Contacts of the helix formed by residues 639 - 655 (chain B) in PDB entry 5ULM
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 639 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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549B ALA* 3.2 33.0 - - + +
551B LYS 4.5 6.0 + - - +
620B ARG* 4.1 11.3 - - - +
637B PHE* 3.7 6.8 - - - +
638B CYS* 1.3 84.4 - - - +
640B GLU* 1.3 64.2 - - - +
641B LEU* 3.3 9.3 + - - +
642B HIS* 2.7 43.2 + - + +
643B CYS* 3.3 10.7 + - - +
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Residues in contact with GLU 640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B THR* 4.2 13.9 + - - -
291B GLU* 5.6 4.1 - - - +
614B ILE* 6.1 0.2 - - - +
619B GLU* 3.2 53.9 - - + +
620B ARG* 4.0 5.8 - - + +
639B THR* 1.3 73.5 - - - +
641B LEU* 1.3 59.7 + - - +
643B CYS* 3.3 5.2 + - - +
644B LYS* 3.0 30.0 + - + +
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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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551B LYS 5.6 0.9 - - - +
552B THR* 3.2 31.0 - - - +
554B VAL* 3.9 19.1 - - + +
639B THR* 3.3 9.1 + - - +
640B GLU* 1.3 81.2 - - - +
642B HIS* 1.3 57.1 + - - +
644B LYS* 3.2 13.3 + - + +
645B LYS* 2.9 56.1 + - + +
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Residues in contact with HIS 642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548B GLU* 2.8 56.3 + - + +
551B LYS* 3.9 12.8 - - + -
554B VAL* 3.6 38.0 - - + +
556B VAL* 4.6 0.7 - - + -
559B PHE* 3.8 21.1 - + + -
637B PHE* 3.8 18.1 - - + -
638B CYS* 3.7 12.5 - - - -
639B THR* 2.7 36.2 + - + +
640B GLU 3.3 0.4 - - - -
641B LEU* 1.3 76.0 - - - +
643B CYS* 1.3 62.4 + - - +
645B LYS* 3.4 5.5 + - - +
646B PHE* 3.2 21.8 + - - +
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Residues in contact with CYS 643 (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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614B ILE* 4.0 11.9 - - - -
619B GLU 3.7 14.6 - - - +
620B ARG 3.6 15.0 - - - +
621B CYS 3.4 35.0 - - - -
622B CYS* 3.7 12.6 - - - -
637B PHE* 3.6 15.3 - - + +
639B THR 3.3 5.7 + - - +
640B GLU 3.5 8.7 - - - +
642B HIS* 1.3 79.6 - - - +
644B LYS* 1.3 61.0 + - - +
646B PHE* 3.2 4.5 + - - +
647B PHE* 3.1 22.0 + - - +
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Residues in contact with LYS 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614B ILE* 3.6 28.8 - - + +
640B GLU* 3.0 18.5 + - + +
641B LEU* 3.2 19.2 + - + +
643B CYS* 1.3 72.9 - - - +
645B LYS* 1.3 65.4 + - + +
647B PHE* 3.4 23.5 + - - +
648B GLU* 3.1 53.1 + - - +
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Residues in contact with LYS 645 (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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554B VAL* 3.9 44.0 - - + +
559B PHE* 4.7 7.0 - - + -
641B LEU* 2.9 43.4 + - + +
642B HIS 3.7 6.5 - - - +
643B CYS 3.3 0.2 - - - -
644B LYS* 1.3 76.2 - - - +
646B PHE* 1.3 58.6 + - - +
648B GLU* 3.4 16.6 + - - +
649B MET* 3.0 38.4 + - + +
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Residues in contact with PHE 646 (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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559B PHE* 4.8 8.4 - + + -
575B LEU* 3.4 47.3 - - + -
577B ILE* 3.8 15.9 - - + -
586B ILE* 4.8 2.5 - - + -
612B VAL* 4.0 20.9 - - + -
622B CYS* 4.0 20.2 - - + -
624B LEU* 4.6 12.3 - - + -
635B ILE* 4.2 12.8 - - + -
637B PHE* 3.3 33.9 - + + -
642B HIS 3.2 3.9 + - - +
643B CYS 3.2 4.9 + - - +
645B LYS* 1.3 74.2 - - - +
647B PHE* 1.3 63.1 + - - +
649B MET* 3.3 6.7 + - - +
650B VAL* 2.9 53.0 + - + +
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Residues in contact with PHE 647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612B VAL* 3.4 46.1 - - + +
613B SER* 4.2 6.5 - - - -
614B ILE* 3.6 32.3 - - + -
622B CYS* 4.2 4.9 - - - -
643B CYS 3.1 12.9 + - - +
644B LYS* 3.5 31.9 - - - +
646B PHE* 1.3 82.3 - - - +
648B GLU* 1.3 64.9 - - + +
650B VAL 3.4 0.5 + - - -
651B ASN* 3.0 53.8 + - - +
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Residues in contact with GLU 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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644B LYS* 3.1 46.0 + - - +
645B LYS* 3.7 22.3 + - - +
647B PHE* 1.3 86.3 - - + +
649B MET* 1.3 59.7 + - + +
651B ASN* 3.5 7.1 + - - +
652B THR* 2.9 33.3 + - - +
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Residues in contact with MET 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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556B VAL 6.2 0.2 - - - +
559B PHE* 4.9 14.6 - - - -
577B ILE* 3.4 47.8 - - + +
645B LYS* 3.0 26.8 + - + +
646B PHE* 3.3 5.4 + - - +
648B GLU* 1.3 75.2 - - + +
650B VAL* 1.3 58.9 + - - +
652B THR* 3.3 9.1 + - - -
653B ILE* 3.1 32.7 + - - +
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Residues in contact with VAL 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577B ILE* 4.3 5.2 - - + -
586B ILE* 3.9 17.7 - - + -
609B VAL* 3.9 26.0 - - + -
611B GLY 4.9 1.1 - - - -
612B VAL* 3.6 28.0 - - + -
646B PHE* 2.9 53.4 + - + +
647B PHE 3.9 0.9 - - - +
649B MET* 1.3 71.8 - - - +
651B ASN* 1.3 66.7 + - - +
653B ILE* 3.2 8.1 + - + +
654B THR* 3.0 27.5 + - + +
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Residues in contact with ASN 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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611B GLY* 5.6 2.0 - - - -
612B VAL* 3.7 17.5 + - - +
647B PHE* 3.0 53.1 + - - +
648B GLU* 3.7 7.3 + - - +
650B VAL* 1.3 73.4 - - - +
652B THR* 1.3 62.0 + - - +
654B THR* 3.3 9.8 + - - -
655B GLU* 3.1 48.9 + - - +
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Residues in contact with THR 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 GLU 2.9 16.7 + - - -
649B MET* 3.5 11.5 - - - -
650B VAL 3.2 0.4 - - - -
651B ASN* 1.3 78.4 - - - +
653B ILE* 1.3 64.4 + - + +
655B GLU* 3.4 22.4 + - - +
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Residues in contact with ILE 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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577B ILE* 4.4 20.2 - - + -
584B LYS* 4.2 32.3 - - + -
585B THR 5.2 3.1 - - - +
586B ILE* 4.0 33.4 - - + -
606B ALA* 4.0 28.3 - - + +
609B VAL* 5.4 0.7 - - + -
649B MET 3.1 12.1 + - - +
650B VAL* 3.2 20.6 + - + +
652B THR* 1.3 78.6 - - + +
654B THR* 1.3 64.4 + - + +
655B GLU 3.7 3.8 + - - +
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Residues in contact with THR 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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606B ALA 4.5 6.5 - - - +
609B VAL* 4.0 42.6 - - + +
610B ARG 4.9 8.0 + - - +
611B GLY* 5.0 3.5 - - - -
650B VAL* 3.0 22.8 + - + +
651B ASN* 3.3 17.5 + - - -
653B ILE* 1.3 79.9 - - + +
655B GLU* 1.3 62.5 + - - +
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Residues in contact with GLU 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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651B ASN* 3.1 43.5 + - - +
652B THR* 3.4 17.2 + - - +
653B ILE 3.4 4.6 - - - +
654B THR* 1.3 85.2 - - - +
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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