Contacts of the helix formed by residues 560 - 567 (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 GLY 560 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559A THR* 1.3 78.8 - - - +
561A PRO* 1.3 74.7 - - - +
562A VAL 3.3 2.7 - - - -
563A THR 3.6 1.2 + - - -
564A ILE* 3.4 18.9 + - - +
587A ILE* 5.7 0.4 - - - -
604A ILE* 3.7 16.6 - - - +
605A ASP 2.9 14.3 + - - -
606A GLU* 3.2 19.1 - - - -
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Residues in contact with PRO 561 (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 THR 3.8 0.6 - - - +
560A GLY* 1.3 83.7 - - - +
562A VAL* 1.3 57.8 + - - +
564A ILE* 3.4 2.1 + - - +
565A LEU* 3.0 29.5 + - - +
580A CYS* 3.8 9.9 - - - +
583A ILE* 3.5 32.3 - - + +
584A ALA* 3.6 17.3 - - + +
587A ILE* 4.8 3.3 - - + -
604A ILE* 5.2 0.2 - - + -
606A GLU* 3.4 8.1 - - - +
630A SER* 3.7 35.2 - - - +
631A PHE* 4.5 6.1 - - + -
634A THR* 3.7 17.0 - - - +
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Residues in contact with VAL 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A PRO* 1.3 75.6 - - - +
563A THR* 1.3 59.4 + - - +
565A LEU* 3.2 3.0 + - + +
566A ASN* 2.8 49.4 + - - +
580A CYS* 4.0 16.2 - - - -
606A GLU* 3.1 19.4 + - - +
608A ALA 3.9 6.1 - - - +
609A LEU* 3.9 14.6 - - + +
623A TYR* 3.8 14.6 - - + +
626A TRP* 5.0 3.1 - - + -
627A ALA* 3.4 40.2 - - + +
630A SER* 4.4 2.2 - - - -
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Residues in contact with THR 563 (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 MSE 4.1 8.7 - - + -
497A VAL* 4.3 2.9 - - + +
559A THR* 3.6 25.4 - - + -
561A PRO 3.4 0.2 - - - -
562A VAL* 1.3 73.6 - - - +
564A ILE* 1.3 66.0 + - - +
566A ASN* 4.0 0.2 - - - -
567A TRP* 3.1 55.1 + - + +
606A GLU* 2.7 22.9 + - - -
607A ALA 3.1 6.8 + - - -
608A ALA* 3.0 33.6 + - + +
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Residues in contact with ILE 564 (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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497A VAL* 4.1 21.8 - - + +
500A PHE* 4.3 19.7 - - + -
501A GLY* 6.0 0.2 - - - -
504A LEU* 4.8 4.7 - - + -
507A PHE* 3.5 33.7 - - + -
528A ILE* 4.5 0.4 - - + -
559A THR* 3.7 31.6 - - + +
560A GLY 3.4 9.1 + - - +
561A PRO 3.7 6.7 - - - +
562A VAL 3.3 0.2 - - - -
563A THR* 1.3 78.6 - - - +
565A LEU* 1.3 63.8 + - - +
567A TRP 3.7 1.2 + - - -
568A SER* 3.1 27.7 + - - -
583A ILE* 4.2 23.8 - - + -
587A ILE* 4.2 12.3 - - + -
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Residues in contact with LEU 565 (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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528A ILE* 4.8 0.9 - - + -
561A PRO 3.0 17.5 + - - +
562A VAL* 3.4 5.4 - - + +
563A THR 3.2 0.2 - - - -
564A ILE* 1.3 77.4 - - - +
566A ASN* 1.3 70.4 + - - +
568A SER* 3.3 8.5 + - - +
570A VAL* 3.2 49.8 - - + +
576A ARG* 4.0 17.5 - - + +
579A THR* 3.5 32.1 - - + -
580A CYS* 3.8 9.9 - - + +
583A ILE* 3.9 11.0 - - + -
626A TRP* 3.6 37.0 - - + -
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Residues in contact with ASN 566 (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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116A ASN* 3.5 16.9 + - - +
562A VAL* 2.8 33.6 + - - +
563A THR 4.1 2.7 - - - +
565A LEU* 1.3 79.4 - - - +
567A TRP* 1.3 63.9 + - + +
568A SER 3.3 7.8 + - - +
576A ARG* 3.9 12.5 + - - -
608A ALA* 2.7 30.4 + - + +
611A GLU* 3.9 12.1 - - + +
612A GLY* 3.5 24.2 - - - +
623A TYR* 3.4 11.2 + - - -
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Residues in contact with TRP 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ASN* 4.0 26.4 - - - +
496A MSE 4.0 20.2 - - + -
497A VAL* 4.2 19.5 - - + +
525A PRO* 3.9 9.9 - - - +
526A PRO* 3.3 19.9 - - - +
563A THR* 3.1 31.9 + - + +
564A ILE 3.9 1.6 - - - -
565A LEU 3.3 0.2 - - - -
566A ASN* 1.3 85.0 - - + +
568A SER* 1.3 58.8 + - - +
607A ALA* 4.0 19.1 - - + -
608A ALA* 3.6 23.5 - - + +
611A GLU* 4.2 8.6 - - + +
649A CYS* 6.1 0.4 - - - -
772A MET* 5.6 1.8 - - + -
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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