Contacts of the helix formed by residues 509 - 518 (chain A) in PDB entry 3FZT
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 509 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507A TYR 4.0 1.1 + - - +
508A GLY* 1.3 73.7 - - - +
510A LEU* 1.3 67.1 + - - +
511A GLY* 3.3 3.9 + - - +
512A HIS* 3.4 37.3 + - - +
513A TYR* 3.0 20.3 + - - +
552A VAL 4.2 3.6 - - - +
553A ARG* 3.3 41.0 - - - +
555A ILE 3.3 7.2 - - - +
556A LEU* 3.8 13.0 - - + -
568A PHE* 4.2 11.5 - - + -
999A 4JZ 5.5 2.6 - - + -
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Residues in contact with LEU 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508A GLY 3.7 1.0 + - - -
509A GLU* 1.3 70.3 - - - +
511A GLY* 1.3 60.1 + - - +
513A TYR* 3.5 3.2 - - + +
514A LEU* 2.8 51.6 + - + +
529A TYR* 3.8 33.7 - - + -
552A VAL* 3.6 24.2 + - + +
555A ILE* 2.7 41.4 + - + +
557A VAL* 3.8 24.4 - - + +
563A VAL* 4.1 7.6 - - + -
618A ILE* 3.9 20.2 - - + -
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Residues in contact with GLY 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509A GLU* 3.3 2.7 - - - +
510A LEU* 1.3 76.8 - - - +
512A HIS* 1.3 58.8 + - - +
514A LEU* 3.3 4.5 + - - +
515A GLU* 3.0 38.7 + - - +
552A VAL* 3.0 36.5 + - - +
553A ARG* 5.3 0.7 - - - -
622A GLY* 4.1 8.7 - - - -
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Residues in contact with HIS 512 (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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509A GLU* 3.4 38.4 + - + +
511A GLY* 1.3 73.3 - - - +
513A TYR* 1.3 59.9 + - - +
515A GLU* 3.1 32.7 + - - +
516A ARG* 3.0 47.9 + - + +
553A ARG* 6.1 0.2 - - + -
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Residues in contact with TYR 513 (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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507A TYR* 3.5 31.9 - + + +
509A GLU 3.0 17.8 + - - +
510A LEU* 3.5 12.1 - - + +
512A HIS* 1.3 75.6 - - - +
514A LEU* 1.3 67.8 + - + +
516A ARG* 3.3 27.8 + - - +
517A ASN* 2.8 53.0 + - - +
521A LEU* 4.2 20.2 - - + +
529A TYR* 3.7 20.6 + + - -
557A VAL* 3.7 32.1 - - + -
560A PRO* 3.9 27.4 - - - +
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Residues in contact with LEU 514 (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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510A LEU* 2.8 50.9 + - + +
511A GLY 3.5 4.0 - - - +
513A TYR* 1.3 74.1 - - + +
515A GLU* 1.3 62.4 + - - +
517A ASN 3.6 0.2 - - - -
518A LYS* 3.0 28.4 + - - +
521A LEU* 3.5 24.9 - - + -
526A LEU* 3.7 20.9 - - + -
529A TYR* 4.4 5.4 - - + -
552A VAL* 4.6 4.0 - - + -
617A GLU 4.2 0.4 - - - +
618A ILE* 3.7 35.9 - - + +
621A PHE* 3.7 18.9 - - + -
622A GLY* 4.1 8.7 - - - +
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Residues in contact with GLU 515 (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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511A GLY* 3.0 22.3 + - - +
512A HIS* 3.3 36.0 - - - +
514A LEU* 1.3 77.2 - - - +
516A ARG* 1.3 62.1 + - + +
517A ASN 3.3 0.7 + - - -
518A LYS* 3.5 20.1 - - - +
621A PHE 3.6 14.8 + - - +
622A GLY* 3.9 15.2 - - - +
624A GLN* 5.4 1.2 - - - +
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Residues in contact with ARG 516 (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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507A TYR* 3.1 33.1 + - - +
509A GLU 6.1 0.2 - - - +
512A HIS* 3.0 39.2 + - + +
513A TYR* 3.6 31.7 - - - +
514A LEU 3.3 0.2 - - - -
515A GLU* 1.3 77.2 - - + +
517A ASN* 1.3 70.4 + - - +
518A LYS* 3.7 1.2 - - - +
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Residues in contact with ASN 517 (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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513A TYR* 2.8 50.1 + - + +
514A LEU 3.2 2.0 + - - -
516A ARG* 1.3 92.6 + - - +
518A LYS* 1.3 64.0 + - - +
519A ASN 3.1 3.4 - - - -
520A SER* 3.0 27.7 + - - +
521A LEU* 3.2 31.3 + - + +
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Residues in contact with LYS 518 (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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514A LEU 3.0 9.1 + - - +
515A GLU* 3.5 17.5 - - - +
516A ARG 3.7 1.1 + - - -
517A ASN* 1.3 76.4 - - - +
519A ASN* 1.3 90.4 + - - +
520A SER 3.4 0.7 + - - -
521A LEU 4.0 3.6 + - - +
621A PHE* 3.6 48.9 - - + -
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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