Contacts of the helix formed by residues 558 - 565 (chain A) in PDB entry 4AY6
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 HIS 558 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554A ASP* 3.2 42.9 + - + +
556A GLY 2.9 8.8 + - - +
557A ASN* 1.3 79.2 + - - +
559A PRO* 1.3 95.0 - - + +
560A THR* 3.1 24.2 + - - -
561A SER* 2.7 16.8 + - - -
562A HIS* 3.0 15.5 + - - -
1200A 12V 4.5 4.3 - - - -
1393E PRO* 4.2 9.2 - - + -
1394E TYR 4.2 16.4 + - - -
1395E DNP 4.4 9.1 - - - -
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Residues in contact with PRO 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A HIS* 1.3 101.7 - - + +
560A THR* 1.3 55.8 + - - +
562A HIS* 2.6 40.5 + - + +
563A LEU* 2.8 17.9 + - - +
921A THR* 3.8 11.0 - - + +
1200A 12V 3.7 41.7 - - - +
1393E PRO* 3.7 24.2 - - + +
1394E TYR* 4.3 8.7 - - - -
1395E DNP 4.4 0.2 - - - +
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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
----------------------------------------------------------
552A SER* 4.2 11.9 - - - +
554A ASP* 3.8 15.3 + - - +
555A PHE* 5.9 0.4 - - + -
558A HIS* 3.0 21.8 + - - -
559A PRO* 1.3 76.4 - - - +
561A SER* 1.3 62.5 + - - +
563A LEU* 3.2 6.7 + - - +
564A MET* 3.1 31.5 + - + +
629A MET* 3.4 38.1 + - + +
653A LEU* 5.6 2.9 - - + -
654A GLY* 4.8 4.9 - - - -
1200A 12V 2.9 23.6 + - - +
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Residues in contact with SER 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A ASP 2.7 21.1 + - - -
555A PHE* 3.5 8.7 - - - -
556A GLY 3.1 30.7 + - - -
558A HIS 2.7 8.9 + - - -
560A THR* 1.3 74.8 - - - +
562A HIS* 1.3 63.4 + - - -
563A LEU 2.9 1.6 + - - -
564A MET* 4.1 7.4 - - - -
565A GLN* 3.0 33.1 + - - +
591A PHE* 4.0 16.2 - - - +
595A VAL* 5.1 3.6 - - - +
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Residues in contact with HIS 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A ASN* 3.0 26.1 + - - -
558A HIS* 3.0 24.9 + - - -
559A PRO* 2.6 26.1 + - + +
561A SER* 1.3 71.7 - - - +
563A LEU* 1.3 59.7 + - + +
565A GLN* 5.3 0.2 - - - -
591A PHE* 3.7 28.2 - + - -
697A ASP* 3.1 27.0 + - - +
698A HIS* 4.8 3.0 + - + -
701A MET* 3.7 20.8 - - + +
809A THR 4.9 2.4 + - - -
898A LYS* 3.3 41.5 + - + +
1200A 12V 3.7 7.6 + - - -
1392E VAL* 5.7 2.7 - - + -
1393E PRO* 4.6 6.5 - - + -
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Residues in contact with LEU 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559A PRO 2.8 16.9 + - - +
560A THR* 3.6 6.1 - - - +
561A SER 2.9 0.8 + - - -
562A HIS* 1.3 81.6 - - + +
564A MET* 1.3 60.0 + - - +
565A GLN 3.6 0.7 - - - -
653A LEU* 3.9 33.7 - - + -
694A PHE* 4.0 22.4 - - + -
695A ILE* 3.4 25.6 - - - +
696A GLY* 3.6 12.2 + - - -
697A ASP* 3.2 26.3 + - - +
698A HIS* 4.6 4.0 - - + -
921A THR* 4.0 31.9 - - + +
924A MET* 4.6 4.5 - - + -
999A THR* 4.9 2.4 - - - +
1200A 12V 4.3 13.0 - - + +
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Residues in contact with MET 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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550A TYR* 5.4 4.0 - - + -
555A PHE* 4.1 21.3 - - + -
560A THR* 3.1 24.8 + - - +
561A SER* 4.1 4.9 - - - -
563A LEU* 1.3 76.2 - - - +
565A GLN* 1.3 73.7 + - - +
566A SER 2.9 5.5 + - - -
567A ILE* 3.0 36.0 + - + -
568A PRO* 3.3 19.5 - - + +
595A VAL* 5.7 1.3 - - + -
629A MET* 3.6 33.7 - - + -
652A TRP* 3.8 13.7 - - + -
653A LEU* 3.8 17.0 - - + -
695A ILE* 4.7 0.4 - - + -
999A THR* 6.2 0.2 - - - -
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Residues in contact with GLN 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A SER* 3.0 24.5 + - - +
563A LEU 3.6 0.4 - - - -
564A MET* 1.3 82.5 - - - +
566A SER* 1.3 61.6 + - - +
567A ILE 3.6 0.2 + - - -
568A PRO* 3.7 9.2 - - - +
590A ASN 4.8 0.5 - - - +
591A PHE* 3.3 34.8 - - - +
594A LYS* 3.6 35.3 - - + +
595A VAL* 4.5 21.4 - - + +
598A GLU* 4.2 3.5 - - - +
697A ASP* 2.7 28.5 + - - +
700A ASN* 3.6 7.1 - - - +
701A MET* 3.4 21.0 - - - +
810A GLY 5.4 0.6 + - - -
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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
------------------------------------------------------------
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