Contacts of the helix formed by residues 557 - 564 (chain A) in PDB entry 5FZ9
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 ASN 557 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0A MET 5.2 4.8 + - - -
26A PHE* 3.5 11.4 - - - -
92A GLU* 2.9 24.3 + - - +
411A TRP* 3.4 39.3 + - + +
415A SER* 6.2 0.6 - - - -
556A MET* 1.3 74.0 - - - +
558A PRO* 1.3 74.0 - - - +
559A ASN* 2.8 37.8 + - - +
560A THR* 3.0 29.5 + - - +
561A LEU* 3.6 2.9 + - - +
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Residues in contact with PRO 558 (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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26A PHE* 3.9 16.4 - - + -
29A PRO* 4.1 7.9 - - + -
411A TRP* 3.4 23.8 - - + -
498A TRP* 4.6 5.4 - - + -
520A TYR* 4.0 24.5 - - + -
556A MET 3.3 5.1 - - - +
557A ASN* 1.3 87.8 - - - +
559A ASN* 1.3 56.8 + - - +
561A LEU* 3.1 15.6 + - + +
562A MET* 3.0 31.8 + - - +
568A VAL* 3.9 26.2 - - + +
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Residues in contact with ASN 559 (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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0A MET 3.9 5.6 - - - +
26A PHE* 3.5 16.3 - - - -
27A LEU* 2.7 57.7 + - - +
29A PRO* 4.9 0.6 - - - +
557A ASN* 2.8 22.3 + - - +
558A PRO* 1.3 71.7 - - - +
560A THR* 1.3 56.8 + - - +
562A MET* 3.5 21.0 - - - +
563A THR* 3.0 33.4 + - - -
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Residues in contact with THR 560 (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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92A GLU* 4.3 4.9 + - - -
533A VAL* 4.8 1.8 - - + -
537A LEU* 3.7 29.8 - - + -
556A MET* 4.4 15.0 - - + -
557A ASN* 3.0 23.3 + - - +
559A ASN* 1.3 80.1 - - - +
561A LEU* 1.3 62.2 + - - +
563A THR* 3.4 6.8 + - - -
564A HIS* 3.1 38.2 + - + +
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Residues in contact with LEU 561 (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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498A TRP* 3.6 39.0 - - + +
522A VAL* 4.8 0.9 - - + -
530A LEU* 3.9 35.9 - - + +
533A VAL* 4.1 19.5 - - + -
534A MET* 5.2 0.4 - - + -
556A MET* 4.1 22.9 - - - -
557A ASN 3.6 2.4 + - - +
558A PRO* 3.1 12.4 + - + +
560A THR* 1.3 77.1 - - - +
562A MET* 1.3 58.2 + - - +
564A HIS* 3.0 17.2 + - - +
565A GLU 3.3 0.2 + - - -
566A VAL* 3.0 39.6 + - + +
568A VAL* 4.0 12.1 - - + -
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Residues in contact with MET 562 (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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27A LEU* 4.4 4.9 - - + +
28A PRO 4.8 1.6 - - - +
29A PRO* 3.9 38.8 - - + -
30A PRO* 4.4 9.0 - - + -
558A PRO 3.0 18.0 + - - +
559A ASN* 3.5 31.6 - - - +
560A THR 3.4 0.2 - - - -
561A LEU* 1.3 75.8 - - - +
563A THR* 1.3 62.6 + - - +
565A GLU* 3.1 14.9 + - - +
566A VAL 3.6 9.6 - - - +
567A PRO* 5.6 0.2 - - + -
568A VAL* 3.8 19.1 - - + +
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Residues in contact with THR 563 (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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559A ASN 3.0 19.5 + - - -
560A THR* 3.6 7.8 - - - -
561A LEU 3.2 0.2 - - - -
562A MET* 1.3 75.6 - - - +
564A HIS* 1.3 73.5 + - + +
565A GLU* 3.2 7.8 + - - +
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Residues in contact with HIS 564 (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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529A GLN* 5.1 1.6 + - - +
533A VAL* 3.8 34.9 - - + +
537A LEU* 4.7 11.2 - - + +
560A THR* 3.1 31.7 + - + +
561A LEU 3.0 7.8 + - - +
563A THR* 1.3 89.0 - - + +
565A GLU* 1.3 70.5 + - - +
566A VAL* 3.3 7.7 + - - +
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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