Contacts of the helix formed by residues 533 - 545 (chain A) in PDB entry 1F7U
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 GLN 533 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A VAL* 4.5 12.1 - - + -
64A MET* 4.5 14.5 - - - +
68A ASP* 4.5 13.7 + - - +
529A ARG 3.5 20.0 + - - +
530A LEU* 3.1 32.5 + - - +
532A GLY* 1.3 77.4 - - - +
534A TYR* 1.3 65.6 + - - +
535A PRO* 3.3 2.9 - - - -
536A ASP* 3.0 19.6 + - + +
537A VAL* 3.0 17.1 + - + +
553A TYR* 4.1 12.5 - - + -
556A LYS* 5.5 4.5 + - - +
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Residues in contact with TYR 534 (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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134A TYR* 3.8 28.7 - + + -
135A GLY* 4.3 9.6 - - - -
531A LEU 3.6 2.1 + - - +
532A GLY 3.5 0.2 - - - -
533A GLN* 1.3 76.7 - - - +
535A PRO* 1.3 69.0 - - + +
537A VAL* 3.1 8.2 + - + +
538A LEU* 3.0 58.6 + - + +
550A VAL* 5.0 6.1 - - + -
553A TYR* 3.4 42.2 + + - +
554A LEU* 4.9 1.8 - - + -
591A VAL* 3.7 12.8 - - + -
594A ASN* 3.6 22.5 + - + +
595A GLY* 3.3 36.2 + - - -
598A LEU* 4.0 5.7 - - - +
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Residues in contact with PRO 535 (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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29A VAL* 3.8 18.6 - - + +
30A ASN* 3.6 31.7 + - + +
31A ILE 5.3 0.4 - - - +
134A TYR* 3.6 26.9 - - + +
135A GLY* 4.0 26.4 - - - +
179A LEU* 6.0 0.2 - - - +
532A GLY 3.6 7.2 - - - +
533A GLN 3.5 3.1 - - - -
534A TYR* 1.3 94.3 - - + +
536A ASP* 1.3 60.0 + - - +
538A LEU* 3.4 3.7 + - - +
539A ARG* 3.1 22.7 + - - +
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Residues in contact with ASP 536 (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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30A ASN* 2.8 22.4 + - - +
32A VAL* 3.4 18.2 - - - +
33A ASP* 4.4 0.3 - - - +
36A ARG* 2.7 41.9 + - - -
60A TRP* 4.1 19.6 - - + +
533A GLN* 3.0 15.2 + - + +
535A PRO* 1.3 76.3 - - - +
537A VAL* 1.3 61.3 + - + +
539A ARG* 3.3 7.0 + - - +
540A ASN* 2.8 32.0 + - - +
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Residues in contact with VAL 537 (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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533A GLN* 3.0 17.1 + - + +
534A TYR* 3.4 14.6 - - + +
536A ASP* 1.3 77.4 - - + +
538A LEU* 1.3 58.0 + - - +
540A ASN* 3.2 6.2 + - - +
541A ALA* 2.7 27.4 + - - +
549A THR* 3.6 27.3 - - + +
550A VAL* 4.0 19.7 - - + -
553A TYR* 3.7 38.8 - - + -
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Residues in contact with LEU 538 (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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135A GLY* 3.2 33.4 - - - +
175A LEU* 3.8 9.9 - - + +
178A LYS* 4.0 21.1 - - + -
179A LEU* 3.8 17.4 - - + +
534A TYR* 3.0 49.8 + - + +
535A PRO 3.8 5.6 - - - +
536A ASP 3.3 0.2 - - - -
537A VAL* 1.3 75.4 - - + +
539A ARG* 1.3 63.0 + - - +
541A ALA* 3.1 5.4 + - - +
542A ILE 3.1 18.4 + - - -
550A VAL* 4.5 7.0 - - + -
598A LEU* 3.3 32.1 - - + -
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Residues in contact with ARG 539 (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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21A VAL* 5.5 7.5 - - - +
24A ASP* 3.6 46.5 + - + +
30A ASN* 5.6 2.0 - - - +
60A TRP* 6.4 1.5 - - - -
179A LEU* 4.4 6.7 - - + +
535A PRO 3.1 11.2 + - - +
536A ASP* 3.5 11.4 - - - +
538A LEU* 1.3 79.6 - - - +
540A ASN* 1.3 65.4 + - - +
542A ILE* 3.2 27.2 - - + +
543A LYS* 3.6 41.1 + - - +
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Residues in contact with ASN 540 (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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60A TRP* 3.6 36.4 - - + -
536A ASP 2.8 18.1 + - - +
537A VAL* 3.7 4.9 - - - +
539A ARG* 1.3 83.4 + - - +
541A ALA* 1.3 58.6 + - - +
543A LYS* 3.1 22.9 + - - +
544A THR* 3.0 37.0 + - - +
549A THR* 3.6 20.1 + - + +
916B H2U 4.6 8.7 + - - +
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Residues in contact with ALA 541 (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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171A PHE* 4.3 4.9 - - + -
175A LEU* 3.5 16.6 - - + +
537A VAL 2.7 18.4 + - - +
538A LEU* 3.1 7.6 + - - +
540A ASN* 1.3 78.1 - - - +
542A ILE* 1.3 57.0 + - - +
544A THR* 3.6 7.4 + - - -
545A HIS* 2.7 28.9 + - - -
546A GLU 3.8 1.3 + - - +
549A THR* 3.9 11.2 - - + +
550A VAL* 3.9 24.5 - - + -
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Residues in contact with ILE 542 (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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175A LEU* 3.5 13.4 - - + +
176A TYR* 3.7 52.5 + - + +
179A LEU* 3.7 39.0 - - + -
181A TRP* 4.5 7.6 - - - +
538A LEU 3.1 4.9 + - - -
539A ARG* 3.2 20.6 - - + +
541A ALA* 1.3 76.8 - - - +
543A LYS* 1.3 60.0 + - + +
545A HIS* 3.1 21.9 + - - -
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Residues in contact with LYS 543 (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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60A TRP* 6.0 0.4 - - - -
539A ARG* 3.6 32.2 - - - +
540A ASN* 3.1 24.0 + - - +
541A ALA 3.1 0.4 - - - -
542A ILE* 1.3 84.5 - - + +
544A THR* 1.3 64.0 - - + +
545A HIS* 4.6 5.0 + - - -
916B H2U 3.4 36.2 + - - -
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Residues in contact with THR 544 (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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467A ARG* 3.4 7.3 + - - -
540A ASN* 3.0 32.1 + - - +
541A ALA* 3.6 2.4 + - - -
543A LYS* 1.3 81.1 - - + +
545A HIS* 1.3 74.4 + - - +
546A GLU* 3.1 24.6 + - - +
549A THR* 2.9 25.1 + - - +
915B A 5.7 4.0 - - - +
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Residues in contact with HIS 545 (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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171A PHE* 4.4 0.4 - - - -
172A LEU* 3.8 35.1 - - + +
176A TYR* 2.7 32.1 + + - -
366A LYS* 4.5 0.7 - - - -
368A ILE* 4.2 9.0 - - + -
398A GLN* 3.1 36.6 + - - -
400A VAL* 3.8 18.8 - - + +
467A ARG* 3.2 27.6 - - - +
541A ALA 2.7 12.7 + - - -
542A ILE* 3.1 24.8 + - - -
543A LYS 4.6 3.8 + - - -
544A THR* 1.3 80.5 - - - +
546A GLU* 1.3 58.8 + - - +
547A PRO* 3.7 2.9 - - - +
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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