Contacts of the strand formed by residues 153 - 158 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150J PRO 4.4 1.6 - - - +
151J ASN* 3.1 28.1 + - - +
152J LYS* 3.4 31.1 + - + +
151K ASN* 5.5 0.4 + - - -
146L ASN* 3.5 5.0 - - - +
148L GLN 4.2 1.4 - - - +
151L ASN* 3.0 55.2 + - - +
152L LYS* 1.4 90.2 + - - +
154L ILE* 1.3 69.1 + - - +
155L TRP* 3.7 25.8 - - + +
165L ARG* 5.2 5.6 - - + -
166L TYR 3.4 9.2 - - - +
167L ASP* 3.7 11.5 + - - +
168L TRP* 3.5 4.5 - - - -
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Residues in contact with ILE 154 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99L ALA* 5.2 8.5 - - + -
103L LEU* 4.6 22.0 - - + -
145L ILE* 5.1 7.9 - - + -
146L ASN* 3.5 23.6 - - - +
147L LYS* 5.5 0.7 - - - -
148L GLN 5.1 2.9 - - - +
153L GLN* 1.3 78.7 - - - +
155L TRP* 1.3 71.7 + - - +
156L LEU* 5.7 1.1 - - + -
164L LYS 3.6 0.3 - - - +
165L ARG* 3.9 0.5 - - - -
166L TYR* 2.9 42.4 + - + +
167L ASP 6.4 0.2 - - - -
168L TRP* 4.0 27.1 - - + -
173L TRP* 5.8 3.1 - - + +
182L LEU* 3.8 32.1 - - + -
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Residues in contact with TRP 155 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96J GLU* 5.3 0.2 - - - -
97J ARG* 5.1 18.6 - - + -
152J LYS* 4.0 38.2 - - + +
168J TRP* 6.2 0.2 - + - -
144L VAL* 2.9 18.4 - - + +
145L ILE* 3.5 1.4 - - - -
146L ASN* 3.1 38.3 + - + +
151L ASN* 5.0 1.5 - - - +
153L GLN* 3.7 20.1 - - + +
154L ILE* 1.3 81.2 - - - +
156L LEU* 1.3 60.5 + - - +
157L SER* 5.3 0.9 - - - +
163L PRO* 3.7 40.6 - - + -
164L LYS 3.3 20.9 - - - -
165L ARG* 3.6 32.5 - - + -
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Residues in contact with LEU 156 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143L TYR* 4.1 16.2 - - + -
144L VAL 3.4 0.7 - - - +
145L ILE* 3.4 34.3 - - + +
154L ILE* 4.1 2.0 - - + -
155L TRP* 1.3 74.1 - - - +
157L SER* 1.4 60.3 + - - +
158L SER* 3.4 14.8 + - - +
163L PRO* 4.5 1.1 - - - -
164L LYS* 2.9 40.6 + - + +
166L TYR* 3.8 30.4 - - + +
182L LEU* 4.5 22.2 - - + +
185L LEU* 5.3 0.9 - - + -
186L LEU* 5.0 11.7 - - + +
189L GLU* 4.4 17.5 - - - +
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Residues in contact with SER 157 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159G PRO 5.1 0.2 + - - -
134L VAL* 5.4 0.7 - - - +
142L THR* 3.3 39.5 + - - +
143L TYR* 3.4 5.1 + - - -
144L VAL* 3.1 38.3 + - - +
155L TRP* 4.1 0.9 - - - -
156L LEU* 1.4 72.0 - - - +
158L SER* 1.4 62.2 + - - +
162L GLY* 3.5 14.1 + - - -
163L PRO* 4.2 10.3 - - - +
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Residues in contact with SER 158 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159G PRO 3.8 0.2 - - - +
142L THR* 3.7 2.8 + - - -
143L TYR* 6.1 1.1 - - - -
156L LEU* 3.4 10.2 + - - +
157L SER* 1.4 72.4 - - - +
159L PRO* 1.3 62.2 - - - +
160L SER* 3.1 16.1 + - - -
161L SER 4.2 2.7 - - - -
162L GLY* 2.8 34.2 + - - +
164L LYS* 3.8 31.3 + - - -
189L GLU* 3.2 30.4 + - - -
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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