Contacts of the strand formed by residues 158 - 165 (chain Q) in PDB entry 3J7Y
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 GLN 158 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39L ARG* 4.5 14.4 - - - +
87L VAL 5.6 0.2 + - - -
100L PHE* 3.1 34.7 - - - +
101L ASP* 4.0 2.5 + - + +
102L SER* 2.6 40.9 + - - +
104L ASN* 3.2 26.2 + - - +
121L THR* 4.4 4.7 + - + -
122L PRO* 4.0 19.0 + - + +
154Q VAL* 3.5 2.2 - - - -
155Q ILE* 2.8 42.7 + - - +
156Q GLU 3.3 2.3 - - - +
157Q GLY* 1.3 78.7 - - - +
159Q GLY* 1.3 61.0 + - - +
160Q VAL* 3.8 0.2 - - - +
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Residues in contact with GLY 159 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100L PHE* 3.6 6.2 - - - -
101L ASP* 3.0 49.3 + - - +
152Q ARG* 4.2 4.7 - - - -
153Q ASN 3.5 7.4 - - - -
154Q VAL* 4.0 14.0 - - - +
157Q GLY 4.2 1.2 + - - -
158Q GLN* 1.3 74.3 - - - +
160Q VAL* 1.3 63.2 + - - +
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Residues in contact with VAL 160 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98L PRO* 3.7 28.7 - - + -
99L ARG 3.7 4.7 - - - +
100L PHE* 3.6 23.6 - - + -
122L PRO* 3.8 4.3 - - + -
145L VAL* 4.1 10.8 - - + -
133Q PHE* 4.1 7.4 - - + -
151Q LEU 3.9 0.5 - - - +
152Q ARG* 3.3 5.0 - - - +
153Q ASN 2.8 34.8 + - - +
155Q ILE* 3.6 31.9 - - + -
159Q GLY* 1.3 79.9 - - - +
161Q GLU* 1.3 65.7 + - - +
162Q ILE* 4.1 11.7 - - + -
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Residues in contact with GLU 161 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98L PRO* 3.4 1.6 - - - +
99L ARG* 2.7 67.8 + - + +
101L ASP* 5.3 0.9 - - - +
138Q ILE* 3.5 21.2 - - + +
150Q ILE* 4.4 9.8 - - + +
151Q LEU 3.3 4.9 - - - +
152Q ARG* 2.9 31.5 + - + +
160Q VAL* 1.3 78.5 - - - +
162Q ILE* 1.3 62.0 + - - +
163Q CYS* 5.9 0.9 - - - -
191Q ARG* 2.9 48.3 + - - +
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Residues in contact with ILE 162 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96L MET* 3.3 26.7 - - - +
97L THR 3.4 9.2 - - - +
98L PRO* 4.0 7.6 - - + -
145L VAL* 3.5 26.7 - - + -
133Q PHE* 3.3 42.2 - - + -
150Q ILE* 3.3 3.3 - - - -
151Q LEU 2.9 30.3 + - - -
160Q VAL* 4.1 2.9 - - + -
161Q GLU* 1.3 80.1 - - - +
163Q CYS* 1.3 72.5 + - - +
164Q PHE* 3.7 23.0 - - + -
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Residues in contact with CYS 163 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3152A C 4.9 10.3 - - - -
92L PRO* 5.6 8.3 - - - -
94L PRO 5.5 0.9 - - - -
95L ARG* 2.8 63.9 + - - +
96L MET* 3.4 9.2 - - - +
97L THR 4.3 1.3 + - - -
99L ARG* 6.3 4.0 - - - -
148Q THR* 5.4 4.7 - - - -
149Q PHE 3.5 5.4 - - - +
150Q ILE* 3.7 31.6 - - + -
161Q GLU 5.9 0.9 - - - -
162Q ILE* 1.3 76.9 - - - +
164Q PHE* 1.3 63.1 + - - +
165Q GLU 4.3 0.2 - - - -
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Residues in contact with PHE 164 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96L MET* 3.9 15.3 - - + -
119Q VAL* 3.3 38.6 - - + -
121Q THR* 3.6 20.2 - - + -
133Q PHE* 3.9 24.5 - + + -
148Q THR* 3.2 6.1 - - - -
149Q PHE* 2.9 62.2 + + + -
151Q LEU* 3.7 17.3 - - + -
162Q ILE* 3.7 35.2 - - + -
163Q CYS* 1.3 76.8 - - - +
165Q GLU* 1.3 64.5 + - - +
166Q LEU 3.5 1.2 + - - -
171Q VAL* 4.6 3.4 - - + -
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Residues in contact with GLU 165 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3151A A 3.5 15.9 + - - -
108E PRO* 5.2 0.2 - - - +
110E TRP* 3.4 12.0 - - + -
116E LYS* 3.2 43.6 - - - +
95L ARG* 4.1 20.1 - - + +
96L MET* 3.9 8.0 - - - +
145Q LEU 5.0 1.6 - - - +
146Q GLY* 4.3 8.0 - - - +
147Q ALA 3.6 7.4 - - - +
148Q THR* 3.7 14.6 - - + +
164Q PHE* 1.3 71.1 - - - +
166Q LEU* 1.3 65.4 + - - +
167Q TYR 3.1 1.6 - - - +
168Q ASN* 2.9 48.6 + - + +
171Q VAL* 4.3 9.5 - - - +
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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