Contacts of the helix formed by residues 993 - 998 (chain B) in PDB entry 3DLS
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 GLY 993 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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991B CYS 3.5 1.0 + - - -
992B GLU* 1.3 88.6 + - - +
994B GLU* 1.3 64.3 + - - -
995B TYR 3.3 2.7 - - - -
996B SER* 3.3 15.6 + - - -
997B GLN* 3.5 16.7 + - - +
1073B ASN* 5.1 2.2 - - - -
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Residues in contact with GLU 994 (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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992B GLU 4.0 1.0 + - - -
993B GLY* 1.3 69.1 - - - -
995B TYR* 1.3 67.2 + - - +
997B GLN* 3.3 23.2 + - + +
998B LYS* 3.5 9.4 + - - +
1071B PHE* 3.4 40.7 - - + +
1072B GLU 5.5 5.6 + - - +
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Residues in contact with TYR 995 (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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991B CYS* 3.7 30.5 - - + +
992B GLU 4.8 0.6 + - - -
993B GLY 3.3 0.8 - - - -
994B GLU* 1.3 77.8 - - - +
996B SER* 1.3 56.5 + - - +
998B LYS* 3.0 5.9 + - - +
999B TYR* 2.8 69.2 + + + +
1001B THR* 2.6 31.2 + - - -
1016B ALA* 3.3 22.2 - - + +
1027B VAL* 3.4 25.8 - - + +
1029B PHE* 4.2 3.6 - + - -
1071B PHE* 3.7 20.6 - + + +
1078B GLN* 3.8 27.8 - - + +
1080B VAL* 3.8 14.8 - - + -
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Residues in contact with SER 996 (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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991B CYS* 2.5 37.9 + - - +
992B GLU* 4.3 1.3 - - - -
993B GLY 3.3 12.4 + - - -
995B TYR* 1.3 78.8 - - - +
997B GLN* 1.3 57.7 + - - +
999B TYR 3.5 14.8 - - - +
1019B LYS* 2.9 19.6 + - - -
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Residues in contact with GLN 997 (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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993B GLY 3.6 15.1 - - - +
994B GLU* 3.4 16.6 - - + +
995B TYR 3.2 0.2 - - - -
996B SER* 1.3 77.4 - - - +
998B LYS* 1.3 56.5 + - + +
1019B LYS* 2.8 21.8 + - - +
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Residues in contact with LYS 998 (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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994B GLU 3.5 7.8 + - - +
995B TYR 3.0 3.8 + - - +
997B GLN* 1.3 79.7 - - + +
999B TYR* 1.3 88.3 + - + +
1018B ASP* 3.2 26.1 + - - +
1019B LYS* 3.1 30.2 + - - +
1020B GLU* 4.8 5.0 + - + +
1023B LYS* 5.2 0.6 - - - +
1069B ASP* 3.3 23.8 + - - +
1071B PHE* 3.8 11.4 - - + -
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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