Contacts of the helix formed by residues 628 - 642 (chain B) in PDB entry 5MKE
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 THR 628 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A SER* 5.0 11.2 - - - +
247A TYR* 3.9 5.8 - - + -
248A TYR* 3.4 36.8 - - + +
382B ILE* 4.5 17.0 - - + +
383B ILE* 5.5 5.4 - - + -
616B TYR* 4.8 0.4 - - - -
626B PHE 3.1 2.2 + - - -
627B SER* 1.3 78.6 - - - +
629B PHE* 1.3 52.6 + - - +
630B GLN* 3.1 8.8 - - - +
631B GLU* 2.5 62.0 + - - +
632B CYS 3.5 1.2 + - - -
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Residues in contact with PHE 629 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A SER* 5.1 3.8 - - - -
1005A CHS 4.3 53.2 - - + +
609B LEU* 3.5 33.7 - - + -
612B ALA* 4.0 7.4 - - + -
613B GLN* 3.7 36.1 - - + -
616B TYR* 3.8 40.0 - + + -
627B SER 3.7 1.6 - - - -
628B THR* 1.3 71.1 - - - +
630B GLN* 1.3 69.4 + - - +
632B CYS* 3.1 15.8 + - + +
633B ILE* 3.4 8.6 + - + -
1010B PLM 4.4 17.3 - - + -
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Residues in contact with GLN 630 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380B TRP* 5.1 8.9 - - - -
382B ILE* 4.0 30.3 + - - +
628B THR* 2.7 14.1 + - - +
629B PHE* 1.3 80.0 - - - +
631B GLU* 1.3 61.9 + - - +
633B ILE* 2.5 44.5 + - + +
634B PHE* 3.5 11.0 + - + -
1009B PLM 2.9 37.2 + - + +
1010B PLM 4.6 19.6 - - + +
654C ARG* 5.7 4.0 + - - +
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Residues in contact with GLU 631 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A TYR* 5.5 2.6 - - - -
248A TYR* 5.3 3.1 + - - -
382B ILE* 5.1 5.9 - - - +
625B ASP* 3.5 38.6 + - - +
626B PHE 4.5 2.1 + - - +
628B THR* 2.5 36.1 + - - +
630B GLN* 1.3 79.1 - - + +
632B CYS* 1.3 56.5 + - - +
634B PHE* 2.9 33.2 + - + +
635B THR* 2.9 15.5 + - - +
638B ARG* 5.9 0.2 + - - -
650C GLU* 6.2 6.5 - - + -
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Residues in contact with CYS 632 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612B ALA* 3.8 23.6 - - + +
616B TYR* 4.5 10.3 - - - -
625B ASP 4.0 5.2 - - - -
626B PHE* 3.2 26.9 - - + -
627B SER* 2.6 42.8 - - - -
628B THR 3.5 0.2 + - - -
629B PHE* 3.1 15.1 + - + +
630B GLN 3.1 0.8 + - - -
631B GLU* 1.3 75.9 - - - +
633B ILE* 1.3 62.1 + - - +
635B THR* 4.0 3.7 - - - +
636B GLN* 3.3 21.8 + - - +
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Residues in contact with ILE 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608B PHE* 3.3 39.9 - - + -
609B LEU* 3.5 31.4 - - + -
612B ALA* 4.1 3.4 - - + -
629B PHE* 3.4 6.3 + - + +
630B GLN* 2.5 32.1 + - + +
632B CYS* 1.3 76.0 - - - +
634B PHE* 1.3 78.0 + - + +
636B GLN* 3.4 9.4 - - - +
637B PHE* 2.9 30.5 + - + -
1009B PLM 4.8 16.2 - - + -
1010B PLM 6.1 4.0 - - + -
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Residues in contact with PHE 634 (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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630B GLN* 3.7 25.8 - - + -
631B GLU* 2.9 18.4 + - + +
633B ILE* 1.3 84.6 - - + +
635B THR* 1.3 51.4 + - - +
636B GLN 2.8 4.5 - - - -
637B PHE* 2.4 33.6 + + - +
638B ARG* 2.7 17.5 + - + +
1009B PLM 4.9 26.2 - - + -
646C PHE* 4.7 17.3 - + + -
650C GLU* 5.5 8.5 - - + -
654C ARG 5.6 2.2 - - - -
658C PRO* 3.8 33.4 - - + -
659C ILE* 4.5 1.8 - - - -
661C PHE* 4.4 16.1 - + + -
662C THR* 3.2 27.6 - - - -
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Residues in contact with THR 635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625B ASP* 2.5 51.0 + - + +
626B PHE* 3.6 28.0 - - + -
631B GLU* 2.9 10.8 + - - +
632B CYS* 4.1 4.3 - - - -
634B PHE* 1.3 75.5 - - - +
636B GLN* 1.3 58.8 + - - +
638B ARG* 3.7 20.9 + - + -
639B ILE* 3.4 31.1 + - + +
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Residues in contact with GLN 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B ILE 3.8 0.6 + - - -
608B PHE* 2.2 86.5 + - + +
611B TYR* 3.6 12.1 - - - +
612B ALA* 3.1 26.2 - - + +
626B PHE* 6.1 1.1 - - + -
632B CYS 3.3 14.8 + - - +
633B ILE* 3.4 2.1 - - - +
634B PHE 2.8 0.4 + - - -
635B THR* 1.3 77.4 - - - +
637B PHE* 1.3 59.9 + - - +
639B ILE* 4.5 2.5 - - - -
640B ILE* 3.9 4.5 + - - +
660B TYR* 5.1 7.6 - - - +
664B PHE* 3.7 30.9 - - + -
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Residues in contact with PHE 637 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604B PHE* 4.9 10.5 - + - -
605B PHE* 6.4 1.1 - + - -
608B PHE* 3.4 26.2 - + - -
633B ILE* 2.9 36.6 - - + -
634B PHE* 2.4 27.8 + + - +
636B GLN* 1.3 66.8 - - - +
638B ARG* 1.3 65.1 + - - +
639B ILE 3.0 2.5 - - - -
640B ILE* 2.9 28.1 - - + +
641B LEU* 3.1 9.3 + - - +
1009B PLM 5.6 4.5 - - + -
661C PHE* 4.6 13.7 - + + -
662C THR* 3.8 35.2 - - + -
665C VAL* 4.4 22.8 - - + +
666C PHE* 5.1 17.9 - + + -
670C PHE* 5.7 7.2 - + - -
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Residues in contact with ARG 638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625B ASP* 3.4 33.4 + - - +
631B GLU* 5.9 0.2 + - - -
634B PHE* 2.7 17.7 + - + +
635B THR* 3.7 22.2 + - + +
636B GLN 3.6 0.4 - - - -
637B PHE* 1.3 73.5 - - - +
639B ILE* 1.3 50.1 + - + +
641B LEU* 3.5 8.3 + - + +
642B GLY 2.5 38.6 + - - +
643B ASP* 2.6 47.8 + - - +
644B ILE* 5.1 3.6 - - + +
645B ASN* 4.7 12.3 + - - +
644C ILE* 5.5 2.6 + - + -
646C PHE* 4.9 29.3 - - + +
647C ALA* 5.7 5.8 - - - +
661C PHE* 5.0 13.6 - - + -
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Residues in contact with ILE 639 (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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641A LEU* 3.7 21.4 - - + +
626B PHE* 4.8 6.3 - - + -
635B THR* 3.4 28.1 + - + +
636B GLN* 5.0 2.2 - - - +
637B PHE 2.9 1.8 + - - -
638B ARG* 1.3 73.3 - - + +
640B ILE* 1.3 61.9 + - - +
641B LEU 2.9 2.0 - - - -
642B GLY* 2.5 27.2 + - - -
644B ILE* 3.3 29.4 - - + -
649B ILE* 4.6 19.3 - - + -
660B TYR* 5.3 9.9 - - + +
661B PHE* 4.5 17.9 - - + -
664B PHE* 4.2 26.0 - - + -
665B VAL* 5.2 1.8 - - + -
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Residues in contact with ILE 640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A LEU* 4.8 8.4 - - - +
604B PHE* 6.2 1.6 - - + -
608B PHE* 5.6 1.3 - - + -
636B GLN 3.9 6.1 - - - +
637B PHE* 2.9 33.6 - - + +
639B ILE* 1.3 79.6 - - - +
641B LEU* 1.3 60.1 + - + +
664B PHE* 4.5 16.6 - - + -
665B VAL* 6.1 1.1 - - - -
669B PHE* 4.2 28.1 - - + -
672B LEU* 3.3 41.7 - - + -
673B LEU* 5.8 0.2 - - + -
665C VAL* 6.5 0.9 - - + -
669C PHE* 4.2 26.8 - - + -
670C PHE* 4.9 6.5 - - + -
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Residues in contact with LEU 641 (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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641A LEU* 4.5 9.2 - - - +
637B PHE 3.1 12.2 + - - +
638B ARG* 3.5 11.2 - - + +
639B ILE 2.7 5.6 + - - -
640B ILE* 1.3 77.8 - - + +
642B GLY* 1.3 63.8 + - - +
643B ASP* 5.3 2.7 - - + +
639C ILE* 3.8 30.7 - - + +
640C ILE* 4.9 6.3 - - - +
641C LEU 4.7 7.5 - - - +
642C GLY* 3.8 27.6 - - - -
643C ASP 4.7 1.1 - - - +
644C ILE* 4.7 14.1 - - + -
661C PHE* 4.8 9.0 - - + -
665C VAL* 3.7 30.1 - - + -
669C PHE* 5.9 8.7 - - + -
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Residues in contact with GLY 642 (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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641A LEU* 3.6 15.7 - - - -
642A GLY* 6.1 0.7 - - - -
638B ARG 2.5 24.5 + - - +
639B ILE 2.5 15.6 + - - -
641B LEU* 1.3 80.3 - - - +
643B ASP* 1.3 71.3 + - - +
644B ILE* 2.9 16.0 + - - +
642C GLY* 6.1 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
------------------------------------------------------------
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