Contacts of the helix formed by residues 637 - 653 (chain A) in PDB entry 1U9J
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 637 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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570A ASN* 4.3 3.4 - - - -
635A LYS 3.7 2.7 + - - +
636A ILE* 1.3 77.0 - - - +
638A MET* 1.3 67.1 + - - +
639A GLN* 4.0 15.6 + - - +
640A GLU* 2.9 38.8 + - - +
641A THR* 3.4 7.8 + - - -
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Residues in contact with MET 638 (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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494A MET* 4.8 2.0 - - - -
537A PHE* 4.0 25.4 - - + -
570A ASN* 3.5 54.3 + - - +
571A GLU 5.4 1.1 - - - +
572A ALA* 5.2 6.3 - - - -
577A LEU* 5.2 1.1 - - + -
580A MET* 3.3 32.3 - - + +
637A ASP* 1.3 71.5 - - - +
639A GLN* 1.3 62.7 + - + +
641A THR* 3.2 10.4 + - - -
642A ILE* 3.0 43.6 + - + +
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Residues in contact with GLN 639 (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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580A MET* 3.1 43.1 + - + +
583A ALA* 6.1 1.6 - - - +
584A SER* 5.1 2.1 - - - -
637A ASP* 3.0 14.2 + - - +
638A MET* 1.3 77.4 - - - +
640A GLU* 1.3 62.6 + - - +
642A ILE* 4.4 5.1 - - - +
643A ASP* 2.9 57.6 + - - +
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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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539A ASP* 4.9 0.2 - - - -
541A ARG* 5.1 6.6 + - - -
636A ILE* 3.6 24.6 - - + +
637A ASP* 2.9 29.3 + - - +
639A GLN* 1.3 79.0 - - - +
641A THR* 1.3 57.8 + - - +
643A ASP* 3.8 4.0 - - - +
644A GLU* 3.0 36.8 + - + +
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Residues in contact with THR 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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494A MET* 3.4 38.6 - - + +
538A THR 4.6 0.7 - - - +
539A ASP* 3.0 46.8 + - - +
570A ASN* 4.6 4.1 + - - +
636A ILE* 3.1 10.9 - - - +
637A ASP 3.4 3.8 + - - -
638A MET* 3.2 15.8 + - + -
640A GLU* 1.3 74.7 - - - +
642A ILE* 1.3 65.9 + - - +
644A GLU* 5.0 0.7 - - - -
645A THR* 2.8 33.3 + - - +
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Residues in contact with ILE 642 (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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494A MET* 4.1 13.9 - - + -
577A LEU* 3.7 29.8 - - + -
580A MET* 3.9 41.3 - - + +
581A LEU* 3.7 28.1 - - + +
584A SER* 4.1 11.2 - - - -
638A MET* 3.0 30.1 + - + +
639A GLN* 3.7 10.3 - - - +
641A THR* 1.3 74.9 - - - +
643A ASP* 1.3 67.4 + - - +
645A THR* 3.9 1.4 - - - -
646A LEU* 3.0 23.7 + - - +
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Residues in contact with ASP 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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584A SER* 3.2 29.4 + - - -
588A HIS* 5.7 0.5 - - - -
639A GLN* 2.9 38.2 + - - +
640A GLU* 3.8 5.2 - - - +
642A ILE* 1.3 80.9 - - - +
644A GLU* 1.3 58.0 + - - +
646A LEU* 3.8 1.4 - - - +
647A ASP* 2.8 32.1 + - - +
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Residues in contact with GLU 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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495A GLY* 5.8 0.4 - - - -
496A PRO* 4.1 27.0 - - + +
539A ASP* 4.0 9.8 - - - +
541A ARG* 2.6 47.1 + - - -
640A GLU* 3.0 21.7 + - + +
641A THR* 4.3 1.8 - - - +
643A ASP* 1.3 74.4 - - - +
645A THR* 1.3 65.8 + - - +
647A ASP* 3.7 7.1 - - + +
648A PHE* 3.0 24.5 + - + +
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Residues in contact with THR 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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494A MET* 3.3 14.2 - - - +
495A GLY* 3.1 48.5 + - - +
496A PRO* 4.6 0.4 - - - +
498A LEU* 4.0 8.1 - - + +
512A ILE* 3.5 30.3 - - + -
516A ILE* 4.1 4.2 - - + +
539A ASP* 5.3 0.3 + - - -
581A LEU* 6.3 0.2 - - - -
641A THR* 2.8 24.0 + - - +
642A ILE 3.9 0.9 - - - -
644A GLU* 1.3 78.0 - - - +
646A LEU* 1.3 60.8 + - - +
648A PHE* 4.2 2.1 - - - +
649A PHE* 3.3 21.7 + - - +
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Residues in contact with LEU 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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516A ILE* 4.2 30.5 - - + +
519A LEU* 5.0 5.2 - - + -
581A LEU* 3.7 22.0 - - + +
584A SER* 3.7 14.8 - - - +
585A PHE* 3.5 40.8 - - + +
588A HIS* 5.3 2.0 - - + -
642A ILE 3.0 16.1 + - - +
643A ASP 3.8 2.7 - - - +
645A THR* 1.3 74.4 - - - +
647A ASP* 1.3 68.0 + - - +
649A PHE* 3.1 1.8 + - - +
650A LEU* 2.9 57.0 + - + +
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Residues in contact with ASP 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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588A HIS* 2.9 30.1 + - + +
643A ASP 2.8 19.9 + - - +
644A GLU* 3.7 9.0 - - - +
646A LEU* 1.3 79.6 - - - +
648A PHE* 1.3 65.5 + - - +
650A LEU* 3.9 1.0 - - - +
651A ARG* 2.6 59.6 + - - +
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Residues in contact with PHE 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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496A PRO* 3.4 26.7 - - + -
497A ARG* 3.3 68.9 - - + -
644A GLU* 3.0 19.3 + - + +
645A THR 4.2 1.1 - - - +
647A ASP* 1.3 80.5 + - - +
649A PHE* 1.3 64.9 + - - +
651A ARG* 3.6 5.4 + - - +
652A THR* 2.8 55.4 + - + -
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Residues in contact with PHE 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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498A LEU* 3.9 30.7 - - + -
513A THR* 5.2 5.8 - - - -
516A ILE* 3.6 28.5 - - + -
517A LEU* 4.0 26.2 - - + -
520A VAL* 3.9 20.2 - - + -
645A THR 3.3 15.8 + - - +
646A LEU 3.1 6.1 + - - +
648A PHE* 1.3 81.4 - - - +
650A LEU* 1.3 67.6 + - + +
652A THR* 3.0 13.9 + - - -
653A VAL* 3.1 36.1 + - + +
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Residues in contact with LEU 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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520A VAL* 3.7 28.9 - - + -
585A PHE* 4.0 23.1 - - + -
588A HIS* 3.6 43.1 - - + +
590A LEU* 4.1 8.5 - - + +
594A PHE* 3.8 28.4 - - + -
646A LEU* 2.9 40.3 + - + +
647A ASP 3.9 2.7 - - - +
649A PHE* 1.3 76.1 - - + +
651A ARG* 1.3 61.3 + - - +
652A THR 3.3 0.7 + - - -
653A VAL* 3.4 19.8 + - - +
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Residues in contact with ARG 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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588A HIS* 4.0 15.3 + - + -
589A PRO* 4.1 17.4 - - - +
590A LEU* 3.7 31.2 - - + +
647A ASP* 2.6 47.2 + - - +
648A PHE* 4.2 4.7 - - - +
650A LEU* 1.3 75.3 - - - +
652A THR* 1.3 60.5 + - - +
653A VAL 4.6 3.4 - - - +
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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 PHE* 2.8 48.4 + - + -
649A PHE* 3.0 6.9 + - - -
651A ARG* 1.3 79.2 - - - +
653A VAL* 1.3 65.8 + - - +
654A ASP* 3.4 3.8 + - - +
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Residues in contact with VAL 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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520A VAL* 4.5 10.1 - - + -
594A PHE* 3.9 25.8 - - + -
649A PHE* 3.1 43.0 + - + +
650A LEU* 3.4 17.3 + - - +
651A ARG 4.6 2.6 - - - +
652A THR* 1.3 78.4 - - - +
654A ASP* 1.3 70.8 + - - +
655A LEU* 3.2 11.9 + - + +
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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