Contacts of the strand formed by residues 166 - 175 (chain G) in PDB entry 5D7I
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 PHE 166 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112G GLN* 4.8 11.9 - - - +
113G ASN* 5.5 9.9 - - + -
136G ASP* 4.7 6.7 - - - -
159G LEU 4.0 0.2 - - - +
160G ASP* 3.6 1.8 + - - -
161G MET* 2.7 49.4 + - + +
164G MET* 3.9 18.6 - - + +
165G ASP* 1.3 78.1 - - - +
167G LYS* 1.3 67.7 + - - +
168G SER* 3.5 30.5 - - - -
140H LYS* 3.6 38.1 - - + +
195H ARG* 3.6 19.1 - - - -
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Residues in contact with LYS 167 (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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14G GLU* 2.9 30.9 + - - +
80G MET* 3.9 25.4 - - + -
109G PRO* 4.3 17.3 - - + -
110G ASP 5.5 1.6 - - - +
111G ILE* 3.8 15.8 - - + +
112G GLN* 4.4 18.6 - - - +
158G VAL* 4.2 10.1 - - + -
159G LEU 3.2 8.3 - - - +
160G ASP* 3.4 34.3 + - + -
165G ASP* 4.3 8.0 + - - +
166G PHE* 1.3 89.7 - - - +
168G SER* 1.3 64.6 + - - +
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Residues in contact with SER 168 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111G ILE* 4.4 5.4 - - - -
135G THR* 4.6 0.5 + - - -
136G ASP* 3.4 26.0 - - - +
157G CYS 3.6 0.7 - - - +
158G VAL* 3.5 5.6 - - - -
159G LEU* 3.0 51.9 + - - +
166G PHE* 3.5 9.2 - - - -
167G LYS* 1.3 76.4 - - - +
169G ASN* 1.3 65.3 + - - +
170G SER* 6.1 0.2 - - - -
195H ARG* 2.9 19.9 + - - -
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Residues in contact with ASN 169 (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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109G PRO* 3.5 8.2 - - - +
111G ILE* 3.7 8.5 - - - +
135G THR* 3.0 4.2 + - - -
136G ASP* 2.9 24.4 + - - +
137G PHE* 3.0 47.4 + - + +
138G ASP 3.7 1.4 + - - -
139G SER* 3.2 33.4 + - - +
156G LYS* 4.9 10.2 + - + +
157G CYS 3.6 4.2 - - - +
158G VAL* 3.3 25.6 - - - +
168G SER* 1.3 75.9 - - - +
170G SER* 1.3 66.2 + - - +
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Residues in contact with SER 170 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133G LEU* 3.9 9.9 - - - -
134G PHE 3.0 14.6 - - - -
135G THR* 3.7 12.1 - - - -
137G PHE* 3.8 6.9 - - - -
156G LYS* 3.1 3.8 - - - -
157G CYS 2.8 20.2 + - - +
159G LEU* 5.0 5.4 - - - +
168G SER 5.3 0.2 - - - -
169G ASN* 1.3 79.7 - - - +
171G ALA* 1.3 57.9 + - - +
142H THR* 6.3 0.4 - - - -
193H ARG* 2.2 59.7 + - - -
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Residues in contact with ALA 171 (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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132G CYS 3.8 0.3 - - - +
133G LEU* 3.8 4.0 - - - +
134G PHE* 2.8 34.5 + - + +
143G VAL* 3.9 29.4 - - + -
154G THR* 3.7 22.4 - - - +
155G ASP 4.1 2.9 - - - +
156G LYS* 4.3 0.4 - - - -
170G SER* 1.3 74.8 - - - +
172G VAL* 1.3 65.9 + - - +
186G PHE* 3.9 10.0 - - + -
193H ARG* 3.6 5.8 - - - +
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Residues in contact with VAL 172 (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 VAL* 3.6 27.6 - - + -
132G CYS 3.4 2.7 - - - +
133G LEU* 4.2 15.0 - - + -
152G TYR 3.8 0.3 - - - +
153G ILE* 3.5 3.5 - - - +
154G THR* 2.9 34.3 + - - +
171G ALA* 1.3 77.1 - - - +
173G ALA* 1.3 63.9 - - - +
174G TRP* 3.9 18.8 - - + -
186G PHE* 4.4 1.3 - - - -
144H VAL* 4.2 22.0 - - + -
146H LEU* 4.5 3.6 - - + -
191H SER* 4.1 12.3 - - - +
193H ARG* 3.5 26.2 - - - +
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Residues in contact with ALA 173 (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 VAL* 3.6 0.5 - - - -
132G CYS* 2.7 39.6 + - + +
152G TYR 3.2 11.0 - - - +
153G ILE* 4.1 10.8 - - + -
172G VAL* 1.3 76.9 - - - +
174G TRP* 1.3 65.4 + - - +
180G PHE* 4.2 6.5 - - + -
185G ALA* 4.2 15.0 - - + -
186G PHE* 3.7 26.9 - - + -
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Residues in contact with TRP 174 (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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130G SER 4.0 7.0 - - - +
131G VAL* 3.7 17.9 - - + -
151G VAL* 3.8 1.7 - - - +
152G TYR* 3.0 75.0 + + + +
154G THR* 4.0 18.4 - - - -
172G VAL* 3.9 11.0 - - + -
173G ALA* 1.3 80.8 - - - +
175G SER* 1.3 70.1 + - - +
180G PHE* 4.0 10.0 - - - -
146H LEU* 3.7 42.6 - - + +
148H THR* 4.5 9.9 - - + +
177H LEU* 4.1 12.6 - - + -
179H GLU* 5.5 1.2 + - - -
189H ALA* 3.6 33.7 - - + -
190H LEU 5.3 0.4 - - - -
191H SER* 4.5 3.6 - - - -
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Residues in contact with SER 175 (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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130G SER 4.6 8.7 + - - +
150G ASP 3.0 20.3 + - - -
151G VAL* 3.7 7.3 - - - +
152G TYR* 5.0 0.7 - - - -
174G TRP* 1.3 86.7 - - - +
176G ASN* 1.3 70.3 + - - +
177G LYS* 3.0 23.5 + - - +
180G PHE* 3.5 36.9 - - - -
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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