Contacts of the strand formed by residues 144 - 148 (chain A) in PDB entry 4KZX
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 THR 144 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A LEU* 4.4 0.4 - - - +
122A LEU* 3.2 9.3 - - + +
124A VAL* 4.2 5.4 - - + -
134A LEU* 3.3 31.8 + - + +
137A ALA* 4.3 12.1 - - - +
142A LEU 3.5 8.1 + - - -
143A PRO* 1.3 76.7 + - - +
145A ILE* 1.3 72.0 + - - +
156A TYR 3.6 17.7 + - - -
157A VAL* 4.0 12.8 - - + -
158A ASP* 2.7 41.4 + - - +
159A ILE* 3.3 0.9 - - - +
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Residues in contact with ILE 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 5.4 0.7 - - + -
61A ALA* 3.8 22.7 - - + +
64A ALA* 4.7 10.3 - - + -
65A ILE* 5.1 1.1 - - + -
121A LEU* 4.0 19.1 - - + -
122A LEU 2.6 8.3 + - - -
123A VAL* 3.4 31.8 - - + -
124A VAL 2.9 22.1 + - - -
144A THR* 1.3 77.4 - - - +
146A ALA* 1.3 71.1 + - - +
158A ASP* 3.9 4.5 - - - +
159A ILE* 2.6 46.9 - - + -
161A ILE* 3.2 25.1 - - + -
178A LEU* 5.7 2.7 - - + -
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Residues in contact with ALA 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A VAL* 5.2 0.9 - - - -
124A VAL* 3.2 17.7 - - + +
127A PRO* 5.2 4.5 - - + -
144A THR* 4.6 0.2 - - + -
145A ILE* 1.3 88.2 - - - +
147A LEU* 1.3 64.8 + - - +
148A CYS* 3.3 14.9 + - - -
157A VAL* 4.2 22.9 - - + -
159A ILE 3.3 8.9 + - - +
160A ALA* 3.5 4.7 - - - -
161A ILE* 3.1 28.5 + - - -
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Residues in contact with LEU 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A ARG* 5.9 0.7 - - - +
124A VAL 2.9 5.3 + - - +
125A THR* 2.0 63.5 - - + +
126A ASP* 5.5 0.2 - - + -
127A PRO* 3.1 23.7 - - - +
146A ALA* 1.3 71.0 - - - +
148A CYS* 1.3 62.4 + - - +
149A ASN 4.1 0.5 + - - -
152A SER* 4.3 0.2 + - - -
161A ILE* 4.0 2.9 - - + +
163A CYS* 2.8 31.4 - - - -
165A ASN* 3.7 29.4 + - + -
171A VAL* 4.1 19.5 - - + -
174A MET* 5.0 7.9 - - + -
175A TRP* 4.8 7.4 - - + +
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Residues in contact with CYS 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A MET* 4.0 16.6 - - + -
127A PRO* 4.3 6.5 - - - -
146A ALA* 3.3 22.2 + - - -
147A LEU* 1.3 84.3 - - - +
149A ASN* 1.3 67.0 + - - +
152A SER* 3.8 17.0 - - - -
153A PRO 4.6 6.5 - - - -
154A LEU* 5.5 1.6 - - - -
157A VAL* 4.9 6.7 - - - -
160A ALA* 3.8 18.6 - - + -
161A ILE 3.1 10.3 + - - +
162A PRO* 2.9 11.1 - - - +
163A CYS* 2.9 21.7 + - - -
165A ASN* 3.4 2.5 - - - -
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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