7 + - - +
661B PRO* 3.7 4.6 - - - +
662B ALA 3.5 12.1 + - - -
665B ARG* 5.0 1.6 + - - +
897D LEU* 3.8 35.8 - - + +
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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