Contacts of the strand formed by residues 153 - 158 (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 GLN 153 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99J ALA* 4.7 0.5 - - - +
147J LYS* 3.7 4.0 - - - +
148J GLN* 2.9 40.2 + - + +
151J ASN* 3.7 28.7 + - + +
152J LYS* 1.3 78.9 - - - +
154J ILE* 1.4 72.5 + - - +
155J TRP* 5.8 0.5 - - - +
165J ARG* 3.9 37.7 - - - +
166J TYR 3.6 11.7 - - - +
167J ASP* 3.2 29.5 + - - +
168J TRP* 3.9 6.5 - - - +
151K ASN* 4.2 11.5 + - - +
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Residues in contact with ILE 154 (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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98J LEU 4.6 4.3 - - - +
99J ALA* 3.5 39.7 - - + +
102J THR* 5.6 5.8 - - + -
103J LEU* 4.2 11.7 - - + -
145J ILE* 4.7 6.3 - - + -
146J ASN 3.7 7.9 - - - +
147J LYS* 3.9 16.8 - - - -
153J GLN* 1.4 80.6 - - - +
155J TRP* 1.4 62.4 + - - +
165J ARG* 4.0 0.5 - - - -
166J TYR* 2.9 41.9 + - + +
168J TRP* 4.5 6.9 - - + +
182J LEU* 3.5 39.0 - - + -
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Residues in contact with TRP 155 (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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144J VAL* 4.1 4.0 - - + +
145J ILE* 4.1 0.3 - - - -
146J ASN* 3.2 50.7 + - - +
148J GLN* 3.7 37.7 - - + +
153J GLN* 4.1 2.1 + - - +
154J ILE* 1.4 75.6 - - - +
156J LEU* 1.3 58.6 + - - +
157J SER* 3.7 29.2 + - - -
163J PRO* 3.6 33.5 - - + +
164J LYS 3.2 26.2 - - - -
165J ARG* 3.8 19.1 - - + +
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Residues in contact with LEU 156 (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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143J TYR* 3.8 25.1 - - + -
144J VAL 3.8 6.1 - - - +
145J ILE* 3.7 29.6 - - + +
154J ILE 4.1 1.0 + - - -
155J TRP* 1.3 74.6 - - - +
157J SER* 1.4 57.3 + - - +
158J SER* 3.6 13.0 + - - -
163J PRO* 3.4 2.4 - - - +
164J LYS* 2.7 46.4 + - + +
166J TYR* 3.9 36.8 - - + +
182J LEU* 3.9 16.4 - - + +
185J LEU* 4.1 20.0 - - + -
186J LEU* 5.8 1.6 - - + -
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Residues in contact with SER 157 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143J TYR* 3.6 7.8 - - - +
144J VAL* 3.1 43.0 + - - +
155J TRP* 3.7 31.8 + - - -
156J LEU* 1.4 68.4 - - - +
158J SER* 1.3 60.6 + - - +
159J PRO* 3.8 6.3 - - - +
163J PRO* 4.3 10.5 - - - +
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Residues in contact with SER 158 (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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143J TYR* 3.2 32.8 + - - -
156J LEU* 3.6 17.9 + - - -
157J SER* 1.3 74.8 + - - +
159J PRO* 1.3 59.0 - - - +
160J SER 3.1 4.4 + - - -
161J SER* 2.9 26.0 + - - -
162J GLY* 2.8 41.6 + - - +
163J PRO* 4.1 1.7 - - - +
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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