Contacts of the strand formed by residues 130 - 138 (chain A) in PDB entry 1JBR
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 PHE 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A TRP* 3.5 24.2 - + - -
26A GLN* 3.3 41.7 - - + -
29A ALA* 4.7 1.8 - - + -
30A GLU* 3.9 35.9 - - + +
33A SER* 6.0 0.7 - - - -
72A LYS* 3.4 30.9 + - - +
75A CYS* 3.9 0.3 - - - -
121A VAL* 3.9 21.5 - - + -
122A ILE 4.3 2.5 - - - -
123A TYR* 4.3 4.5 - - + -
128A LYS 3.4 5.1 + - - +
129A VAL* 1.3 74.1 - - - +
131A CYS* 1.3 60.5 + - - +
132A GLY* 3.3 38.4 - - - -
133A ILE* 4.2 6.3 - - + -
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Residues in contact with CYS 131 (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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3A TRP* 4.5 4.3 - - - -
70A PHE* 3.2 34.7 - - + +
72A LYS* 4.0 7.8 + - - +
75A CYS* 2.0 53.8 - - + -
93A LEU* 3.8 17.7 - - - -
122A ILE* 2.9 20.3 + - + +
123A TYR* 3.9 4.3 - - - -
124A THR* 3.9 4.3 - - - -
129A VAL 3.6 11.7 - - - -
130A PHE* 1.3 78.4 - - - +
132A GLY* 1.3 59.4 + - - +
146A LEU* 5.3 0.2 - - - +
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Residues in contact with GLY 132 (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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3A TRP* 3.7 10.5 - - - -
70A PHE* 4.2 8.7 - - - -
122A ILE* 2.8 29.5 + - - +
130A PHE* 3.3 23.3 - - - -
131A CYS* 1.3 82.8 - - - +
133A ILE* 1.3 64.1 + - - +
134A VAL 4.2 0.4 - - - -
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Residues in contact with ILE 133 (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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3A TRP* 3.7 33.1 - - + -
5A CYS* 4.0 16.8 - - - -
24A TYR* 3.9 25.1 - - + -
25A SER 4.7 2.0 - - - +
26A GLN* 4.9 0.7 - - - -
29A ALA* 3.6 28.0 - - + -
98A THR* 3.9 14.8 - - + -
119A ALA* 4.4 2.5 - - + -
120A ARG 3.3 13.7 - - - +
121A VAL* 4.5 2.9 - - - -
130A PHE* 4.2 11.9 - - + -
132A GLY* 1.3 79.0 - - - +
134A VAL* 1.3 71.4 + - - +
146A LEU* 3.8 3.0 - - - +
147A CYS* 3.0 26.7 + - - +
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Residues in contact with VAL 134 (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 PHE* 5.0 1.6 - - + -
68A ILE* 4.1 15.3 - - + -
70A PHE* 4.0 18.8 - - + -
119A ALA* 3.4 1.6 - - - -
120A ARG* 2.9 34.2 + - + +
122A ILE* 3.8 32.3 - - + -
133A ILE* 1.3 83.1 - - - +
135A ALA* 1.3 67.2 + - - +
144A LEU* 3.7 29.4 - - + -
145A ARG 3.0 17.0 - - - +
146A LEU* 4.2 4.5 - - + -
147A CYS* 3.7 1.6 - - - -
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Residues in contact with ALA 135 (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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5A CYS* 3.8 15.5 - - + -
6A ILE 5.1 4.8 - - - +
7A ASN* 5.6 1.3 - - + -
22A LEU* 6.3 0.2 - - + -
118A PRO* 3.2 18.6 - - + +
119A ALA* 4.0 5.8 - - + -
134A VAL* 1.3 79.3 - - - +
136A HIS* 1.3 69.5 + - - +
137A GLN* 3.3 0.9 + - - -
144A LEU* 3.6 6.5 - - - -
145A ARG* 2.8 30.8 + - - +
147A CYS* 3.8 15.5 - - - -
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Residues in contact with HIS 136 (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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6A ILE 4.0 5.7 - - - +
7A ASN* 2.8 22.6 + - - +
118A PRO 3.1 31.1 + - - +
120A ARG* 3.6 21.1 + - - -
135A ALA* 1.3 75.1 - - - +
137A GLN* 1.3 59.7 + - - +
139A GLY 3.5 14.6 - - - +
140A ASN* 3.4 24.5 + - - -
141A GLN* 3.2 22.5 - - - +
142A GLY 3.0 25.7 + - - -
143A ASP 3.1 7.4 - - - -
144A LEU* 3.4 25.6 - - + +
17C A23 4.5 17.8 + + - -
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Residues in contact with GLN 137 (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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6A ILE 4.0 1.6 - - - +
7A ASN* 3.7 3.1 - - - -
8A GLN* 2.8 45.4 + - - +
135A ALA 3.3 1.4 + - - -
136A HIS* 1.3 72.7 - - - +
138A ARG* 1.3 60.9 - - + +
141A GLN 4.7 0.4 + - - -
143A ASP* 2.8 28.8 + - + +
145A ARG* 2.7 56.6 + - + +
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Residues in contact with ARG 138 (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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8A GLN* 2.9 36.8 + - + +
17A TRP* 3.4 67.6 - - + +
137A GLN* 1.3 85.7 - - + +
139A GLY* 1.3 69.5 + - - +
141A GLN* 3.0 20.6 + - - +
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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