Contacts of the helix formed by residues 619 - 636 (chain A) in PDB entry 1U1H
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 GLU 619 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A ASP* 4.6 5.9 - - - +
614A PRO* 3.6 27.9 - - + +
616A ARG* 2.9 43.0 + - + +
617A LYS 3.0 1.2 - - - -
618A SER* 1.3 79.5 - - - +
620A HIS* 1.3 65.5 + - - +
621A ALA 3.6 0.4 - - - -
622A PHE* 3.8 11.8 + - + +
623A TYR 3.5 12.0 + - - -
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Residues in contact with HIS 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A LEU* 3.9 38.3 - - + +
614A PRO* 3.0 26.5 + - + -
615A LEU 4.2 2.6 + - - -
616A ARG 3.2 22.5 + - - -
617A LYS* 3.0 34.6 + - + +
618A SER 3.3 0.2 - - - -
619A GLU* 1.3 76.9 - - - +
621A ALA* 1.3 68.2 + - - +
623A TYR* 2.8 16.1 + - - +
624A LEU* 3.0 21.5 + - + +
655A ASP* 5.9 2.4 + - - -
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Residues in contact with ALA 621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A LYS 4.7 0.4 + - - -
618A SER 4.8 5.3 + - - +
619A GLU 3.6 0.2 - - - -
620A HIS* 1.3 78.0 - - - +
622A PHE* 1.3 62.7 + - - +
624A LEU* 3.4 10.4 + - - +
625A ASP* 3.0 24.5 + - - +
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Residues in contact with PHE 622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A HIS* 3.8 23.6 - + - -
618A SER 5.4 1.3 + - - +
619A GLU* 3.8 15.3 + - + +
620A HIS 3.2 0.4 - - - -
621A ALA* 1.3 77.9 - - - +
623A TYR* 1.3 65.5 + - + +
625A ASP* 3.3 21.1 + - + +
626A TRP* 3.1 39.0 + + - -
771A SO4 3.8 22.7 - - - -
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Residues in contact with TYR 623 (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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562A VAL* 3.8 4.9 - - + +
566A ASN* 3.4 10.1 + - - -
576A ARG* 3.9 5.2 - - - -
609A LEU 2.5 29.2 + - - -
610A ARG* 4.8 0.4 - - - -
612A GLY* 3.2 38.9 + - - -
613A LEU* 3.6 34.1 - - + -
614A PRO* 3.6 17.0 - - + -
619A GLU 3.5 3.8 + - - +
620A HIS 2.8 13.4 + - - +
622A PHE* 1.3 76.1 - - + +
624A LEU* 1.3 74.1 + - + +
625A ASP 3.0 0.2 + - - -
626A TRP* 3.3 49.9 + + - +
627A ALA* 2.9 32.7 + - + +
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Residues in contact with LEU 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609A LEU* 5.4 8.3 - - + +
610A ARG* 6.0 1.1 - - - -
613A LEU* 4.2 15.5 - - + -
620A HIS* 3.0 20.3 + - + +
621A ALA* 3.8 9.9 - - - +
623A TYR* 1.3 99.4 - - + +
625A ASP* 1.3 61.5 + - - +
627A ALA* 3.8 4.9 - - + +
628A VAL* 3.0 31.0 + - + +
655A ASP 5.2 3.6 - - - +
656A ILE* 4.4 27.1 - - + -
659A SER* 3.5 31.6 - - - +
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Residues in contact with ASP 625 (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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581A TYR* 5.3 1.7 + - - -
621A ALA 3.0 13.5 + - - +
622A PHE* 3.3 17.8 - - + +
623A TYR 3.0 0.2 - - - -
624A LEU* 1.3 78.2 - - - +
626A TRP* 1.3 61.6 + - - +
628A VAL* 3.9 2.5 - - - +
629A HIS* 2.9 33.6 + - - +
632A ARG* 5.5 5.5 + - - -
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Residues in contact with TRP 626 (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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562A VAL* 5.0 3.4 - - + -
565A LEU* 3.6 20.4 - - + -
576A ARG* 4.1 15.0 - - + -
577A HIS* 3.3 31.3 - - + +
580A CYS* 3.5 33.0 - - + -
581A TYR* 3.3 24.2 - - + +
622A PHE* 3.1 41.4 + + - -
623A TYR* 3.3 43.5 + + - +
625A ASP* 1.3 79.4 - - - +
627A ALA* 1.3 66.0 + - + +
629A HIS* 3.7 2.1 - - - +
630A SER* 2.7 38.7 + - - -
771A SO4 3.6 24.5 + - - -
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Residues in contact with ALA 627 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A VAL* 3.4 28.4 - - + +
609A LEU* 4.1 14.8 - - + +
623A TYR* 2.9 35.0 + - + +
624A LEU* 3.8 9.6 - - + +
626A TRP* 1.3 87.1 - - + +
628A VAL* 1.3 63.4 + - + +
630A SER* 3.3 4.5 - - - -
631A PHE* 3.2 16.1 + - - +
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Residues in contact with VAL 628 (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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609A LEU* 5.3 8.3 - - + -
624A LEU* 3.0 19.9 + - + +
625A ASP* 3.9 2.5 - - - +
627A ALA* 1.3 78.3 - - + +
629A HIS* 1.3 68.7 + - - +
631A PHE* 2.9 17.4 + - - +
632A ARG* 2.9 18.8 + - - +
659A SER* 3.4 33.0 - - - +
662A ASP* 3.2 41.1 - - + +
663A MSE 3.6 15.7 - - + -
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Residues in contact with HIS 629 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A ALA* 4.2 11.2 - - + -
407A GLY 4.1 10.3 - - - -
408A SER* 4.4 4.3 - - - -
409A ASP* 2.7 34.2 + - + +
581A TYR* 3.2 25.4 + + - +
625A ASP* 2.9 23.1 + - - +
626A TRP* 3.7 4.9 - - - +
628A VAL* 1.3 74.8 - - - +
630A SER* 1.3 66.4 + - - +
632A ARG* 2.8 30.4 + - - +
633A ILE* 2.8 41.5 + - + +
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Residues in contact with SER 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A PRO* 3.7 11.2 - - - -
580A CYS* 3.2 32.5 - - - +
581A TYR* 3.3 15.4 - - - -
584A ALA* 3.2 24.7 - - - +
626A TRP 2.7 23.2 + - - -
627A ALA 3.3 6.5 - - - -
629A HIS* 1.3 76.5 - - - +
631A PHE* 1.3 62.6 + - - +
633A ILE* 3.5 10.9 - - - +
634A THR* 3.3 11.3 + - - -
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Residues in contact with PHE 631 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A PRO* 4.2 5.3 - - + +
604A ILE* 3.7 39.9 - - + -
606A GLU* 4.3 14.8 - - + +
609A LEU* 6.0 0.7 - - + -
627A ALA 3.2 8.3 + - - +
628A VAL* 2.9 11.4 + - - +
630A SER* 1.3 77.9 - - - +
632A ARG* 1.3 64.3 + - - +
634A THR* 2.8 28.8 - - - -
635A ASN* 3.7 19.6 + - - -
644A ILE* 4.6 7.6 - - + -
646A THR* 3.6 29.6 - - + -
663A MSE 3.7 58.6 - - + -
664A ASP 5.1 0.2 - - - -
665A ALA* 4.5 8.1 - - + -
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Residues in contact with ARG 632 (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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408A SER* 4.4 5.5 - - - -
409A ASP* 3.5 32.4 - - + +
410A HIS* 4.1 36.5 + - - +
411A ARG* 5.2 2.0 - - + +
625A ASP* 5.5 5.1 + - - -
628A VAL* 2.9 22.2 + - - +
629A HIS* 2.8 44.9 + - - +
631A PHE* 1.3 69.6 - - - +
633A ILE* 1.3 65.7 + - - +
634A THR 2.7 6.2 + - - -
635A ASN* 2.7 20.1 + - - +
636A CYS* 2.9 12.1 + - - +
662A ASP* 2.7 36.7 + - - +
663A MSE 3.5 21.1 - - - +
664A ASP* 4.8 4.3 - - - -
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Residues in contact with ILE 633 (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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404A ALA* 4.9 10.3 - - + -
409A ASP* 4.0 20.8 - - - +
581A TYR* 3.4 43.1 - - + +
584A ALA* 3.9 14.8 - - + -
585A LEU* 3.9 25.8 - - + -
588A LYS* 2.9 32.8 - - + +
629A HIS* 2.8 42.1 + - + +
630A SER* 3.5 8.5 - - - +
632A ARG* 1.3 71.5 - - - +
634A THR* 1.3 59.5 + - - +
635A ASN 3.3 0.7 + - - -
636A CYS* 3.9 6.1 + - - -
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Residues in contact with THR 634 (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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561A PRO* 3.7 17.9 - - - +
584A ALA 4.0 9.7 + - - -
587A ILE* 4.0 13.9 - - + +
588A LYS* 3.2 28.5 - - - +
591A VAL* 3.6 19.5 - - + +
592A GLU* 5.4 0.3 - - - +
604A ILE* 3.2 36.6 - - + -
630A SER 3.3 10.3 + - - -
631A PHE* 2.8 16.0 + - - -
632A ARG 2.7 1.2 + - - -
633A ILE* 1.3 80.0 - - - +
635A ASN* 1.3 55.1 + - - +
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Residues in contact with ASN 635 (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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411A ARG* 3.5 17.2 - - - +
588A LYS* 5.2 0.7 - - - -
591A VAL* 4.1 13.0 - - + -
592A GLU* 5.8 2.0 - - - -
604A ILE* 3.2 29.1 - - - +
631A PHE* 3.7 17.1 + - - -
632A ARG* 2.7 17.0 + - - +
634A THR* 1.3 78.2 - - + +
636A CYS* 1.3 59.2 + - - +
637A GLY 3.0 8.3 + - - +
638A VAL* 3.2 21.4 - - + +
644A ILE* 3.1 37.3 - - + +
663A MSE 5.7 0.5 - - - +
664A ASP 5.3 2.3 - - - +
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Residues in contact with CYS 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A LYS* 5.9 4.0 - - - -
409A ASP* 3.1 51.4 - - + +
410A HIS 4.1 4.2 - - - +
411A ARG* 3.7 26.2 - - - +
412A ARG* 3.9 12.3 + - - +
588A LYS* 4.7 12.1 - - - -
632A ARG* 2.9 9.4 + - - +
633A ILE* 3.9 9.1 + - - -
634A THR 3.9 0.8 - - - -
635A ASN* 1.3 76.1 - - - +
637A GLY* 1.3 61.9 + - - +
638A VAL 3.5 2.4 + - - +
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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