Contacts of the helix formed by residues 528 - 543 (chain B) in PDB entry 1U5T
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 528 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433B MET* 5.6 0.9 - - - +
435B ILE* 2.9 30.7 - - + +
436B THR* 5.6 0.9 - - - -
439B ASP* 5.9 6.7 - - + +
443B MET* 4.7 18.4 - - + +
519B SER* 5.5 0.4 - - - -
526B ASN 3.0 8.2 + - - -
527B TRP* 1.3 75.8 - - - +
529B LEU* 1.3 74.2 + - + +
530B GLY 3.1 2.4 + - - -
531B ILE* 2.9 16.5 - - - +
532B LEU* 3.3 4.3 + - - -
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Residues in contact with LEU 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ARG* 5.1 21.8 - - + -
107A LYS* 4.2 13.9 - - + -
511B LEU* 4.3 19.1 - - + -
515B THR* 4.5 10.2 + - - +
519B SER* 5.7 1.2 + - - -
528B THR* 1.3 75.1 - - + +
530B GLY* 1.3 54.6 + - - +
532B LEU* 2.5 48.7 + - + +
533B MET* 2.6 38.3 + - + -
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Residues in contact with GLY 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ARG* 6.1 0.6 - - - +
436B THR* 4.0 9.1 - - - +
439B ASP* 5.0 10.1 + - - -
528B THR* 3.1 3.0 + - - -
529B LEU* 1.3 81.5 - - - +
531B ILE* 1.3 57.8 + - - +
533B MET* 3.1 13.2 + - - +
534B GLU* 2.6 35.8 + - - +
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Residues in contact with ILE 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B ILE* 3.1 55.2 - - + +
435B ILE* 3.4 28.0 - - + -
436B THR* 3.2 25.0 - - + +
484B ILE* 4.7 12.8 - - + -
486B CYS* 4.8 2.5 - - + -
527B TRP* 3.8 3.5 - - + -
528B THR* 2.9 24.9 - - - +
530B GLY* 1.3 74.1 - - - +
532B LEU* 1.3 63.5 + - - +
534B GLU* 4.1 9.6 - - + -
535B VAL* 3.0 24.1 + - + +
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Residues in contact with LEU 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B LEU* 3.5 20.2 - - + -
511B LEU* 3.5 29.6 - - + -
514B LEU* 3.3 28.7 - - + -
515B THR* 4.1 28.3 - - - +
518B LEU* 4.7 10.5 - - + -
527B TRP* 3.6 22.0 - - + -
528B THR 3.3 6.4 + - - +
529B LEU* 2.5 32.7 + - + +
531B ILE* 1.3 71.1 - - - +
533B MET* 1.3 62.4 + - - +
535B VAL* 3.0 5.7 + - - +
536B LEU* 2.9 25.8 + - + +
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Residues in contact with MET 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LYS* 3.3 37.5 - - + -
161A VAL* 4.7 10.3 - - + -
162A PRO* 4.9 16.7 - - + +
511B LEU* 3.9 27.8 - - + -
529B LEU* 2.6 30.4 + - + +
530B GLY* 3.2 13.9 - - - +
532B LEU* 1.3 78.1 - - - +
534B GLU* 1.3 62.3 + - + +
536B LEU* 3.4 10.8 + - - +
537B GLN* 3.4 21.0 + - - +
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Residues in contact with GLU 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A SER 5.4 1.4 - - - +
162A PRO* 3.9 14.4 - - - +
436B THR* 5.4 7.0 - - - -
483B ARG* 2.8 43.1 + - - -
484B ILE* 2.7 52.3 - - + +
485B LEU 6.0 0.4 - - - +
530B GLY* 2.6 25.3 + - - +
531B ILE* 3.7 11.2 - - + +
533B MET* 1.3 70.4 - - + +
535B VAL* 1.3 65.9 + - - +
537B GLN* 3.3 14.6 + - - +
538B ASN* 3.4 7.4 + - - -
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Residues in contact with VAL 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B ILE* 4.7 1.8 - - + -
492B PHE* 3.1 40.4 - - + -
495B VAL* 6.1 0.2 - - + -
496B LYS* 4.8 12.3 - - + +
499B LEU* 4.1 27.6 - - + -
527B TRP* 4.3 13.9 - - + -
531B ILE* 3.0 21.2 + - + +
532B LEU 3.0 3.2 + - - +
534B GLU* 1.3 75.4 - - + +
536B LEU* 1.3 67.8 + - - +
537B GLN 3.0 1.6 - - - -
538B ASN* 2.8 16.1 + - + +
539B CYS* 2.8 27.7 + - - -
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Residues in contact with LEU 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B LEU* 4.6 5.8 - - + -
503B ILE* 3.7 20.6 - - + -
511B LEU* 3.8 28.0 - - + -
514B LEU* 4.1 17.5 - - + -
532B LEU* 2.9 21.9 + - + +
533B MET* 3.5 10.5 - - - +
534B GLU 3.2 0.2 - - - -
535B VAL* 1.3 76.8 - - - +
537B GLN* 1.3 63.6 + - + +
539B CYS* 3.6 8.1 - - - +
540B VAL* 3.3 25.4 + - - +
545B LEU* 4.0 4.9 - - + -
556B TYR* 3.4 50.9 - - + +
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Residues in contact with GLN 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A PRO* 4.2 22.9 - - + +
163A ASN* 2.7 35.4 + - - +
533B MET 3.4 7.2 + - - +
534B GLU* 3.3 10.4 + - - +
535B VAL 3.0 1.0 - - - -
536B LEU* 1.3 79.1 - - + +
538B ASN* 1.3 71.2 + - - +
540B VAL* 3.6 13.7 - - - +
541B ASP* 2.8 45.9 + - - +
549B LYS* 5.2 9.5 - - - +
556B TYR* 5.6 4.3 - - - +
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Residues in contact with ASN 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B VAL* 5.4 1.6 - - - +
481B ASN* 2.6 40.9 + - - +
484B ILE* 5.0 8.1 - - + +
492B PHE* 4.2 16.0 - - + -
496B LYS* 3.4 28.8 + - + -
534B GLU 3.4 6.5 + - - +
535B VAL* 2.8 21.5 + - - +
537B GLN* 1.3 68.9 - - - +
539B CYS* 1.3 56.6 + - - +
541B ASP* 2.3 40.6 + - - +
542B GLU* 2.9 19.8 + - - +
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Residues in contact with CYS 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B LYS* 4.0 24.6 - - + +
499B LEU* 5.6 3.4 - - - -
500B VAL* 5.0 4.3 - - + -
535B VAL* 2.8 28.3 - - - -
536B LEU* 3.6 11.4 - - - +
538B ASN* 1.3 76.1 - - - +
540B VAL* 1.3 51.8 + - - +
542B GLU* 4.3 1.8 - - - -
543B GLY 2.5 32.1 + - - -
544B ASP* 2.6 29.7 + - + -
545B LEU* 3.3 32.5 - - + -
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Residues in contact with VAL 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B LEU 3.3 13.3 + - - +
537B GLN* 3.6 21.3 - - - +
538B ASN 2.5 4.6 + - - -
539B CYS* 1.3 77.3 - - - +
541B ASP* 1.3 75.4 + - - +
543B GLY* 3.2 11.3 + - - -
545B LEU* 4.1 13.4 - - + +
547B ILE* 3.6 37.6 - - + +
549B LYS* 6.1 2.7 - - - +
556B TYR* 4.1 20.4 - - + +
18D PRO* 4.1 17.0 - - + +
19D ASN* 4.0 7.8 - - - +
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Residues in contact with ASP 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481B ASN* 5.0 5.2 - - - +
537B GLN* 2.8 37.6 + - - +
538B ASN* 2.3 26.7 + - - +
540B VAL* 1.3 74.0 - - - +
542B GLU* 1.3 62.3 + - - +
543B GLY 2.8 6.1 + - - -
18D PRO* 5.4 2.5 - - - +
19D ASN* 3.1 21.1 - - - +
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Residues in contact with GLU 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481B ASN* 4.2 18.2 + - - -
496B LYS* 4.3 12.2 + - - +
538B ASN* 2.9 23.7 + - - +
539B CYS* 3.8 4.5 - - - +
541B ASP* 1.3 77.9 - - - +
543B GLY* 1.3 66.1 + - - +
544B ASP* 3.4 21.5 - - - +
564B SER* 4.7 5.0 + - - -
19D ASN* 4.1 8.9 + - - +
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Residues in contact with GLY 543 (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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539B CYS 2.5 11.5 + - - -
540B VAL 3.5 9.2 - - - -
541B ASP 2.8 4.9 - - - -
542B GLU* 1.3 81.4 - - - +
544B ASP* 1.3 61.2 + - - +
545B LEU 3.5 4.3 - - - -
559B ASN* 3.8 18.0 + - - -
564B SER* 4.6 9.4 + - - -
19D ASN* 3.7 20.4 - - - -
22D THR* 4.6 1.1 - - - -
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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
------------------------------------------------------------
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