Contacts of the strand formed by residues 153 - 160 (chain A) in PDB entry 3JW3
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 TYR 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A LEU* 4.1 24.5 - - + -
27A SER* 3.3 22.5 + - - -
28A GLU* 4.1 12.2 + - + -
115A THR* 3.8 18.6 - - + -
116A LYS 3.2 12.6 - - - +
117A ILE* 3.8 16.8 - - + -
118A HIS* 4.6 0.2 - - - -
142A LYS* 3.9 0.9 - - - +
143A GLY* 2.7 38.6 + - - +
144A LEU 2.6 43.5 + - - -
145A THR* 4.4 1.9 + - - -
149A ASN* 4.0 4.3 + - + +
151A TYR 3.3 18.8 - - - -
152A THR* 1.3 79.1 - - - +
154A TYR* 1.3 66.1 + - - +
155A TYR* 3.4 22.9 - + - -
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Residues in contact with TYR 154 (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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115A THR* 3.2 7.6 - - - -
116A LYS 2.9 32.8 + - - +
118A HIS* 3.4 32.5 - + - +
140A VAL* 3.8 16.6 - - + -
141A GLU* 3.5 6.3 - - - -
142A LYS* 3.4 55.5 - - + +
152A THR* 3.9 15.7 - - + -
153A TYR* 1.3 88.9 - - - +
155A TYR* 1.3 61.4 + - - +
156A HIS* 3.4 25.3 - + + +
142B LYS* 6.2 4.3 - - + -
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Residues in contact with TYR 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A SER* 3.3 27.9 + - - -
28A GLU* 3.6 11.5 - - + -
31A TYR* 3.3 60.0 - + + +
114A ILE 4.2 2.5 - - - -
115A THR* 3.4 21.5 - - + -
139A PHE* 3.8 12.6 - + + +
140A VAL* 3.1 6.9 - - - +
141A GLU* 2.9 50.6 + - + +
142A LYS 4.6 2.9 - - - -
143A GLY* 3.6 19.9 - - - -
144A LEU 4.9 0.9 - - - -
153A TYR* 3.4 20.4 - + - -
154A TYR* 1.3 71.6 - - - +
156A HIS* 1.3 58.8 + - - +
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Residues in contact with HIS 156 (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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31A TYR* 4.9 1.2 + - - -
112A LEU 4.2 0.2 - - - -
113A TYR* 3.6 1.2 - - - +
114A ILE* 3.0 37.4 + - + +
116A LYS* 3.6 39.2 - - + +
118A HIS* 5.4 1.8 + - - -
137A GLU* 2.7 30.1 + - - +
139A PHE 3.3 4.9 - - - -
140A VAL* 3.9 19.0 - - + +
154A TYR* 3.4 32.1 - - + +
155A TYR* 1.3 74.7 - - - +
157A VAL* 1.3 69.0 + - - +
158A TYR* 3.8 16.4 + - + -
142B LYS* 5.2 11.2 - - + -
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Residues in contact with VAL 157 (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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31A TYR* 4.1 6.5 - - - +
111A LYS* 4.0 26.9 - - + -
112A LEU 3.1 7.4 - - - +
113A TYR* 3.6 28.5 - - + -
137A GLU* 3.4 6.2 - - - +
138A VAL* 2.8 38.8 + - + -
139A PHE* 2.9 39.8 + - + -
156A HIS* 1.3 79.1 - - - +
158A TYR* 1.3 68.8 + - - +
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Residues in contact with TYR 158 (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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111A LYS* 3.4 7.6 - - - +
112A LEU* 2.8 53.7 + - + -
114A ILE* 3.9 21.1 - - + -
116A LYS* 2.9 20.1 + - - -
132A MET* 3.7 23.1 - - + -
135A TRP* 3.5 18.0 - - + -
136A LYS 3.2 7.9 - - - +
137A GLU* 3.4 41.4 + - + -
138A VAL 4.5 0.2 - - - +
156A HIS* 3.8 19.3 - - + -
157A VAL* 1.3 76.1 - - - +
159A GLU* 1.3 63.4 + - - +
139B PHE* 4.2 5.2 - + - -
141B GLU* 2.8 32.7 + - + -
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Residues in contact with GLU 159 (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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110A ASP 3.7 4.3 - - - +
111A LYS* 3.6 32.4 + - + -
135A TRP* 3.4 4.0 - - - -
136A LYS 2.9 19.6 + - - -
138A VAL* 3.2 36.4 - - + +
158A TYR* 1.3 77.9 - - - +
160A LYS* 1.3 62.2 + - - +
161A GLN* 2.8 26.6 + - - +
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Residues in contact with LYS 160 (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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109A VAL 3.9 15.7 - - - +
110A ASP 2.9 20.9 + - - +
133A THR 4.8 1.8 + - - -
134A ASN* 3.5 21.1 - - - +
135A TRP* 3.4 32.6 - - + +
159A GLU* 1.3 75.9 - - - +
161A GLN* 1.3 65.1 + - - +
162A GLN* 3.7 50.7 - - + +
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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