Contacts of the helix formed by residues 521 - 532 (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 GLU 521 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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518A LEU 3.9 9.2 - - - +
519A LEU* 3.5 5.6 - - - +
520A LYS* 1.3 84.3 + - - +
522A PRO* 1.3 75.3 - - + +
523A ALA* 4.4 4.3 - - + +
524A ALA* 3.0 19.3 + - + +
525A LYS* 3.1 11.1 + - - +
567A VAL* 6.3 0.2 - - + -
568A LEU* 3.8 20.5 - - + +
577A LEU* 5.1 2.3 - - - +
581A ARG* 3.0 29.6 + - - -
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Residues in contact with PRO 522 (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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520A LYS 3.5 4.2 - - - +
521A GLU* 1.3 85.3 - - + +
523A ALA* 1.3 61.8 + - - +
525A LYS* 3.4 12.3 + - + +
526A LEU* 3.2 31.2 + - + +
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Residues in contact with ALA 523 (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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521A GLU* 3.3 2.3 - - + +
522A PRO* 1.3 78.6 - - - +
524A ALA* 1.3 62.4 + - - +
526A LEU* 3.6 2.6 + - - -
527A LEU 3.3 9.2 + - - -
560A GLN* 3.2 21.6 + - - +
563A SER* 5.3 2.2 - - - -
564A CYS* 3.1 33.0 - - - +
567A VAL* 4.2 23.1 - - + -
568A LEU* 4.5 4.0 - - + -
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Residues in contact with ALA 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A LEU* 3.7 24.0 - - + +
521A GLU* 3.0 15.9 + - - +
523A ALA* 1.3 78.2 - - - +
525A LYS* 1.3 64.7 + - - +
527A LEU* 3.2 3.5 + - - +
528A ILE* 2.9 28.8 + - - +
564A CYS* 4.4 1.1 - - - -
568A LEU* 3.7 23.5 - - + +
584A LEU* 3.9 18.5 - - + +
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Residues in contact with LYS 525 (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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101A GLU* 4.2 18.2 + - - +
116A PRO* 3.9 35.3 - - + +
519A LEU 4.0 7.4 - - - +
520A LYS* 2.9 37.8 + - - +
521A GLU 3.1 11.7 + - - +
522A PRO* 3.4 12.3 + - + +
524A ALA* 1.3 77.4 - - - +
526A LEU* 1.3 62.9 + - + +
528A ILE* 3.3 5.7 + - - +
529A ARG* 3.0 31.6 + - - +
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Residues in contact with LEU 526 (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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64A MET* 3.8 27.7 - - + +
522A PRO* 3.2 21.6 + - + +
523A ALA* 3.7 2.0 - - - +
524A ALA 3.2 0.2 - - - -
525A LYS* 1.3 79.3 - - + +
527A LEU* 1.3 63.3 + - - +
529A ARG* 3.3 29.8 + - - +
530A LEU* 3.1 24.9 + - - +
560A GLN* 3.7 31.4 - - - +
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Residues in contact with LEU 527 (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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523A ALA 3.3 11.1 + - - +
524A ALA 3.2 9.0 + - - +
526A LEU* 1.3 78.6 - - - +
528A ILE* 1.3 62.8 + - - +
530A LEU* 3.2 6.2 + - + +
531A LEU* 3.0 29.5 + - + +
557A LEU* 3.8 22.9 - - + +
560A GLN* 3.7 12.5 - - + +
561A VAL* 3.8 31.9 - - + +
564A CYS* 4.1 16.4 - - + -
584A LEU* 3.6 33.0 - - + +
585A TYR* 4.8 8.1 - - + -
588A ALA* 4.2 15.5 - - + -
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Residues in contact with ILE 528 (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 PRO* 3.5 26.7 - - + +
117A GLN* 5.6 0.9 - - - -
119A LEU* 3.7 20.9 - - + +
120A ALA* 3.8 28.3 - - + +
123A VAL* 5.1 3.9 - - + +
124A ILE* 4.9 2.7 - - + -
519A LEU* 4.0 31.4 - - + +
524A ALA 2.9 20.3 + - - +
525A LYS* 3.5 9.9 - - - +
526A LEU 3.2 0.2 - - - -
527A LEU* 1.3 72.6 - - - +
529A ARG* 1.3 65.1 + - - +
531A LEU* 3.1 21.8 + - + +
532A GLY* 3.3 9.5 + - - -
584A LEU* 3.7 17.5 - - + -
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Residues in contact with ARG 529 (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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64A MET* 2.9 50.6 + - - +
67A GLY* 3.2 19.8 + - - -
68A ASP* 2.6 40.0 + - - +
113A PHE* 4.4 12.0 - - - -
114A PHE* 5.4 2.0 - - + +
116A PRO* 4.5 15.0 - - + -
119A LEU* 4.0 22.9 - - + +
525A LYS* 3.0 23.1 + - - +
526A LEU* 3.7 22.2 - - - +
528A ILE* 1.3 76.2 - - - +
530A LEU* 1.3 63.5 + - - +
532A GLY* 3.2 10.9 + - - -
533A GLN* 3.5 17.5 + - - +
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Residues in contact with LEU 530 (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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64A MET* 3.5 37.2 - - + -
526A LEU 3.1 10.1 + - - +
527A LEU* 3.3 9.6 - - + +
529A ARG* 1.3 78.9 - - - +
531A LEU* 1.3 61.0 + - - +
533A GLN* 3.1 29.6 + - - +
553A TYR* 2.8 28.8 + - + -
556A LYS* 3.7 26.7 - - + +
557A LEU* 4.3 21.5 - - + +
560A GLN* 3.5 32.1 - - + -
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Residues in contact with LEU 531 (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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123A VAL* 4.2 4.9 - - + -
124A ILE* 4.5 7.2 - - + -
127A ILE* 4.0 11.4 - - + -
134A TYR* 2.9 25.9 + - - -
527A LEU* 3.0 18.4 + - + +
528A ILE* 3.1 10.3 + - + +
530A LEU* 1.3 75.5 - - - +
532A GLY* 1.3 60.6 + - - +
533A GLN 3.1 1.4 + - - -
534A TYR* 3.6 5.7 + - - +
553A TYR* 3.9 2.7 - - - -
557A LEU* 3.9 17.7 - - + -
584A LEU* 3.8 30.1 - - + +
587A ALA* 3.8 22.0 - - + -
588A ALA* 3.5 28.3 - - + +
591A VAL* 4.0 15.4 - - + +
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Residues in contact with GLY 532 (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* 4.4 1.4 - - - +
31A ILE* 3.5 23.8 - - - +
32A VAL* 3.5 18.4 - - - +
119A LEU* 5.9 2.2 - - - -
123A VAL* 4.2 8.2 - - - +
134A TYR* 3.6 9.6 + - - -
528A ILE 3.3 5.6 + - - -
529A ARG* 3.2 7.4 + - - -
530A LEU 3.2 1.0 - - - -
531A LEU* 1.3 77.1 - - - +
533A GLN* 1.3 61.3 + - - +
534A TYR 3.5 0.4 - - - -
535A PRO* 3.6 10.6 - - - +
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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