Contacts of the helix formed by residues 559 - 567 (chain B) in PDB entry 1JSC
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 559 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B PRO* 3.3 10.3 - - - +
137B LYS 2.8 11.8 + - - -
138B HIS* 3.1 37.4 + - - +
141B GLY* 3.6 16.4 - - - -
145B MET* 5.1 1.3 - - - +
529B LEU* 3.9 15.9 - - + -
530B PRO* 4.5 10.1 - - + -
533B ILE* 3.6 13.7 - - + +
556B THR* 3.0 22.5 + - - +
558B THR* 1.3 79.4 - - + +
560B LEU* 1.3 64.8 + - - +
561B SER 3.2 0.7 - - - -
562B SER* 2.6 44.3 + - - -
563B ALA 3.0 9.2 + - - -
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Residues in contact with LEU 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529B LEU* 3.5 31.6 - - + +
553B PHE* 3.7 26.2 - - + -
557B LEU 3.1 17.0 + - - +
558B THR 3.0 0.4 - - - -
559B GLU* 1.3 77.9 - - - +
561B SER* 1.3 62.9 + - - +
563B ALA* 3.1 20.6 + - + +
564B VAL* 3.3 10.0 + - - +
570B VAL* 6.4 0.2 - - + -
572B ILE* 4.5 6.3 - - + -
608B LEU* 4.0 17.9 - - + -
609B ALA* 4.7 4.3 - - - -
612B MET* 3.5 25.8 - - + -
614B LEU* 3.8 31.5 - - + +
640B LEU* 4.5 8.3 - - + -
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Residues in contact with SER 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554A ASN* 4.4 1.9 + - - -
601A LEU* 3.8 14.7 - - - +
603A PRO* 4.8 7.4 - - - -
137B LYS* 2.7 35.2 + - - +
558B THR 3.3 11.4 + - - -
560B LEU* 1.3 76.5 - - - +
562B SER* 1.3 60.3 + - - +
564B VAL* 3.3 4.6 + - - +
565B GLN* 3.0 28.4 + - - +
612B MET* 3.7 33.9 - - - -
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Residues in contact with SER 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B VAL* 6.3 0.7 - - - -
135B LEU 3.7 17.0 + - - +
136B PRO* 3.4 5.0 - - - +
137B LYS* 3.4 22.5 + - - +
145B MET* 5.1 4.7 - - - -
533B ILE* 4.5 7.0 - - - -
559B GLU* 2.6 40.5 + - - -
561B SER* 1.3 77.7 + - - +
563B ALA* 1.3 57.3 + - - +
565B GLN* 3.3 4.7 + - - +
566B ALA* 2.9 32.8 + - - +
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Residues in contact with ALA 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529B LEU* 5.1 1.8 - - + -
533B ILE* 3.9 19.9 - - + +
559B GLU 3.0 5.7 + - - +
560B LEU* 3.3 13.0 - - + +
562B SER* 1.3 77.5 - - - +
564B VAL* 1.3 62.4 + - - +
566B ALA* 3.3 1.5 + - - -
567B GLY* 3.0 18.5 + - - -
568B THR* 3.1 37.0 + - - +
570B VAL* 4.2 11.4 - - + -
614B LEU* 5.5 2.7 - - + -
638B PRO* 4.7 7.5 - - + +
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Residues in contact with VAL 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601A LEU* 3.6 19.1 - - + -
560B LEU 3.3 9.8 + - - +
561B SER 3.3 6.7 + - - +
562B SER 3.3 0.2 - - - -
563B ALA* 1.3 76.5 - - - +
565B GLN* 1.3 63.5 + - - +
567B GLY* 3.0 14.0 + - - -
612B MET 3.7 20.2 - - - +
613B GLY* 3.7 24.5 - - - +
614B LEU* 3.9 12.1 - - + -
638B PRO* 4.2 13.5 - - + -
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Residues in contact with GLN 565 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599A HIS 3.5 19.7 + - - -
600A GLN* 2.5 32.8 + - - +
601A LEU* 3.0 34.0 + - + +
135B LEU* 3.9 24.8 - - - +
137B LYS* 3.9 0.7 + - - -
561B SER 3.0 16.3 + - - +
562B SER* 3.7 5.4 - - - +
564B VAL* 1.3 77.2 - - - +
566B ALA* 1.3 59.2 + - - +
567B GLY 3.2 0.9 + - - -
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Residues in contact with ALA 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B VAL* 4.3 26.5 - - + -
135B LEU 5.9 0.2 - - - +
533B ILE* 4.9 2.7 - - + -
537B VAL* 5.1 3.8 - - + +
562B SER 2.9 17.9 + - - +
563B ALA 4.0 2.7 - - - +
565B GLN* 1.3 75.7 - - - +
567B GLY* 1.3 63.4 + - - +
568B THR* 3.3 19.5 + - + +
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Residues in contact with GLY 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563B ALA 3.0 4.6 + - - -
564B VAL* 3.0 13.7 + - - -
565B GLN 3.2 1.6 + - - -
566B ALA* 1.3 78.7 - - - +
568B THR* 1.3 58.2 + - - +
569B PRO* 3.1 14.0 - - - +
638B PRO* 5.8 3.8 - - - -
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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