Contacts of the strand formed by residues 140 - 147 (chain L) 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 GLY 140 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136L VAL* 3.8 4.0 - - - +
139L VAL* 1.3 78.2 - - - +
141L TRP* 1.3 67.6 + - - -
158L ILE 3.0 11.7 - - - -
160L LYS 3.3 15.3 - - - -
177L VAL* 2.9 31.8 + - - +
178L TRP* 3.4 11.6 - - - +
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Residues in contact with TRP 141 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89L LEU* 3.4 58.3 - - + +
90L HIS* 3.5 33.7 - + - -
93L PHE* 3.8 13.5 - + + -
136L VAL* 3.7 9.9 - - - +
140L GLY* 1.3 78.8 - - - -
142L ALA* 1.3 61.9 + - - +
143L ILE* 4.1 9.9 - - + -
157L GLN* 3.5 3.5 - - - -
158L ILE* 2.8 39.1 + - + +
160L LYS 3.3 11.9 - - - -
161L HIS* 2.9 26.7 - + - -
174L ALA* 3.9 14.8 - - + -
175L LEU 3.1 13.2 - - - +
176L ASP* 3.4 42.8 - - + -
177L VAL* 4.1 2.6 - - - +
178L TRP* 3.7 1.8 - - - +
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Residues in contact with ALA 142 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129L PHE* 3.4 25.8 - - + +
132L ALA* 4.3 5.6 - - + -
133L ALA* 3.6 39.0 - - + +
141L TRP* 1.3 74.7 - - - +
143L ILE* 1.3 60.6 + - - +
156L LEU 3.4 7.9 - - - +
157L GLN* 4.7 1.1 - - - +
175L LEU 2.9 30.5 + - - +
177L VAL* 5.0 0.4 - - - +
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Residues in contact with ILE 143 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89L LEU* 4.7 8.3 - - + -
129L PHE* 3.8 5.6 - - - -
141L TRP* 4.1 13.7 - - + -
142L ALA* 1.3 79.6 - - - +
144L LEU* 1.3 60.5 + - - +
145L VAL* 3.7 21.5 - - + -
154L LEU 3.8 0.5 - - - +
155L ILE* 3.3 5.9 - - - +
156L LEU* 3.0 52.1 + - + +
158L ILE* 3.6 18.2 - - + -
165L HIS* 3.6 28.0 - - + +
166L ALA 5.8 0.2 - - - +
171L VAL* 4.2 14.4 - - + -
173L LEU 3.3 6.1 - - - +
174L ALA* 3.9 20.4 - - + -
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Residues in contact with LEU 144 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111L ILE* 4.5 22.0 - - + -
115L ILE* 5.0 3.1 - - + -
119L PHE* 4.6 1.8 - - + -
125L PHE* 3.7 33.4 - - + -
129L PHE* 3.8 9.8 - - + -
143L ILE* 1.3 72.8 - - - +
145L VAL* 1.3 62.4 + - - +
153L LEU* 4.1 21.1 - - + -
154L LEU 3.4 19.3 - - - +
155L ILE* 4.4 3.1 - - + +
171L VAL* 3.6 2.9 - - - -
172L LEU* 2.6 44.7 + - + -
173L LEU* 2.7 32.7 + - + +
203L TRP* 5.2 0.4 - - + -
206L VAL* 4.8 2.0 - - + -
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Residues in contact with VAL 145 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143L ILE* 3.7 30.1 - - + -
144L LEU* 1.3 79.7 - - - +
146L TYR* 1.3 63.0 + - - +
147L GLU* 4.5 3.4 - - + +
153L LEU* 3.3 7.8 - - - +
154L LEU* 3.0 45.6 + - + +
156L LEU* 4.2 17.5 - - + -
166L ALA* 5.2 1.3 - - + +
169L ALA* 4.1 21.8 - - + -
170L GLN 2.9 15.3 - - - +
171L VAL* 3.8 13.2 - - + -
172L LEU* 4.1 6.1 - - - -
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Residues in contact with TYR 146 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218I ILE* 4.8 4.3 - - + -
114L LEU* 5.1 3.6 - - + -
145L VAL* 1.3 74.3 - - - +
147L GLU* 1.3 57.1 + - - +
148L PRO* 3.0 40.1 - - + +
151L GLU* 2.9 48.0 - - + +
152L GLN* 3.5 9.4 - - - -
153L LEU* 4.2 6.5 - - + -
169L ALA* 3.6 1.7 - - - -
170L GLN* 2.8 25.9 + - + +
172L LEU* 4.1 10.6 - - + +
210L LEU* 4.3 15.7 - - + -
213L ALA* 3.5 46.0 + - + -
214L LEU* 3.8 27.5 + - + +
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Residues in contact with GLU 147 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I TYR* 2.4 32.9 + - - +
84I LEU* 4.0 15.7 - - + -
88I ILE* 4.0 13.8 - - + +
220I LEU* 5.3 0.3 - - - +
145L VAL* 3.8 4.6 + - + -
146L TYR* 1.3 71.4 - - - +
148L PRO* 1.3 57.0 - - + +
149L LEU* 2.9 27.1 + - - +
150L GLU* 2.9 22.7 + - - +
151L GLU* 2.8 36.4 + - - -
152L GLN* 2.6 20.5 + - + +
154L LEU* 3.9 23.8 - - + -
166L ALA* 5.4 0.4 - - + -
169L ALA* 4.6 6.7 - - + -
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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