Contacts of the strand formed by residues 153 - 160 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B LEU* 4.0 28.0 - - + -
27B SER* 3.5 21.7 + - - -
28B GLU* 3.9 12.2 + - + -
115B THR* 3.8 18.2 - - + -
116B LYS 3.1 14.4 - - - +
117B ILE* 3.9 15.9 - - + -
118B HIS 4.6 0.2 - - - +
142B LYS* 3.7 4.6 - - - +
143B GLY* 2.8 37.6 + - - +
144B LEU 2.7 43.6 + - - -
145B THR* 4.2 2.3 + - - -
149B ASN* 4.2 1.4 + - + -
151B TYR 3.3 18.8 - - - -
152B THR* 1.3 76.0 - - - +
154B TYR* 1.3 65.4 + - - +
155B TYR* 3.3 24.7 + + - -
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Residues in contact with TYR 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A GLU* 4.7 3.4 - - - -
140A VAL* 5.3 3.3 - - - +
115B THR* 3.3 5.0 - - - -
116B LYS 2.9 32.6 + - - +
118B HIS* 3.5 32.5 - + - +
140B VAL* 4.1 13.9 - - + -
141B GLU 3.4 6.1 - - - +
142B LYS* 3.7 47.0 - - + +
152B THR* 3.9 17.1 - - + +
153B TYR* 1.3 79.3 - - - +
155B TYR* 1.3 64.1 + - - +
156B HIS* 3.6 24.1 + - + +
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Residues in contact with TYR 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B SER* 3.5 22.2 + - - -
28B GLU* 3.7 12.0 - - + -
31B TYR* 3.4 56.6 - + + +
114B ILE 4.2 2.2 - - - -
115B THR* 3.3 21.1 - - - -
139B PHE* 3.8 6.8 - - + +
140B VAL* 3.0 8.0 - - - +
141B GLU* 2.8 62.9 + - + +
142B LYS 4.5 0.2 - - - -
143B GLY* 3.5 19.2 - - - -
144B LEU 4.8 1.1 + - - -
153B TYR* 3.3 24.1 + + - -
154B TYR* 1.3 71.2 - - - +
156B HIS* 1.3 60.4 + - - +
157B VAL* 5.2 0.7 - - - -
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Residues in contact with HIS 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B TYR* 4.7 1.6 + - - -
112B LEU 4.2 0.7 - - - -
113B TYR* 3.6 1.4 - - - +
114B ILE* 3.0 38.3 + - + +
116B LYS* 3.4 35.7 - - + +
118B HIS* 5.5 1.4 + - - -
137B GLU* 2.6 26.2 + - - +
139B PHE 3.4 3.6 - - - -
140B VAL* 3.6 16.2 - - + +
154B TYR* 3.6 32.2 - + + +
155B TYR* 1.3 72.1 - - - +
157B VAL* 1.3 70.5 + - - +
158B TYR* 3.6 26.8 + - + -
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Residues in contact with VAL 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A THR* 6.0 0.7 - - - +
31B TYR* 4.1 7.4 - - - +
111B LYS* 3.7 32.3 - - + -
112B LEU 3.2 7.0 - - - +
113B TYR* 3.8 26.9 - - + -
137B GLU* 3.4 5.7 - - - +
138B VAL* 2.8 40.7 + - + -
139B PHE* 2.9 41.5 + - + -
156B HIS* 1.3 80.7 - - - +
158B TYR* 1.3 59.9 + - - +
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Residues in contact with TYR 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B LYS* 3.3 8.4 - - - +
112B LEU* 2.8 53.5 + - + -
114B ILE* 3.2 27.8 - - + -
116B LYS* 3.4 27.1 + - - -
132B MET* 3.7 24.2 - - + -
135B TRP* 3.7 20.5 - - + -
136B LYS 3.2 7.2 - - - +
137B GLU* 3.5 36.3 + - + -
156B HIS* 3.6 20.5 + - + -
157B VAL* 1.3 76.2 - - - +
159B GLU* 1.3 63.4 + - - +
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Residues in contact with GLU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A THR* 4.1 16.7 + - - +
2B ARG* 4.0 10.2 + - - -
110B ASP 3.7 4.7 - - - +
111B LYS* 3.4 38.3 + - + -
135B TRP* 3.5 3.5 - - - -
136B LYS 2.8 32.3 + - - +
138B VAL* 3.8 28.0 - - + +
158B TYR* 1.3 80.1 - - - +
160B LYS* 1.3 61.1 + - - +
161B GLN* 3.3 13.9 - - - +
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Residues in contact with LYS 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B LEU 5.7 1.0 + - - -
107B PRO 4.5 12.7 + - - -
108B TYR 5.4 1.0 - - - -
109B VAL 3.3 22.7 + - - -
110B ASP* 2.9 29.9 + - - +
134B ASN* 3.4 12.6 - - + +
135B TRP* 3.5 32.5 - - + +
159B GLU* 1.3 74.2 - - - +
161B GLN* 1.3 66.5 + - - +
162B GLN* 3.4 43.9 + - + +
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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