Contacts of the strand formed by residues 154 - 165 (chain G) in PDB entry 4GEK
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 154 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126G ALA 3.4 15.9 - - - +
127G SER 3.9 0.2 - - - -
128G MET 3.8 12.8 - - - +
129G VAL* 3.8 15.0 - - + -
150G ILE* 2.9 26.2 + - + +
151G TYR* 3.4 6.5 + - - +
152G GLN 3.8 1.7 - - - +
153G GLY* 1.3 78.6 - - - +
155G ASN* 1.3 62.7 + - - +
156G PRO* 4.5 0.2 - - - +
158G GLY* 4.1 6.5 - - - +
159G ALA 3.8 34.8 - - - +
223G PHE* 3.6 37.0 - - + -
242G LYS* 2.8 37.7 + - + -
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Residues in contact with ASN 155 (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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58G THR* 3.7 16.8 - - - +
125G ASN* 2.9 48.2 + - - +
126G ALA 2.8 19.0 + - - +
127G SER* 4.4 3.4 - - - +
153G GLY 3.6 0.9 + - - +
154G LEU* 1.3 77.4 - - - +
156G PRO* 1.3 84.0 - - + +
157G GLY 3.3 0.2 + - - -
158G GLY* 2.8 16.9 + - - +
242G LYS* 3.8 5.1 - - - +
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Residues in contact with PRO 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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55G GLN* 6.2 0.3 - - - +
154G LEU 3.9 1.1 - - - +
155G ASN* 1.3 97.3 - - + +
157G GLY* 1.3 58.6 + - - +
158G GLY 3.4 0.3 + - - -
242G LYS* 4.3 12.0 - - + +
243G ALA 3.2 17.5 - - - +
244G GLU* 4.3 1.6 - - - -
245G ASP 3.4 40.6 - - - +
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Residues in contact with GLY 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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53G PHE* 3.4 25.6 - - - +
55G GLN* 5.9 1.2 + - - -
156G PRO* 1.3 71.2 - - - +
158G GLY* 1.3 65.3 + - - +
241G LEU* 5.3 1.0 - - - +
242G LYS 2.9 21.4 + - - -
243G ALA 3.0 4.9 + - - -
244G GLU* 3.8 21.1 - - - +
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Residues in contact with GLY 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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53G PHE* 4.5 0.7 - - - -
127G SER* 3.2 21.8 - - - -
154G LEU* 4.1 12.4 - - - +
155G ASN* 2.8 18.1 + - - -
156G PRO 3.2 1.2 + - - -
157G GLY* 1.3 82.1 - - - +
159G ALA* 1.3 58.9 + - - -
240G ALA 4.0 0.2 - - - +
241G LEU* 3.6 2.9 - - - -
242G LYS* 2.9 27.3 + - - +
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Residues in contact with ALA 159 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G LEU* 4.0 22.9 - - + -
53G PHE* 3.7 23.8 - - + -
127G SER 3.1 8.1 + - - +
128G MET* 3.1 9.1 - - + +
129G VAL 2.9 25.5 + - - +
154G LEU* 3.8 6.6 - - - +
158G GLY* 1.3 75.0 - - - +
160G LEU* 1.3 59.9 + - - +
239G VAL* 4.6 1.8 - - + -
240G ALA 3.3 4.7 - - - +
241G LEU* 3.9 14.6 - - + -
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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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129G VAL* 3.2 34.8 - - + +
131G LEU* 4.2 15.3 - - + +
147G LEU* 3.8 18.6 - - + -
150G ILE* 4.2 11.0 - - + -
154G LEU* 4.3 1.0 - - + +
159G ALA* 1.3 74.3 - - - +
161G VAL* 1.3 78.3 + - - +
162G LEU* 4.4 7.6 - - + +
218G LEU* 3.6 30.7 - - + -
223G PHE* 3.9 24.2 - - + -
238G LEU 3.7 0.7 - - - +
239G VAL* 3.3 6.4 - - - +
240G ALA* 2.8 35.5 + - + +
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Residues in contact with VAL 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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42G ILE* 5.1 0.4 - - + -
46G ILE* 4.0 20.0 - - + -
49G LEU* 3.6 31.4 - - + -
128G MET* 4.2 15.3 - - + -
129G VAL 2.9 10.0 + - - +
130G VAL* 4.6 7.2 - - + -
131G LEU 2.8 31.9 + - - +
132G ASN* 5.0 0.2 - - - +
160G LEU* 1.3 77.5 - - - +
162G LEU* 1.3 55.3 + - - +
163G SER* 3.8 9.0 - - - +
229G TRP* 3.9 19.7 - - + -
237G SER* 3.3 24.9 - - - +
238G LEU 3.4 3.6 - - - +
239G VAL* 4.8 1.8 - - + -
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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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131G LEU* 3.5 22.9 - - + +
135G LEU* 3.9 32.5 - - + -
147G LEU* 4.6 6.7 - - + -
160G LEU* 4.0 12.1 - - + -
161G VAL* 1.3 73.5 - - - +
163G SER* 1.3 58.6 + - - +
164G GLU* 4.0 13.7 - - + +
214G HIS* 3.9 25.8 - - + +
218G LEU* 4.3 29.4 - - + -
237G SER* 3.4 1.0 - - - -
238G LEU* 2.7 50.4 + - + +
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Residues in contact with SER 163 (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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42G ILE* 3.6 4.6 - - - +
131G LEU 2.9 8.6 + - - +
132G ASN* 2.7 31.2 + - - -
133G PHE* 2.8 42.6 + - - -
161G VAL* 3.8 5.2 - - - +
162G LEU* 1.3 69.9 - - - +
164G GLU* 1.3 69.0 + - - +
236G GLY 3.2 12.1 - - - -
237G SER* 2.7 22.6 + - - -
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Residues in contact with GLU 164 (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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133G PHE* 3.5 9.7 - - - -
134G THR 3.9 0.5 + - - -
135G LEU* 3.3 19.5 + - - +
136G GLN* 2.9 53.1 + - - +
143G ARG* 5.5 0.3 - - - -
162G LEU* 4.0 13.6 + - + +
163G SER* 1.3 83.0 - - - +
165G LYS* 1.3 69.4 + - - +
166G PHE* 3.7 17.4 + - + -
208G THR* 5.4 0.7 - - - +
209G ASP* 4.9 4.2 + - - +
214G HIS* 3.6 28.6 + - + +
235G PHE* 3.6 0.5 - - - -
236G GLY 2.9 32.8 + - - +
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Residues in contact with LYS 165 (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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133G PHE* 4.0 3.2 - - - -
136G GLN* 2.9 18.5 + - - +
164G GLU* 1.3 81.8 - - - +
166G PHE* 1.3 67.2 + - - +
178G PHE* 6.3 1.0 - - - -
181G HIS* 4.5 4.6 + - - -
203G GLU* 2.8 43.4 + - + +
204G ASN* 6.0 0.2 + - - -
206G MET* 5.6 4.7 - - + -
208G THR* 3.3 34.2 - - + +
209G ASP 4.2 1.9 + - - +
234G ASN* 3.6 34.5 - - - +
235G PHE* 3.6 29.6 - - + -
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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