Contacts of the helix formed by residues 418 - 431 (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 MET 418 (chain A).
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Specific contacts
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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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Residues in contact with GLU 419 (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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415A ASN* 3.2 24.1 + - - +
416A GLY 4.1 12.2 - - - +
417A ASN 3.8 2.0 - - - -
418A MET* 1.3 75.1 - - - +
420A ASN* 1.3 74.7 + - - +
422A VAL* 4.2 0.2 - - - +
423A GLY* 2.8 25.8 + - - -
495A GLU* 5.3 4.3 - - - +
496A TYR* 3.8 0.6 + - - -
534A TRP* 4.7 6.2 - - - +
535A ILE 5.0 1.4 - - - -
536A SER* 3.9 7.8 + - - -
537A GLY* 3.5 38.5 + - - +
538A ALA 4.5 0.3 + - - -
539A ALA 5.4 0.2 + - - -
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Residues in contact with ASN 420 (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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418A MET 3.2 0.6 - - - -
419A GLU* 1.3 87.5 - - - +
421A ALA* 1.3 65.7 + - - +
424A ARG* 3.0 23.6 + - - +
482A PRO* 4.5 9.1 - - - +
485A ILE* 3.7 30.0 - - + +
491A LYS* 6.4 0.4 - - - +
492A LEU* 3.6 19.7 - - + +
495A GLU* 2.9 25.6 + - - +
496A TYR* 3.4 5.5 + - - +
534A TRP* 6.0 1.6 - - - +
536A SER 5.6 0.5 - - - +
537A GLY* 5.1 4.9 - - - -
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Residues in contact with ALA 421 (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 4.0 19.5 - - - +
132A VAL* 4.7 6.0 - - + +
135A ALA* 4.6 5.8 - - + -
418A MET* 3.3 12.3 + - + +
420A ASN* 1.3 77.6 - - - +
422A VAL* 1.3 62.2 + - - +
424A ARG* 3.3 9.7 + - - +
425A LEU* 3.2 27.9 + - + +
492A LEU* 3.9 12.7 - - + +
496A TYR* 3.2 26.3 + - + -
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Residues in contact with VAL 422 (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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117A LEU* 3.7 23.0 - - + +
120A VAL* 5.8 1.3 - - + -
121A LEU* 4.4 15.7 - - + -
135A ALA* 4.9 6.7 - - + -
414A VAL* 4.0 15.0 - - + +
415A ASN* 3.0 52.5 - - + +
418A MET 3.0 17.1 + - - +
421A ALA* 1.3 73.5 - - - +
423A GLY* 1.3 61.3 + - - +
425A LEU* 3.3 8.5 + - + +
426A TYR* 2.8 26.9 + - - +
539A ALA* 4.0 3.6 - - + -
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Residues in contact with GLY 423 (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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419A GLU 2.8 21.0 + - - -
420A ASN 3.9 0.9 - - - -
422A VAL* 1.3 78.2 - - - +
424A ARG* 1.3 54.9 + - - +
426A TYR* 3.6 5.1 - - - +
427A VAL* 2.9 36.7 + - - +
485A ILE* 3.8 7.9 - - - -
538A ALA* 4.0 18.4 - - - -
539A ALA* 4.4 5.6 - - - -
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Residues in contact with ARG 424 (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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127A GLU* 5.7 2.8 + - - -
129A ILE* 3.8 25.9 - - - +
132A VAL* 4.9 13.9 - - - +
420A ASN 3.0 14.7 + - - +
421A ALA* 3.4 11.7 - - - +
422A VAL 3.2 0.2 - - - -
423A GLY* 1.3 76.1 - - - +
425A LEU* 1.3 66.5 + - + +
427A VAL* 3.3 5.6 - - - +
428A GLU* 3.0 47.6 + - - +
485A ILE* 2.9 39.1 + - + +
486A VAL* 3.6 25.0 + - + -
489A ASP* 2.9 38.1 + - - +
492A LEU* 4.8 9.6 - - - +
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Residues in contact with LEU 425 (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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120A VAL* 3.7 40.5 - - + +
121A LEU* 4.0 21.1 - - + -
128A ASP* 5.5 1.6 - - - +
132A VAL* 3.9 39.0 - - + -
135A ALA* 5.4 2.5 - - + -
136A LYS* 4.7 4.0 - - + +
421A ALA 3.2 15.8 + - - +
422A VAL* 3.7 7.2 - - - +
424A ARG* 1.3 81.1 - - + +
426A TYR* 1.3 63.7 + - - +
428A GLU* 3.5 16.0 + - - +
429A ALA* 3.1 24.3 + - - +
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Residues in contact with TYR 426 (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* 3.6 31.3 - - + +
116A VAL* 3.6 29.4 - - + -
117A LEU* 4.3 13.5 - - + -
120A VAL* 4.7 2.6 - - - +
422A VAL 2.8 17.5 + - - +
423A GLY 3.6 3.1 - - - +
425A LEU* 1.3 78.2 - - - +
427A VAL* 1.3 70.7 + - + +
429A ALA* 3.0 4.7 + - - +
430A ALA* 2.8 50.6 + - + +
431A PHE* 5.2 2.5 - - + -
538A ALA 4.2 2.0 - - - -
539A ALA* 3.8 23.8 - - + -
556A ALA* 4.2 9.2 + - + -
557A GLY* 3.9 28.6 - - - -
560A GLN* 4.0 13.3 + - - -
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Residues in contact with VAL 427 (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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423A GLY 2.9 19.0 + - - +
424A ARG* 3.3 15.3 - - - +
426A TYR* 1.3 79.1 - - + +
428A GLU* 1.3 65.5 + - - +
431A PHE* 3.0 40.3 + - + +
481A TYR* 3.8 35.9 - - + -
486A VAL* 4.2 17.9 - - + -
538A ALA* 3.8 20.2 - - + -
556A ALA* 4.0 15.3 - - + -
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Residues in contact with GLU 428 (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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424A ARG* 3.0 44.3 + - - +
425A LEU* 3.8 18.9 - - - +
427A VAL* 1.3 83.4 - - + +
429A ALA* 1.3 58.5 + - - +
486A VAL* 3.8 26.9 - - + +
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Residues in contact with ALA 429 (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 VAL* 4.1 12.8 - - + -
120A VAL* 3.7 21.3 - - + -
425A LEU 3.1 15.7 + - - +
426A TYR 3.0 4.7 + - - +
428A GLU* 1.3 80.5 - - - +
430A ALA* 1.3 57.8 + - - +
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Residues in contact with ALA 430 (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 VAL* 4.3 13.9 - - + -
426A TYR* 2.8 45.8 + - + +
429A ALA* 1.3 75.6 - - - +
431A PHE* 1.3 64.2 + - - +
432A ALA 4.0 1.4 + - - -
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Residues in contact with PHE 431 (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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426A TYR* 5.2 3.1 - + + -
427A VAL* 3.0 30.9 + - + +
429A ALA 3.9 0.4 - - - -
430A ALA* 1.3 78.4 - - - +
432A ALA* 1.3 71.6 + - - +
433A GLY* 3.3 11.1 + - - -
435A SER* 3.5 32.3 - - - -
436A LYS* 4.2 15.5 - - + -
480A GLY* 4.1 10.8 - - - -
481A TYR* 3.7 37.2 - + - -
556A ALA* 3.6 26.0 - - + -
559A LEU* 4.0 32.8 - - + -
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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