Contacts of the strand formed by residues 140 - 147 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136X VAL* 4.0 2.3 - - - +
139X VAL* 1.3 79.8 - - - +
141X TRP* 1.3 65.8 + - - -
158X ILE 3.1 10.5 - - - -
160X LYS 3.2 17.3 - - - -
177X VAL* 2.9 29.7 + - - -
178X TRP* 3.3 14.4 - - - +
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Residues in contact with TRP 141 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89X LEU* 3.4 54.4 - - + +
90X HIS* 3.3 37.7 - + - -
93X PHE* 3.8 18.6 - + + -
136X VAL* 3.6 10.1 - - - +
140X GLY* 1.3 78.8 - - - -
142X ALA* 1.3 62.0 + - - +
143X ILE* 4.1 9.0 - - + -
157X GLN* 3.7 0.9 - - - -
158X ILE* 2.8 46.5 + - + +
160X LYS 3.3 11.0 - - - -
161X HIS* 2.8 23.7 - + - -
174X ALA* 3.9 15.9 - - + -
175X LEU 3.2 9.0 - - - -
176X ASP* 3.5 41.7 - - + -
177X VAL* 3.7 7.2 - - - -
178X TRP* 3.8 1.4 - - - +
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Residues in contact with ALA 142 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129X PHE* 3.6 20.5 - - + +
132X ALA* 4.4 4.5 - - + -
133X ALA* 3.4 43.5 - - + +
141X TRP* 1.3 74.0 - - - +
143X ILE* 1.3 62.7 + - - +
155X ILE* 5.6 0.4 - - + -
156X LEU 3.6 6.7 - - - -
157X GLN* 4.8 1.3 - - - +
174X ALA* 3.5 0.2 - - - -
175X LEU* 2.7 33.0 + - + -
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Residues in contact with ILE 143 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89X LEU* 4.5 6.3 - - + -
129X PHE* 3.7 5.6 - - - -
141X TRP* 4.1 14.6 - - + -
142X ALA* 1.3 81.1 - - - +
144X LEU* 1.3 59.3 + - - +
145X VAL* 3.4 27.6 - - + -
155X ILE* 3.4 7.1 - - - +
156X LEU* 3.0 49.2 + - + +
158X ILE* 3.8 25.1 - - + -
165X HIS* 3.8 16.2 - - + +
166X ALA 6.0 0.2 - - - +
171X VAL* 4.3 12.8 - - + -
173X LEU 3.0 7.9 - - - +
174X ALA* 3.6 21.5 - - + -
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Residues in contact with LEU 144 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111X ILE* 4.1 25.6 - - + -
115X ILE* 4.7 3.6 - - + -
119X PHE* 4.3 2.9 - - + -
125X PHE* 3.8 33.7 - - + -
129X PHE* 3.8 9.4 - - + -
143X ILE* 1.3 74.0 - - - +
145X VAL* 1.3 65.0 + - - +
153X LEU* 4.1 22.0 - - + -
154X LEU 3.5 20.4 - - - +
155X ILE* 4.2 3.8 - - + -
171X VAL* 3.7 0.7 - - - -
172X LEU* 2.8 37.4 + - + +
173X LEU* 2.7 32.1 + - + +
203X TRP* 5.0 0.2 - - + -
206X VAL* 4.8 3.4 - - + -
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Residues in contact with VAL 145 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143X ILE* 3.4 34.8 - - + -
144X LEU* 1.3 78.5 - - - +
146X TYR* 1.3 63.9 + - - +
147X GLU 4.5 1.1 - - - +
153X LEU* 3.3 6.9 - - - +
154X LEU* 2.9 59.3 + - + +
156X LEU* 4.2 17.7 - - + -
166X ALA* 5.3 0.7 - - + +
169X ALA* 4.1 18.8 - - + -
170X GLN 3.1 14.6 - - - +
171X VAL* 4.2 8.3 - - + -
172X LEU* 4.2 5.4 - - - -
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Residues in contact with TYR 146 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218U ILE* 5.5 1.6 - - + -
114X LEU* 4.2 10.1 - - + -
118X PHE* 5.5 0.9 - + - -
145X VAL* 1.3 74.3 - - - +
147X GLU* 1.3 58.4 + - - +
148X PRO* 3.0 27.4 - - + +
151X GLU* 3.4 39.1 + - + +
152X GLN* 3.5 20.4 - - - -
153X LEU* 4.0 9.0 - - + -
169X ALA* 3.7 1.0 - - - -
170X GLN* 2.8 24.8 + - + +
172X LEU* 4.0 10.2 - - + +
210X LEU* 3.9 12.3 - - + -
213X ALA* 3.6 46.7 - - + -
214X LEU* 3.3 29.0 - - + +
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Residues in contact with GLU 147 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18U TYR* 2.8 26.2 + - - +
84U LEU* 3.9 15.3 - - + -
88U ILE* 4.1 10.7 - - + +
220U LEU* 4.8 0.2 - - - +
145X VAL* 3.8 2.2 - - + -
146X TYR* 1.3 72.0 - - - +
148X PRO* 1.3 64.4 - - + +
149X LEU* 2.8 28.9 + - - +
150X GLU* 2.9 23.2 + - - -
151X GLU* 2.8 30.4 + - - -
152X GLN* 2.7 19.3 + - + +
154X LEU* 3.5 33.4 - - + -
166X ALA* 5.4 0.2 - - + -
167X ALA 5.3 0.2 - - - +
169X ALA* 4.6 8.0 - - + +
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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