Contacts of the strand formed by residues 140 - 147 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136H VAL* 3.8 5.5 - - - +
139H VAL* 1.3 77.5 - - - +
141H TRP* 1.3 64.2 + - - -
158H ILE 3.1 11.7 - - - -
160H LYS 3.3 15.0 - - - -
176H ASP* 3.5 1.4 - - - +
177H VAL* 2.9 33.0 + - - +
178H TRP* 3.3 12.0 - - - +
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Residues in contact with TRP 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89H LEU* 3.5 49.1 - - + +
90H HIS* 3.4 31.4 - + - -
93H PHE* 3.7 25.4 - + + -
136H VAL* 3.7 12.7 - - - +
140H GLY* 1.3 75.5 - - - -
142H ALA* 1.3 62.3 + - - +
143H ILE* 4.1 9.2 - - + -
157H GLN* 3.7 0.7 - - - -
158H ILE* 2.8 41.7 + - + +
160H LYS 3.1 17.7 - - - -
161H HIS* 2.8 23.5 - + - -
174H ALA* 3.8 17.0 - - + -
175H LEU 3.3 8.7 - - - -
176H ASP* 3.3 46.1 + - + -
177H VAL* 4.1 1.1 - - - -
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Residues in contact with ALA 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H PHE* 3.4 21.9 - - + +
132H ALA* 4.6 4.5 - - + -
133H ALA* 3.2 44.2 - - + +
136H VAL* 5.1 0.4 - - - -
141H TRP* 1.3 72.8 - - - +
143H ILE* 1.3 62.0 + - - +
155H ILE* 5.6 0.7 - - + -
156H LEU 3.6 6.7 - - - +
157H GLN* 5.0 0.9 - - - +
175H LEU* 2.8 33.0 + - + +
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Residues in contact with ILE 143 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89H LEU* 4.6 7.0 - - + -
129H PHE* 3.9 5.1 - - - -
141H TRP* 4.1 15.0 - - + -
142H ALA* 1.3 81.1 - - - +
144H LEU* 1.3 60.1 + - - +
145H VAL* 3.6 23.1 - - + -
154H LEU 3.8 0.3 - - - +
155H ILE* 3.2 7.2 - - - +
156H LEU* 2.9 47.4 + - + +
158H ILE* 3.7 27.8 - - + -
165H HIS* 3.8 15.5 - - + +
166H ALA 5.8 0.4 - - - +
171H VAL* 4.2 15.3 - - + -
173H LEU 3.2 5.4 - - - +
174H ALA* 3.6 22.0 - - + -
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Residues in contact with LEU 144 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111H ILE* 4.2 24.7 - - + -
115H ILE* 5.0 2.0 - - + -
119H PHE* 4.3 2.7 - - + -
125H PHE* 3.9 33.2 - - + -
129H PHE* 3.9 9.8 - - + -
143H ILE* 1.3 73.4 - - - +
145H VAL* 1.3 62.8 + - - +
153H LEU* 4.0 26.0 - - + -
154H LEU 3.5 19.1 - - - +
155H ILE* 4.1 4.9 - - + +
171H VAL* 3.7 0.9 - - - +
172H LEU* 2.8 36.7 + - + -
173H LEU* 2.7 31.0 + - + +
203H TRP* 5.2 0.4 - - + -
206H VAL* 4.8 1.6 - - + -
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Residues in contact with VAL 145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143H ILE* 3.6 29.8 - - + -
144H LEU* 1.3 79.7 - - - +
146H TYR* 1.3 64.1 + - - +
147H GLU* 4.6 2.7 - - + +
153H LEU* 3.2 7.6 - - - +
154H LEU* 2.8 53.5 + - + +
156H LEU* 4.2 16.2 - - + -
166H ALA* 4.9 1.8 - - + +
169H ALA* 4.1 22.2 - - + -
170H GLN 3.1 14.1 - - - +
171H VAL* 3.8 12.6 - - + -
172H LEU* 4.1 6.3 - - - -
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Residues in contact with TYR 146 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A PRO* 5.6 2.1 - - - +
218E ILE* 5.5 0.4 - - + -
114H LEU* 4.2 10.3 - - + -
118H PHE* 5.5 0.2 - + - -
145H VAL* 1.3 74.3 - - - +
147H GLU* 1.3 62.5 + - - +
148H PRO* 3.2 17.0 - - + +
151H GLU* 3.0 59.8 + - + +
152H GLN* 3.6 8.5 - - - -
153H LEU* 4.1 6.1 - - + -
169H ALA* 3.6 2.1 - - - -
170H GLN* 2.8 29.7 + - + +
172H LEU* 3.9 9.8 - - + +
210H LEU* 3.6 17.5 - - + -
213H ALA* 3.8 40.6 - - + -
214H LEU* 3.5 31.3 - - + +
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Residues in contact with GLU 147 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18E TYR* 2.5 32.1 + - - +
84E LEU* 4.0 17.3 - - + -
88E ILE* 4.2 12.6 - - + +
220E LEU* 5.1 1.4 - - - +
145H VAL* 3.8 3.9 + - + -
146H TYR* 1.3 72.7 - - - +
148H PRO* 1.3 57.0 - - + +
149H LEU* 2.7 27.7 + - - +
150H GLU* 3.0 21.5 + - - -
151H GLU* 2.8 38.3 + - - -
152H GLN* 2.8 17.9 + - + +
154H LEU* 3.9 24.5 - - + -
166H ALA* 5.3 0.2 - - + -
167H ALA 5.3 0.2 - - - +
169H ALA* 4.6 7.0 - - + -
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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