Contacts of the helix formed by residues 688 - 698 (chain B) in PDB entry 5YDJ
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 LYS 688 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566B GLU* 6.3 0.2 - - - +
684B ALA* 3.0 26.3 + - + +
687B LYS* 1.3 114.0 - - + +
689B TYR* 1.3 63.9 + - - +
690B LEU 3.7 0.2 - - - -
691B PRO* 3.8 6.2 - - - +
692B GLN* 3.5 24.0 + - - +
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Residues in contact with TYR 689 (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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530B ALA* 4.2 13.5 - - + +
684B ALA 3.0 14.5 + - - +
685B PHE* 3.8 28.0 - + + +
688B LYS* 1.3 72.4 - - + +
690B LEU* 1.3 63.2 + - - +
692B GLN* 3.2 25.7 - - + +
693B LEU* 3.0 55.7 + - + +
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Residues in contact with LEU 690 (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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523B VAL* 4.8 13.7 - - + -
527B ALA* 3.9 28.3 - - + +
530B ALA* 4.1 1.8 - - + -
531B ILE* 4.5 6.5 - - + -
558B TYR* 6.0 0.4 - - + -
685B PHE* 2.8 46.3 + - + +
686B TRP* 3.5 34.1 - - + +
689B TYR* 1.3 75.2 - - - +
691B PRO* 1.3 66.2 - - + +
693B LEU* 3.2 15.8 + - + +
694B VAL* 3.0 32.4 + - + +
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Residues in contact with PRO 691 (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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686B TRP 3.3 26.0 - - - +
687B LYS* 3.5 17.7 - - + +
688B LYS 3.8 10.5 - - - +
689B TYR 3.5 3.4 - - - -
690B LEU* 1.3 91.0 - - + +
692B GLN* 1.3 60.1 + - - +
694B VAL* 3.6 5.3 + - + +
695B ALA* 3.3 22.7 + - - +
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Residues in contact with GLN 692 (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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688B LYS* 3.5 16.6 + - - +
689B TYR* 3.2 30.4 + - + +
691B PRO* 1.3 76.4 - - - +
693B LEU* 1.3 58.9 + - - +
695B ALA* 4.1 7.6 - - - +
696B ALA* 3.2 25.1 + - - +
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Residues in contact with LEU 693 (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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526B ALA* 3.9 22.2 - - + +
527B ALA* 3.9 11.9 - - + -
530B ALA* 3.9 22.9 - - + -
689B TYR* 3.0 37.2 + - + +
690B LEU* 3.2 15.5 + - + +
692B GLN* 1.3 75.9 - - - +
694B VAL* 1.3 57.3 + - - +
696B ALA* 2.9 10.2 + - + +
697B THR* 2.8 58.5 + - + +
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Residues in contact with VAL 694 (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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523B VAL* 4.9 9.4 - - + -
524B ASN* 4.1 16.6 - - - +
527B ALA* 4.2 17.7 - - + -
690B LEU* 3.0 28.6 + - + +
691B PRO* 4.0 5.4 - - + +
693B LEU* 1.3 75.3 - - - +
695B ALA* 1.3 52.6 + - - +
697B THR* 3.5 7.0 - - - -
698B SER* 2.6 49.7 + - - +
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Residues in contact with ALA 695 (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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691B PRO 3.3 14.8 + - - +
692B GLN* 4.1 7.6 - - - +
693B LEU 3.2 0.8 - - - -
694B VAL* 1.3 77.2 - - - +
696B ALA* 1.3 65.2 + - - +
698B SER* 3.9 14.1 + - - +
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Residues in contact with ALA 696 (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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692B GLN 3.2 13.4 + - - +
693B LEU* 2.9 14.2 + - + +
695B ALA* 1.3 80.6 - - - +
697B THR* 1.3 63.5 + - + +
698B SER 4.6 0.9 - - - +
699B ASN* 4.9 2.4 - - - +
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Residues in contact with THR 697 (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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524B ASN* 3.2 27.7 + - - -
526B ALA* 3.8 18.8 - - + -
693B LEU* 2.8 41.3 + - + +
694B VAL* 3.3 2.4 + - - -
696B ALA* 1.3 76.0 - - + +
698B SER* 1.3 69.1 + - - +
699B ASN* 3.1 18.9 + - - +
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Residues in contact with SER 698 (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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524B ASN* 4.4 16.4 - - - +
694B VAL* 2.6 37.0 + - - +
695B ALA* 3.9 14.4 - - - +
696B ALA 4.6 0.7 - - - +
697B THR* 1.3 73.8 + - - +
699B ASN* 1.3 60.9 + - - +
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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