Contacts of the strand formed by residues 155 - 162 (chain G) in PDB entry 7GCH
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 LEU 155 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21F GLU* 3.6 7.3 - - - +
22F ALA* 3.1 27.7 + - + -
23F VAL 5.8 1.3 - - - +
25F GLY 6.2 2.7 - - - +
26F SER 6.3 0.4 - - - +
27F TRP* 4.3 31.4 - - + +
30F GLN* 3.8 21.1 - - + -
70F GLU 4.4 10.8 - - - +
71F PHE* 3.0 24.7 + - + -
139F THR* 4.8 1.3 - - - -
140F GLY 3.8 18.6 - - - +
141F TRP* 3.4 49.4 - - + +
154G ARG* 1.3 70.6 - - - +
156G GLN* 1.3 65.7 - - - +
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Residues in contact with GLN 156 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F ILE* 4.1 16.3 - - + +
19F GLY* 4.5 7.7 + - - -
20F GLU* 3.3 25.0 + - - +
21F GLU* 3.9 6.3 + - - +
22F ALA* 4.6 1.6 - - - -
139F THR* 3.4 8.0 - - - +
140F GLY 2.8 39.5 + - - +
144F THR* 4.1 21.7 - - + +
152G PRO* 3.6 18.6 - - + +
154G ARG* 2.9 33.0 + - - +
155G LEU* 1.3 79.1 - - - +
157G GLN* 1.3 61.2 + - - +
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Residues in contact with GLN 157 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E PRO* 5.1 1.2 - - - +
9E VAL 3.5 20.9 + - - +
10E LEU* 4.2 11.7 - - + +
16F ILE* 4.2 2.0 - - - -
19F GLY* 3.0 7.2 - - - -
20F GLU* 2.7 60.5 + - - +
21F GLU 3.3 17.4 + - - -
22F ALA* 3.7 13.5 - - + +
23F VAL* 4.8 1.5 + - - +
26F SER* 5.1 0.7 + - - -
27F TRP* 2.8 34.7 + - + +
137F VAL* 4.6 2.5 - - + -
138F THR 3.3 8.3 - - - -
139F THR* 3.6 17.0 - - + -
156G GLN* 1.3 72.1 - - - +
158G ALA* 1.3 62.3 - - - +
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Residues in contact with ALA 158 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E LEU* 6.2 0.2 - - - -
16F ILE* 3.6 23.3 - - + -
18F ASN 4.8 1.3 - - - +
19F GLY* 4.4 5.2 - - - -
20F GLU* 4.5 5.8 - - - -
137F VAL* 3.2 6.9 - - - -
138F THR* 2.8 43.0 + - + +
157G GLN* 1.3 81.8 - - - +
159G SER* 1.3 59.9 + - - +
160G LEU* 3.5 3.3 - - - +
188G VAL* 4.3 21.3 - - + -
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Residues in contact with SER 159 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E LEU* 5.5 10.5 - - - -
20F GLU* 4.7 8.0 + - - -
135F THR* 3.6 16.3 - - - +
136F CYS 3.3 11.9 - - - -
137F VAL* 3.9 10.8 - - - -
158G ALA* 1.3 72.6 - - - +
160G LEU* 1.3 66.5 + - - +
186G SER* 4.9 0.5 + - - -
188G VAL* 3.8 13.2 - - - +
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Residues in contact with LEU 160 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F THR 4.3 0.2 - - - -
135F THR* 3.7 8.4 - - - +
136F CYS* 3.0 39.1 + - - +
137F VAL 4.1 0.9 - - - +
138F THR* 3.9 21.1 - - + +
158G ALA 3.5 14.4 - - - +
159G SER* 1.3 79.3 + - - +
161G PRO* 1.3 72.8 - - + +
162G LEU 4.1 0.5 + - - -
183G ALA* 4.2 12.1 - - + +
184G GLY* 4.1 17.9 - - - +
186G SER* 4.0 2.7 - - - +
188G VAL* 3.9 20.2 - - + +
189G SER* 5.9 0.9 - - - -
190G SER* 5.4 2.7 - - - +
199G LEU* 4.3 5.8 - - + -
228G TYR* 3.9 21.8 - - + +
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Residues in contact with PRO 161 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F GLY* 4.4 14.8 - - - +
134F THR 3.2 9.2 - - - +
135F THR* 4.6 4.9 - - - +
160G LEU* 1.3 89.3 - - + +
162G LEU* 1.3 67.6 + - - +
163G LEU* 4.1 9.5 - - + +
183G ALA* 3.1 22.6 - - - -
184G GLY 3.2 17.6 + - - +
186G SER* 3.6 22.4 - - - +
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Residues in contact with LEU 162 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F PHE* 3.8 29.2 - - + +
131F ALA 3.7 23.8 - - - +
132F ALA* 4.4 0.7 - - - -
133F GLY* 2.8 25.6 + - - -
134F THR* 3.1 10.2 + - - +
136F CYS* 3.6 34.5 - - + -
160G LEU 4.1 0.2 + - - -
161G PRO* 1.3 75.1 - - - +
163G LEU* 1.3 64.6 + - - +
181G ILE* 4.3 13.7 - - + -
182G CYS 3.4 7.6 - - - +
183G ALA* 3.9 14.8 - - + -
199G LEU* 4.2 17.5 - - + -
201G CYS* 3.8 3.8 - - - -
210G VAL* 4.5 4.9 - - + -
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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