Contacts of the helix formed by residues 677 - 686 (chain N) in PDB entry 5G04
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 THR 677 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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676N TRP* 1.3 78.3 - - - +
678N LEU* 1.3 61.3 + - - +
679N GLU* 3.5 16.8 - - - +
680N GLU* 3.1 37.3 + - - +
681N LEU* 2.9 27.4 + - - +
711N GLY* 4.0 27.4 - - - +
713N PHE* 4.2 2.0 - - - -
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Residues in contact with LEU 678 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677N THR* 1.3 73.4 - - - +
679N GLU* 1.3 65.7 + - + +
682N SER* 2.9 33.1 + - - -
689N VAL* 4.2 22.9 - - + -
692N LEU* 3.4 10.1 - - + +
693N ARG* 3.5 33.0 - - + +
696N MET* 3.9 19.5 - - + -
710N PRO 4.1 7.6 - - - +
711N GLY* 3.8 24.1 - - - -
712N THR* 4.1 6.0 - - - +
713N PHE* 4.1 13.7 - - + -
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Residues in contact with GLU 679 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677N THR* 3.5 17.1 + - - +
678N LEU* 1.3 82.1 - - + +
680N GLU* 1.3 64.9 + - + +
682N SER* 3.4 9.2 - - - -
683N LYS* 3.0 27.2 + - - +
689N VAL* 6.4 0.9 - - - -
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Residues in contact with GLU 680 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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675N SER 4.6 2.8 - - - +
676N TRP* 3.5 33.8 - - + -
677N THR* 3.1 37.6 + - - +
679N GLU* 1.3 81.1 - - + +
681N LEU* 1.3 57.6 + - - +
683N LYS* 3.3 8.0 + - - +
684N ALA* 3.0 22.2 + - - +
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Residues in contact with LEU 681 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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666N ILE* 3.5 39.7 - - + +
669N TYR* 4.4 16.8 - - + -
670N PHE* 5.8 1.1 - - + -
676N TRP* 3.7 21.9 - - + -
677N THR 2.9 13.9 + - - +
678N LEU 3.9 3.6 - - - +
680N GLU* 1.3 73.0 - - - +
682N SER* 1.3 57.7 + - - +
684N ALA* 4.2 2.0 - - - -
685N VAL* 2.8 55.6 + - + +
692N LEU* 3.7 18.8 - - + -
713N PHE* 3.4 34.1 - - + -
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Residues in contact with SER 682 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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678N LEU 2.9 22.5 + - - -
679N GLU* 3.4 12.0 - - - -
680N GLU 3.3 0.2 - - - -
681N LEU* 1.3 75.6 - - - +
683N LYS* 1.3 56.7 + - - +
686N LYS* 2.9 32.0 + - - +
687N MET 3.6 17.6 + - - +
689N VAL* 4.2 22.7 - - - +
692N LEU* 3.3 17.3 - - - +
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Residues in contact with LYS 683 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610N GLU* 3.9 2.6 - - - +
679N GLU 3.0 14.2 + - - +
680N GLU* 3.4 12.1 - - - +
681N LEU 3.2 0.2 - - - -
682N SER* 1.3 75.1 - - - +
684N ALA* 1.3 60.7 + - - +
686N LYS* 3.4 48.1 - - - +
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Residues in contact with ALA 684 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610N GLU* 3.1 20.2 - - - +
669N TYR* 2.8 47.1 + - + -
676N TRP* 3.7 21.1 - - + -
680N GLU 3.0 15.8 + - - +
681N LEU* 3.3 6.2 + - - +
683N LYS* 1.3 77.7 - - - +
685N VAL* 1.3 57.6 + - - +
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Residues in contact with VAL 685 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609N LEU* 3.7 27.4 - - + -
610N GLU 3.1 21.9 + - - +
662N VAL 4.6 1.1 - - - +
665N VAL* 3.7 21.1 - - + -
666N ILE* 4.2 6.7 - - + -
669N TYR* 4.0 16.4 - - + -
681N LEU* 2.8 45.5 + - + +
684N ALA* 1.3 73.1 - - - +
686N LYS* 1.3 66.2 + - - +
687N MET* 3.2 22.6 + - + +
692N LEU* 4.6 3.4 - - + -
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Residues in contact with LYS 686 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608N LYS* 3.1 23.5 - - + +
609N LEU 5.0 0.2 - - - -
610N GLU* 3.6 34.1 - - + +
682N SER 2.9 17.4 + - - +
683N LYS* 3.4 37.9 - - - +
684N ALA 3.5 0.2 - - - -
685N VAL* 1.3 77.1 - - - +
687N MET* 1.3 62.6 + - - +
688N PRO* 3.9 4.2 - - - +
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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