Contacts of the helix formed by residues 639 - 655 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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549A ALA* 3.2 32.8 - - - +
551A LYS 4.5 6.5 + - - +
620A ARG* 4.1 11.3 - - - +
637A PHE* 3.7 6.2 - - - +
638A CYS* 1.3 84.7 - - - +
640A GLU* 1.3 64.2 + - - +
641A LEU* 3.3 8.6 + - - +
642A HIS* 2.7 43.7 + - + +
643A CYS* 3.3 10.9 + - - +
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Residues in contact with GLU 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A THR* 4.3 13.0 + - - -
619A GLU* 3.2 52.8 - - + +
620A ARG* 4.0 6.0 - - + +
639A THR* 1.3 73.7 - - - +
641A LEU* 1.3 64.9 + - - +
643A CYS* 3.3 5.5 + - - +
644A LYS* 3.0 25.0 + - + +
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Residues in contact with LEU 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551A LYS 5.6 0.9 - - - +
552A THR* 3.2 29.8 - - - +
554A VAL* 3.9 18.8 - - + +
639A THR* 3.3 8.7 + - - +
640A GLU* 1.3 81.8 - - - +
642A HIS* 1.3 57.2 + - - +
644A LYS* 3.2 13.1 + - + +
645A LYS* 2.9 54.6 + - + +
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Residues in contact with HIS 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A GLU* 2.8 56.4 + - + +
551A LYS* 3.9 12.6 - - + -
554A VAL* 3.6 37.6 - - + +
556A VAL* 4.6 0.9 - - + -
559A PHE* 3.7 21.9 - + + -
637A PHE* 3.8 18.1 - - + -
638A CYS* 3.7 13.7 - - - -
639A THR* 2.7 35.4 + - + +
640A GLU 3.3 0.2 - - - -
641A LEU* 1.3 75.0 - - - +
643A CYS* 1.3 63.4 + - - +
645A LYS* 3.4 5.5 + - - +
646A PHE* 3.2 21.5 + - - +
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Residues in contact with CYS 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614A ILE* 4.0 12.6 - - - -
619A GLU 3.7 15.5 - - - +
620A ARG 3.6 15.3 - - - +
621A CYS 3.4 34.1 - - - -
622A CYS* 3.7 13.0 - - - -
637A PHE* 3.6 14.0 - - + -
639A THR 3.3 5.8 + - - +
640A GLU 3.5 8.5 - - - +
642A HIS* 1.3 79.8 - - - +
644A LYS* 1.3 61.2 + - - +
646A PHE* 3.2 4.7 + - - +
647A PHE* 3.1 21.5 + - - +
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Residues in contact with LYS 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614A ILE* 3.6 28.4 - - + +
640A GLU* 3.0 18.5 + - + +
641A LEU* 3.2 18.4 + - + +
643A CYS* 1.3 74.0 - - - +
645A LYS* 1.3 65.9 + - + +
647A PHE* 3.4 24.5 + - - +
648A GLU* 3.0 53.9 + - - +
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Residues in contact with LYS 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554A VAL* 3.9 43.7 - - + +
559A PHE* 4.7 1.8 - - + -
641A LEU* 2.9 42.9 + - + +
642A HIS 3.7 6.1 - - - +
643A CYS 3.3 0.2 - - - -
644A LYS* 1.3 76.4 - - - +
646A PHE* 1.3 58.1 + - - +
648A GLU* 3.4 17.2 + - - +
649A MET* 3.0 43.5 + - + +
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Residues in contact with PHE 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559A PHE* 4.8 2.0 - + + -
575A LEU* 3.4 47.1 - - + -
577A ILE* 3.8 15.7 - - + -
586A ILE* 4.8 2.7 - - + -
612A VAL* 4.0 20.4 - - + -
622A CYS* 4.0 19.7 - - + -
624A LEU* 4.6 12.1 - - + -
635A ILE* 4.2 14.1 - - + -
637A PHE* 3.3 33.7 - + + -
642A HIS 3.2 4.5 + - - +
643A CYS 3.5 4.3 - - - +
645A LYS* 1.3 75.1 - - - +
647A PHE* 1.3 61.7 + - - +
649A MET* 3.3 13.1 + - + +
650A VAL* 2.9 53.6 + - + +
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Residues in contact with PHE 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612A VAL* 3.4 45.7 - - + +
613A SER* 4.2 6.1 - - - -
614A ILE* 3.6 33.7 - - + -
622A CYS* 4.2 4.0 - - - -
643A CYS 3.1 13.1 + - - +
644A LYS* 3.5 32.8 - - - +
646A PHE* 1.3 80.8 - - - +
648A GLU* 1.3 63.2 + - + +
650A VAL 3.3 1.6 + - - -
651A ASN* 3.0 53.7 + - - +
453B ARG* 3.5 31.9 - - - -
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Residues in contact with GLU 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644A LYS* 3.0 47.1 + - - +
645A LYS* 3.7 21.9 + - - +
647A PHE* 1.3 88.0 - - + +
649A MET* 1.3 60.0 + - + +
651A ASN* 3.5 8.0 + - - +
652A THR* 2.9 32.0 + - - +
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Residues in contact with MET 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556A VAL 5.9 0.4 - - - +
559A PHE* 3.6 38.8 - - + -
577A ILE* 4.0 32.3 - - + -
645A LYS* 3.0 27.9 + - + +
646A PHE* 3.7 9.2 - - - +
648A GLU* 1.3 76.9 - - + +
650A VAL* 1.3 57.9 + - - +
652A THR* 3.3 8.7 + - - -
653A ILE* 3.1 32.9 + - + +
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Residues in contact with VAL 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577A ILE* 4.3 5.6 - - + -
586A ILE* 3.9 17.7 - - + -
609A VAL* 3.9 24.9 - - + -
611A GLY* 4.9 1.3 - - - -
612A VAL* 3.6 28.7 - - + -
624A LEU* 4.4 0.2 - - + -
646A PHE* 2.9 52.4 + - + +
647A PHE 3.9 0.9 - - - +
649A MET* 1.3 72.8 - - - +
651A ASN* 1.3 65.7 + - - +
653A ILE* 3.2 8.3 + - + +
654A THR* 3.0 27.6 + - + +
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Residues in contact with ASN 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611A GLY* 5.7 1.6 - - - -
612A VAL* 3.7 17.5 + - - +
647A PHE* 3.0 52.4 + - - +
648A GLU* 3.7 7.1 - - - +
650A VAL* 1.3 74.9 - - - +
652A THR* 1.3 62.8 + - - +
654A THR* 3.3 10.1 + - - -
655A GLU* 3.1 45.9 + - - +
450B PHE* 4.9 6.1 - - - -
453B ARG* 4.2 21.4 + - - +
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Residues in contact with THR 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648A GLU* 2.9 17.6 + - - +
649A MET* 3.5 11.7 - - - -
650A VAL 3.2 0.4 - - - -
651A ASN* 1.3 77.2 - - - +
653A ILE* 1.3 64.3 + - + +
654A THR 3.4 0.2 + - - -
655A GLU* 3.4 21.8 + - - +
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Residues in contact with ILE 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577A ILE* 4.4 19.7 - - + -
584A LYS* 4.2 31.4 - - + -
585A THR 5.2 2.7 - - - +
586A ILE* 4.0 33.7 - - + -
606A ALA* 4.0 28.4 - - + +
609A VAL* 5.4 1.1 - - + -
649A MET 3.1 13.0 + - - +
650A VAL* 3.2 21.5 + - + +
652A THR* 1.3 78.4 - - + +
654A THR* 1.3 65.6 + - + +
655A GLU 3.7 3.8 + - - +
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Residues in contact with THR 654 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606A ALA 4.5 6.7 - - - +
609A VAL* 4.0 41.3 - - + +
610A ARG 4.9 9.0 + - - +
611A GLY* 5.0 3.4 - - - -
650A VAL* 3.0 23.9 + - + +
651A ASN* 3.3 17.0 + - - -
653A ILE* 1.3 79.7 - - + +
655A GLU* 1.3 62.1 + - - +
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Residues in contact with GLU 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651A ASN* 3.1 42.5 + - - +
652A THR* 3.4 16.8 + - - +
653A ILE 3.4 4.8 - - - +
654A THR* 1.3 84.3 - - - +
453B ARG* 4.2 14.7 - - - -
457B VAL* 3.2 44.0 - - + +
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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
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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