Contacts of the strand formed by residues 116 - 124 (chain A) in PDB entry 1JCZ
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 ALA 116 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A LEU* 5.3 0.2 - - + -
96A HIS 3.2 15.9 - - - +
97A TRP* 4.2 9.9 - - + -
105A SER* 3.5 14.9 - - - +
114A PHE* 3.3 0.8 - - - +
115A ALA* 1.3 78.9 - - - +
117A GLU* 1.3 65.9 + - - +
147A LEU 3.9 0.3 - - - -
148A ILE* 2.9 46.6 + - + +
218A ILE* 5.6 0.2 - - + -
223A LEU* 4.5 6.7 - - + -
226A LEU* 4.4 12.1 - - + -
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Residues in contact with GLU 117 (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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95A LEU* 3.3 5.4 - - - +
96A HIS* 3.0 36.9 + - + +
105A SER* 3.6 13.0 - - - -
106A GLU* 2.8 29.6 + - - +
107A HIS* 2.8 32.6 + - - -
116A ALA* 1.3 80.3 - - - +
118A LEU* 1.3 63.6 - - - +
119A HIS* 2.7 34.7 + - + +
145A ALA* 3.5 7.6 - - + +
146A VAL 3.3 14.8 - - - +
147A LEU* 3.7 11.2 - - + +
148A ILE* 4.2 4.7 - - - -
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Residues in contact with LEU 118 (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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93A LEU* 4.0 26.2 - - + -
94A HIS 3.4 16.4 - - - +
95A LEU* 3.8 22.9 - - + -
117A GLU* 1.3 72.8 - - - +
119A HIS* 1.3 68.0 + - - +
120A ILE* 4.0 22.7 - - + -
144A LEU 3.5 0.7 - - - +
145A ALA* 3.2 1.7 - - - -
146A VAL* 2.9 44.4 + - + +
148A ILE* 4.0 2.8 - - + +
157A TYR* 3.4 29.4 - - + +
160A ILE* 5.6 1.1 - - + -
184A LEU* 3.9 25.1 - - + -
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Residues in contact with HIS 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LEU* 3.0 5.2 - - - +
94A HIS* 2.9 43.8 + - + +
96A HIS* 3.1 10.9 + + - -
106A GLU* 3.0 30.5 - - + -
107A HIS* 4.5 0.4 + - - -
117A GLU* 2.7 30.6 + - + -
118A LEU* 1.3 84.4 - - - +
120A ILE* 1.3 62.3 + - - +
121A VAL 3.8 0.9 + - - -
143A VAL* 3.9 6.1 - - + -
144A LEU 3.3 2.5 - - - -
145A ALA* 3.8 4.3 - - + -
199A THR* 4.8 0.2 - - + -
209A TRP* 3.6 31.7 - + - -
801A ACY 3.0 6.2 + - - +
901A ZN 2.1 32.5 - - - -
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Residues in contact with ILE 120 (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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51A TYR* 4.5 2.7 - - + +
70A LEU* 3.8 26.0 - - + -
74A MET* 4.3 6.7 - - + -
92A GLN 3.8 2.0 - - - -
93A LEU* 4.0 6.5 - - + -
118A LEU* 4.0 23.8 - - + -
119A HIS* 1.3 73.5 - - - +
121A VAL* 1.3 60.7 + - - +
122A HIS* 3.1 33.0 + - + +
143A VAL* 3.4 1.4 - - - -
144A LEU* 2.9 44.6 + - + +
146A VAL* 5.3 0.9 - - + -
181A ILE* 4.0 21.5 - - + +
184A LEU* 5.3 0.2 - - + -
185A LEU* 4.0 26.2 - - + -
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Residues in contact with VAL 121 (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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90A ALA* 3.6 4.3 - - - +
91A THR* 2.9 41.8 + - + +
92A GLN* 2.8 41.5 + - - +
94A HIS* 3.8 20.0 - - + +
119A HIS 4.4 0.7 - - - +
120A ILE* 1.3 70.5 - - - +
122A HIS* 1.3 73.6 + - - +
141A LEU* 4.6 15.7 - - + -
142A ALA 4.0 1.8 - - - -
143A VAL* 4.2 21.5 - - + -
198A LEU* 5.6 2.0 - - + -
801A ACY 4.4 8.7 - - + +
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Residues in contact with HIS 122 (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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51A TYR* 2.8 32.7 + - - -
78A HIS* 4.5 1.8 - - - -
79A ILE* 3.5 29.0 - - + +
88A TYR* 3.7 21.1 - - + -
89A SER 3.0 10.5 - - - +
90A ALA* 3.4 28.0 - - + +
91A THR* 4.4 1.1 - - - +
120A ILE* 3.1 35.4 + - + -
121A VAL* 1.3 74.9 - - - +
123A TYR* 1.3 60.8 + - - +
141A LEU* 3.4 13.1 - - - +
142A ALA 2.9 36.4 + - - +
144A LEU* 4.0 4.7 - - + +
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Residues in contact with TYR 123 (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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72A SER* 3.7 20.4 - - - -
88A TYR* 3.1 6.4 - - - -
89A SER* 2.8 59.3 + - - -
90A ALA 4.0 11.9 - - - -
91A THR* 4.2 6.7 - - - -
122A HIS* 1.3 74.8 - - - +
124A ASN* 1.3 68.8 + - - +
125A SER* 2.9 26.5 + - - -
128A TYR 3.8 5.6 - - - -
129A PRO 3.8 10.3 + - - -
130A ASP* 3.6 28.8 - - - +
131A ALA* 3.6 35.7 - - + -
134A ALA* 3.9 3.1 - - + -
140A GLY 3.3 10.8 - - - +
141A LEU* 3.9 6.1 - - + -
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Residues in contact with ASN 124 (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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86A SER* 3.4 28.0 + - - -
87A ARG 3.7 5.1 - - - +
88A TYR* 3.5 14.1 + - + -
123A TYR* 1.3 69.2 - - - +
125A SER* 1.3 56.6 + - - +
126A ASP* 3.1 13.0 + - - +
127A LEU* 3.1 35.7 + - - +
128A TYR* 2.9 39.0 + - + +
134A ALA* 4.3 0.2 - - - +
139A GLU* 3.2 31.8 + - - +
140A GLY 2.9 10.4 + - - +
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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