Contacts of the helix formed by residues 405 - 418 (chain A) in PDB entry 1R1H
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 ALA 405 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A THR* 5.3 1.2 - - - +
403A GLU 3.8 0.8 + - - -
404A THR* 1.3 79.0 + - - +
406A THR* 1.3 67.9 + - - +
407A TRP* 3.8 28.5 - - + +
408A ARG* 3.0 26.4 + - - +
409A ARG 3.1 9.5 + - - -
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Residues in contact with THR 406 (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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142A CYS 4.0 10.3 - - - +
143A ILE* 4.1 11.4 - - + +
145A GLU* 2.8 35.7 + - + +
384A ARG* 5.4 1.7 + - - -
404A THR 3.4 1.6 + - - -
405A ALA* 1.3 71.1 - - - +
407A TRP* 1.3 64.0 + - - +
408A ARG 3.1 0.2 + - - -
409A ARG* 3.2 33.3 + - - +
410A CYS* 2.9 40.1 + - - -
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Residues in contact with TRP 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A GLU* 3.4 26.7 - - + -
115A VAL* 4.0 14.8 - - + -
118A LYS* 3.6 45.2 - - + +
139A TYR* 3.3 24.5 - - - +
143A ILE* 4.0 13.2 - - + +
405A ALA* 3.8 16.4 - - + +
406A THR* 1.3 78.8 - - - +
408A ARG* 1.3 111.0 + - + +
410A CYS* 3.8 0.9 - - - +
411A ALA* 2.8 31.4 + - + +
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Residues in contact with ARG 408 (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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111A ASP* 3.1 37.2 + - - +
114A GLU* 2.9 33.0 + - - +
115A VAL* 4.1 10.7 - - - +
404A THR* 3.6 21.5 - - + +
405A ALA* 3.0 19.2 + - + +
407A TRP* 1.3 123.1 - - + +
409A ARG* 1.3 66.2 + - - +
411A ALA* 3.3 4.1 + - - +
412A ASN* 3.0 32.1 + - - +
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Residues in contact with ARG 409 (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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142A CYS* 5.0 0.4 - - - -
145A GLU* 5.7 0.2 - - - -
380A SER 5.0 0.4 + - - -
384A ARG* 5.9 2.4 - - - +
387A LYS* 3.7 28.9 - - - +
403A GLU* 3.7 40.2 + - - +
404A THR* 2.5 58.6 + - + -
405A ALA 3.1 2.0 + - - +
406A THR* 3.4 39.9 + - - +
408A ARG* 1.3 77.7 - - - +
410A CYS* 1.3 61.2 + - - +
412A ASN* 3.5 7.5 + - - +
413A TYR* 2.9 28.5 + - - +
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Residues in contact with CYS 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A TYR* 4.1 7.2 - - + -
142A CYS* 2.0 68.4 - - + -
143A ILE* 3.6 19.7 - - + -
406A THR* 2.9 27.3 + - - +
407A TRP 3.8 1.6 - - - +
409A ARG* 1.3 78.7 - - - +
411A ALA* 1.3 65.6 - - - +
413A TYR* 3.2 2.5 + - - +
414A VAL* 3.0 28.4 + - - +
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Residues in contact with ALA 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A GLU* 4.6 9.2 - - + +
117A LEU* 3.8 31.1 - - + +
118A LYS 4.6 2.7 - - - +
121A LEU* 4.3 1.1 - - + -
139A TYR* 3.9 10.7 - - + -
407A TRP* 2.8 21.3 + - + +
408A ARG* 3.7 6.3 - - - +
410A CYS* 1.3 75.2 - - - +
412A ASN* 1.3 57.5 + - - +
414A VAL* 2.7 30.3 - - - +
415A ASN* 3.0 12.8 + - - +
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Residues in contact with ASN 412 (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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113A LEU* 5.6 0.9 - - - +
114A GLU* 2.7 40.7 + - - +
117A LEU* 4.6 5.7 - - - +
404A THR* 5.9 1.8 - - - +
408A ARG* 3.0 23.0 + - - +
409A ARG* 3.6 7.6 - - - +
411A ALA* 1.3 75.5 - - - +
413A TYR* 1.3 60.9 + - - +
415A ASN* 3.5 9.4 + - - +
416A GLY* 2.8 27.2 + - - -
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Residues in contact with TYR 413 (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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138A LEU* 4.1 22.9 - - + -
142A CYS* 5.0 1.6 - - - -
409A ARG 2.9 17.6 + - - +
410A CYS* 3.2 8.0 + - - +
412A ASN* 1.3 75.9 - - - +
414A VAL* 1.3 65.1 + - + +
416A GLY* 3.2 2.5 + - - -
417A ASN* 3.0 52.6 + - - -
506A TYR* 3.9 28.5 - + - +
510A ILE* 3.3 30.5 + - + +
513A ASN* 3.0 31.9 + - - +
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Residues in contact with VAL 414 (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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121A LEU* 3.3 28.9 - - + -
135A ALA* 4.2 9.2 - - + +
138A LEU* 3.8 24.7 - - + +
139A TYR* 3.6 35.0 - - + +
142A CYS* 5.6 0.9 - - + -
410A CYS* 3.0 13.2 + - + +
411A ALA 2.7 26.0 - - - +
413A TYR* 1.3 74.3 - - + +
415A ASN* 1.3 60.2 + - - +
417A ASN 3.2 0.2 + - - -
418A MET* 2.8 39.2 + - - +
422A VAL* 4.0 8.5 - - + -
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Residues in contact with ASN 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LEU* 4.5 1.2 - - - +
117A LEU* 3.6 18.2 - - + +
411A ALA 3.0 13.9 + - - +
412A ASN* 3.5 10.0 + - - +
414A VAL* 1.3 83.8 - - - +
416A GLY* 1.3 61.1 + - - +
419A GLU* 3.2 30.3 + - - +
422A VAL* 3.0 33.8 - - + +
537A GLY* 5.9 0.9 - - - -
539A ALA* 2.9 33.0 + - - +
540A VAL* 4.9 6.0 - - - +
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Residues in contact with GLY 416 (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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412A ASN 2.8 19.5 + - - -
413A TYR* 3.2 3.1 + - - -
415A ASN* 1.3 73.7 - - - +
417A ASN* 1.3 63.0 + - - +
419A GLU* 4.1 13.7 - - - +
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Residues in contact with ASN 417 (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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138A LEU* 4.8 1.8 - - + -
413A TYR* 3.0 54.7 + - + +
414A VAL 4.1 1.1 - - - +
416A GLY* 1.3 81.2 - - - +
418A MET* 1.3 68.7 - - + +
419A GLU* 3.8 2.6 + - - -
496A TYR* 4.1 8.0 - - - -
499A LEU* 5.6 2.9 - - - +
501A TYR* 5.4 0.4 + - - +
513A ASN* 3.7 37.7 - - - +
517A SER* 4.5 8.8 + - - -
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Residues in contact with MET 418 (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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131A ALA 3.4 26.2 - - - +
134A LYS* 4.1 6.5 - - + -
135A ALA* 3.4 33.2 - - + +
138A LEU* 4.2 11.4 - - + -
414A VAL 2.8 18.5 + - - +
415A ASN 3.7 2.0 - - - -
417A ASN* 1.3 81.6 - - + +
419A GLU* 1.3 63.6 + - - +
420A ASN 3.2 3.3 + - - -
421A ALA* 3.3 5.6 + - + -
422A VAL* 3.0 22.4 + - + +
496A TYR* 3.4 46.7 - - + +
499A LEU* 5.7 0.4 - - + -
501A TYR* 4.0 24.2 - - + +
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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