Contacts of the strand formed by residues 152 - 159 (chain P) in PDB entry 1P7G
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 152 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15M THR* 3.7 12.1 - - - +
16M LYS* 3.0 48.0 + - + +
18M TYR* 2.6 35.3 + - - +
58M LEU* 4.0 6.9 - - - +
65M ARG* 5.7 0.7 + - - -
118P PHE* 3.6 21.5 - - + -
146P TYR* 3.5 9.0 - - - -
147P GLU* 2.7 38.6 + - + +
150P GLU 4.6 0.9 - - - +
151P GLU* 1.3 76.1 - - - +
153P LEU* 1.3 63.1 + - - +
154P LEU* 3.9 22.3 - - + +
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Residues in contact with LEU 153 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65M ARG* 4.7 4.3 + - - -
111P ILE* 4.6 3.8 - - + -
114P LEU* 3.4 43.5 - - + +
115P ILE* 3.7 16.8 - - + +
118P PHE* 3.7 23.0 - - + +
119P PHE* 3.9 23.0 - - + -
144P LEU* 4.2 11.7 - - + -
145P VAL 3.5 6.5 - - - +
146P TYR* 4.2 11.0 - - + -
152P GLN* 1.3 78.0 - - - +
154P LEU* 1.3 70.2 + - - +
172P LEU* 3.7 29.4 - - + -
210P LEU* 4.3 6.5 - - + -
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Residues in contact with LEU 154 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18M TYR* 4.1 5.6 - - - +
58M LEU* 4.0 20.0 - - + -
61M LEU* 5.3 0.4 - - + -
65M ARG* 5.0 9.4 - - - +
80M LEU* 4.2 18.8 - - + -
84M LEU* 3.4 33.0 - - + -
119P PHE* 4.9 1.6 - - - -
143P ILE 3.8 0.2 - - - +
144P LEU* 3.6 3.0 - - - +
145P VAL* 2.8 47.3 + - + +
147P GLU* 3.6 21.1 - - + -
152P GLN* 3.9 21.8 - - + +
153P LEU* 1.3 83.4 - - - +
155P ILE* 1.3 68.1 + - - +
156P LEU* 4.8 3.1 - - + -
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Residues in contact with ILE 155 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61M LEU* 5.7 0.5 - - - +
65M ARG* 5.0 1.2 - - - +
77M LEU* 3.3 24.1 - - + +
80M LEU* 4.4 2.1 - - - +
119P PHE* 3.9 15.6 - - + -
125P PHE* 3.9 11.7 - - + -
128P GLU* 3.7 29.3 + - + +
129P PHE* 3.5 43.5 - - + +
132P ALA* 4.0 27.6 - - + -
142P ALA* 5.3 0.2 - - + -
143P ILE 3.2 11.0 - - - +
144P LEU* 3.9 18.6 - - + -
154P LEU* 1.3 73.2 - - - +
156P LEU* 1.3 72.5 + - - +
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Residues in contact with LEU 156 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77M LEU* 4.4 9.9 - - + +
80M LEU* 3.7 27.1 - - + -
81M SER* 4.6 16.4 - - - +
84M LEU* 5.4 1.6 - - + -
132P ALA* 5.1 0.4 - - - +
142P ALA* 3.6 2.8 - - - -
143P ILE* 2.9 44.9 + - + +
145P VAL* 4.3 23.6 - - + -
154P LEU* 4.8 5.6 - - + +
155P ILE* 1.3 85.6 - - - +
157P GLN* 1.3 65.5 + - - +
158P ILE* 4.6 0.7 - - + -
164P MSE 3.9 10.8 - - - +
165P HIS* 4.4 2.2 - - - -
166P ALA* 3.7 40.2 - - + +
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Residues in contact with GLN 157 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73M ILE 5.1 0.2 + - - -
74M ARG* 3.5 44.3 + - - +
77M LEU* 4.1 18.1 + - + +
78M ARG* 4.7 0.8 - - - +
81M SER* 5.7 0.5 - - - -
132P ALA* 2.9 35.3 - - + +
135P ASN* 2.8 26.5 - - - +
136P VAL* 3.6 17.9 - - + +
137P GLU 5.1 0.8 - - - +
141P TRP 3.6 2.9 - - - +
142P ALA* 4.8 0.4 - - - +
156P LEU* 1.3 74.8 - - - +
158P ILE* 1.3 60.8 + - - +
159P GLU* 5.7 2.0 - - - +
164P MSE 3.1 40.9 - - + +
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Residues in contact with ILE 158 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89P LEU* 4.5 0.7 - - + -
136P VAL* 3.9 6.9 - - - +
140P GLY* 3.1 4.3 - - - -
141P TRP* 2.7 51.0 + - + +
143P ILE* 3.7 33.2 - - + -
156P LEU* 4.6 2.9 - - + -
157P GLN* 1.3 80.1 - - - +
159P GLU* 1.3 72.9 + - - +
161P HIS* 3.6 29.8 - - - +
162P ASN 4.1 0.2 - - - +
163P LEU 3.4 6.7 - - - +
164P MSE 3.9 2.5 - - - +
165P HIS* 3.6 48.5 - - + +
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Residues in contact with GLU 159 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78M ARG* 3.5 21.9 + - - -
160N LYS* 2.9 34.4 + - - +
136P VAL* 5.3 3.4 - - + -
137P GLU* 4.0 12.6 - - - +
139P VAL 3.7 5.6 - - - +
157P GLN* 5.7 2.9 - - + +
158P ILE* 1.3 73.6 - - - +
160P LYS* 1.3 75.4 + - + +
161P HIS 3.0 2.8 + - - -
162P ASN 3.5 0.3 + - - -
163P LEU* 3.1 48.1 + - + +
164P MSE 3.5 29.5 - - + +
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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