Contacts of the helix formed by residues 691 - 701 (chain F) in PDB entry 4YJL
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 691 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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647F ALA 5.2 0.4 + - - -
650F GLU* 3.7 13.9 + - - -
653F ARG* 3.3 49.8 - - - +
657F ARG* 3.5 6.8 + - - +
687F LEU 4.2 3.4 - - - +
689F ALA 3.4 1.1 - - - +
690F ARG* 1.3 80.4 + - - +
692F PRO* 1.4 72.2 - - - +
693F LYS* 3.5 5.3 + - - +
694F ASP* 2.8 33.5 + - + +
695F GLN* 2.9 30.6 + - - +
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Residues in contact with PRO 692 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690F ARG 4.2 3.4 - - - +
691F ASN* 1.4 87.6 - - - +
693F LYS* 1.3 57.3 + - - +
695F GLN* 3.4 17.1 + - - +
696F GLU* 2.9 37.5 + - + +
732F ASN* 6.2 0.2 - - - +
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Residues in contact with LYS 693 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650F GLU* 4.4 6.3 + - - -
654F GLN* 4.8 3.7 + - - -
657F ARG* 3.6 44.2 - - - +
691F ASN* 3.2 9.1 + - - +
692F PRO* 1.3 81.2 - - - +
694F ASP* 1.3 58.8 + - - +
696F GLU* 3.4 6.9 + - - +
697F ALA* 3.1 26.8 + - + +
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Residues in contact with ASP 694 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653F ARG* 2.7 34.1 + - - +
657F ARG* 2.8 37.8 + - - +
662F LEU* 3.5 29.1 - - + +
687F LEU* 3.8 12.9 - - - +
691F ASN* 2.8 18.3 + - - +
693F LYS* 1.3 70.6 - - - +
695F GLN* 1.3 60.9 + - - +
697F ALA* 3.8 3.5 - - - +
698F LEU* 3.0 36.6 + - + +
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Residues in contact with GLN 695 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688F SER 2.8 29.5 - - - +
690F ARG* 3.3 7.8 + - - -
691F ASN 2.9 27.6 + - - +
692F PRO* 3.4 24.9 - - - +
694F ASP* 1.3 74.0 - - - +
696F GLU* 1.3 59.7 + - - +
698F LEU* 3.4 2.8 + - - +
699F TRP* 3.0 35.5 + - - -
728F ASN* 4.3 2.5 - - - +
729F LEU* 4.0 18.5 - - + +
732F ASN* 3.2 53.1 + - + +
734F PRO* 5.2 0.2 - - - -
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Residues in contact with GLU 696 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692F PRO* 2.9 22.7 + - + +
693F LYS* 3.6 6.6 - - - +
695F GLN* 1.3 70.0 - - - +
697F ALA* 1.3 60.2 + - - +
699F TRP* 3.2 3.1 + - - +
700F ASP* 2.9 38.3 + - - +
734F PRO* 3.7 31.6 - - + +
736F LYS* 3.3 29.7 + - - +
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Residues in contact with ALA 697 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662F LEU* 4.3 9.4 - - + -
693F LYS* 3.1 18.0 + - + +
694F ASP* 3.8 7.2 - - - +
695F GLN 3.4 0.2 - - - -
696F GLU* 1.3 75.5 - - - +
698F LEU* 1.3 58.1 + - - +
700F ASP* 3.2 9.3 + - - +
701F MET* 2.8 51.9 + - + +
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Residues in contact with LEU 698 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662F LEU* 4.1 24.7 - - + -
666F LEU* 4.0 13.5 - - + -
684F LEU* 3.6 32.1 - - + -
687F LEU 5.1 0.2 - - - -
688F SER* 3.9 22.4 - - - +
694F ASP 3.0 24.7 + - - +
695F GLN 3.8 3.8 - - - +
697F ALA* 1.3 72.2 - - - +
699F TRP* 1.3 65.3 + - - +
701F MET* 3.2 4.9 + - + -
702F GLY 3.2 4.3 + - - -
703F ALA* 2.9 46.2 + - + +
707F LEU* 6.3 0.4 - - + -
725F ALA* 6.4 0.2 - - + -
729F LEU* 3.9 24.9 - - + -
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Residues in contact with TRP 699 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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695F GLN 3.0 25.6 + - - -
696F GLU 3.2 8.0 + - - +
698F LEU* 1.3 74.6 - - - +
700F ASP* 1.3 57.1 + - - +
702F GLY* 2.9 21.7 + - - -
703F ALA 4.9 1.1 - - - +
704F VAL* 3.8 35.5 + - + +
729F LEU* 2.9 43.6 + - + +
730F MET* 4.2 11.0 - - - -
732F ASN 3.5 9.0 + - - -
733F ARG* 3.6 46.2 - - + -
734F PRO* 3.5 21.8 - - + -
737F TYR* 3.6 49.1 + + + -
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Residues in contact with ASP 700 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696F GLU* 2.9 27.6 + - - +
697F ALA* 3.5 8.5 - - - +
699F TRP* 1.3 73.2 - - - +
701F MET* 1.3 60.0 - - + +
702F GLY 3.2 1.4 + - - -
736F LYS* 2.8 31.2 + - - -
737F TYR* 2.7 30.1 + - - -
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Residues in contact with MET 701 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662F LEU* 3.7 22.7 - - + -
663F GLN* 3.3 49.6 - - + +
666F LEU* 3.6 22.6 - - + +
697F ALA* 2.8 48.0 + - + +
698F LEU* 3.8 6.7 - - + +
699F TRP 3.2 0.6 - - - -
700F ASP* 1.3 78.5 - - + +
702F GLY* 1.3 60.2 + - - +
703F ALA 3.7 0.2 + - - -
706F MET* 4.8 4.9 - - - +
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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