Contacts of the strand formed by residues 133 - 140 (chain F) in PDB entry 5IJ7
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 133 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B LEU* 4.5 4.5 - - + -
83F PHE* 3.8 8.1 - - - -
102F VAL* 4.0 21.6 - - + -
103F GLY* 3.9 11.1 + - - +
104F SER 2.9 9.3 + - - +
105F ASN* 3.5 38.6 - - - -
106F ARG 3.6 11.0 - - - +
107F VAL* 3.9 16.4 - - + -
126F ASP* 3.4 26.0 - - + -
131F GLU* 3.6 23.1 - - + -
132F ASN* 1.3 81.0 - - - +
134F TYR* 1.3 60.6 + - - +
135F THR 4.8 0.2 - - - +
151F VAL* 3.8 20.0 - - + -
152F ALA* 3.7 27.4 - - - +
153F GLY 4.1 0.2 - - - -
157F ILE 5.2 0.9 - - - -
159F ARG* 4.4 12.8 - - + -
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Residues in contact with TYR 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F PHE* 3.6 48.0 - + - +
84F GLY* 3.9 0.5 + - - -
102F VAL* 4.0 5.6 - - - -
132F ASN* 3.6 27.1 + - - +
133F PHE* 1.3 81.7 - - - +
135F THR* 1.3 60.1 + - - +
152F ALA 3.0 4.4 + - - +
153F GLY* 3.9 6.1 - - - -
154F SER* 3.4 33.0 - - - -
178F ALA* 4.1 11.1 - - + +
179F ILE 3.6 24.0 - - - +
180F ASN* 3.9 14.4 - - - -
350F TRP* 6.6 0.2 - + - -
351F TYR* 3.4 28.0 + + + +
353F ARG* 4.8 1.7 + - - -
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Residues in contact with THR 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84F GLY* 5.2 2.0 - - - -
102F VAL* 3.8 10.5 - - - +
133F PHE* 3.8 0.4 - - - +
134F TYR* 1.3 78.3 + - - +
136F CYS* 1.3 73.6 + - - +
151F VAL* 3.4 3.8 - - - +
152F ALA 3.2 34.2 + - - +
179F ILE* 4.1 7.9 - - + +
180F ASN 3.7 14.1 - - - +
181F GLU* 3.7 20.9 + - - +
182F LEU* 3.4 43.6 + - + +
353F ARG* 5.4 1.5 + - - -
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Residues in contact with CYS 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84F GLY* 4.9 1.3 - - - -
85F VAL 4.7 1.8 - - - -
86F GLN* 3.2 48.5 - - - +
100F ALA* 4.2 21.8 - - - -
102F VAL* 3.8 19.2 - - + +
135F THR* 1.3 81.2 + - - +
137F ALA* 1.3 63.1 - - - +
149F LEU* 4.0 5.4 - - + -
150F ALA 3.0 14.8 - - - +
151F VAL* 3.6 15.9 - - + -
182F LEU* 4.2 5.9 - - - +
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Residues in contact with ALA 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86F GLN* 4.6 8.3 - - - +
136F CYS* 1.3 77.2 - - - +
138F TRP* 1.3 59.1 + - - +
149F LEU* 3.5 6.8 - - - -
150F ALA* 2.8 32.7 + - + +
182F LEU* 3.7 27.1 - - + +
183F LYS* 4.4 3.8 - - - -
184F PHE* 3.5 27.5 - - + +
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Residues in contact with TRP 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B VAL* 4.5 2.5 - - + -
86F GLN* 3.0 34.2 + - + +
87F PHE 3.4 19.5 - - - +
88F ASN* 3.7 31.9 - - + +
89F TRP 5.2 0.9 - - - +
90F HIS* 3.3 23.0 - - + +
98F VAL* 3.9 22.0 - - + -
99F PHE 4.2 0.7 - - - -
100F ALA* 3.6 26.1 - - + +
109F LEU* 3.8 24.7 - - + -
137F ALA* 1.3 73.6 - - - +
139F THR* 1.3 61.2 + - - +
147F PRO* 4.2 15.7 - - + -
148F LEU 3.3 18.4 - - - -
149F LEU* 3.6 22.6 - - + +
163F PRO* 4.3 13.5 - - + -
184F PHE* 3.6 12.6 - - - +
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Residues in contact with THR 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90F HIS* 3.5 16.8 + - - -
138F TRP* 1.3 74.1 - - - +
140F TYR* 1.3 70.5 + - - +
147F PRO* 3.4 7.3 - - - +
148F LEU* 2.8 50.5 + - + +
160F ILE* 5.5 0.7 - - + -
184F PHE* 3.4 39.8 - - + +
189F PRO* 2.8 32.6 + - - +
206F ILE* 5.4 3.4 - - + -
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Residues in contact with TYR 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ARG* 3.4 46.1 + - - -
65B ILE* 3.6 33.4 - - + -
90F HIS* 3.5 29.2 - + + -
139F THR* 1.3 83.5 + - - +
141F ASP* 1.3 69.2 + - - +
142F SER* 3.7 13.4 + - - -
146F HIS 3.3 9.6 - - - +
147F PRO* 4.5 0.4 - - + -
148F LEU* 4.2 7.3 - - - +
187F ARG 4.4 4.9 + - - -
189F PRO* 3.4 59.7 - - + +
190F ASN* 5.0 2.4 - - - +
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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