Contacts of the helix formed by residues 114 - 119 (chain j) in PDB entry 5KZ5
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 VAL 114 (chain j).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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682 PRO* 3.9 21.1 - - + -
692 LEU 4.6 3.1 + - - +
712 PRO* 5.7 0.4 - - + -
82j LYS* 3.5 30.1 - - + +
83j GLY 4.3 5.2 - - - +
113j THR* 1.3 72.0 - - - +
115j GLU* 1.4 64.7 + - - +
117j ALA* 3.1 18.7 + - + +
118j LEU* 3.3 9.4 + - + +
160l LYS* 3.7 38.6 - - + +
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Residues in contact with GLU 115 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85J GLY* 5.7 0.2 - - - -
86J HIS* 3.5 47.8 - - + +
171J LYS* 5.7 2.9 + - - -
172J ASN* 5.9 1.8 - - - +
173J TRP* 5.8 5.2 - - + -
113j THR* 3.4 2.9 - - - +
114j VAL* 1.4 76.6 - - - +
116j GLU* 1.4 55.6 + - - +
118j LEU* 3.4 12.8 + - - +
119j THR* 2.9 30.2 + - - -
160l LYS* 3.5 34.2 + - - +
161l LYS* 5.4 3.1 + - - +
164l ALA* 4.9 6.1 - - + +
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Residues in contact with GLU 116 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672 THR* 5.0 5.2 - - + +
173J TRP* 5.2 9.4 - - - -
184J GLU* 3.0 40.6 - - - +
206J SER* 5.5 2.8 - - - -
207J GLY 5.1 6.3 + - - +
112j LYS* 3.2 41.1 - - + +
113j THR* 3.3 13.2 + - - +
115j GLU* 1.4 73.8 - - - +
117j ALA* 1.3 60.4 + - - +
119j THR* 3.1 9.6 + - - +
120j ILE* 3.0 25.3 + - - +
124j ASP* 4.0 15.0 - - - +
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Residues in contact with ALA 117 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672 THR* 3.3 38.3 + - - +
682 PRO* 4.4 3.8 - - + -
113j THR 3.0 7.7 + - - +
114j VAL* 3.1 17.0 + - + +
116j GLU* 1.3 75.7 - - - +
118j LEU* 1.3 57.7 + - - +
120j ILE* 3.0 31.1 - - - +
147j LYS* 4.9 1.6 - - - +
150j LEU* 3.9 19.4 - - + +
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Residues in contact with LEU 118 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178J ASP* 4.3 6.6 - - - +
114j VAL* 3.3 8.4 + - + +
115j GLU* 3.4 13.4 + - - +
117j ALA* 1.3 77.0 - - - +
119j THR* 1.4 58.3 + - - +
120j ILE 3.4 0.7 - - - -
147j LYS* 3.8 24.0 + - + +
154j LYS* 3.8 25.8 - - - +
162j GLY* 4.2 14.4 - - - +
165j GLU* 3.4 27.1 - - + +
166j LYS* 3.5 17.0 - - + +
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Residues in contact with THR 119 (chain j).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173J TRP* 5.5 1.7 - - - -
178J ASP* 3.2 33.3 + - - +
179J GLY* 3.1 32.1 + - - +
180J VAL* 3.7 7.6 - - + -
184J GLU* 3.5 24.0 - - - +
115j GLU 2.9 15.4 + - - -
116j GLU* 3.1 17.1 + - - +
118j LEU* 1.4 77.7 - - - +
120j ILE* 1.4 63.6 + - - +
121j LYS* 3.3 8.0 + - - -
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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