Contacts of the strand formed by residues 149 - 158 (chain C) in PDB entry 6H2V
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 ALA 149 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118C LYS* 2.9 28.6 + - - -
120C PHE 3.4 4.7 - - - -
121C ASP 4.1 4.0 - - - +
123C VAL* 3.8 11.0 - - + +
145C ALA 2.8 20.8 + - - +
147C GLU 3.5 0.2 - - - -
148C MET* 1.3 73.1 - - - +
150C ARG* 1.4 58.1 + - - +
152C ALA 3.3 28.3 - - - +
153C VAL* 3.5 11.2 - - + -
209C PHE* 3.3 10.5 - - + -
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Residues in contact with ARG 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C VAL* 3.6 18.4 - - - +
118C LYS* 2.8 56.4 + - + +
119C SER* 3.5 14.8 + - - +
120C PHE 2.8 18.1 + - - +
121C ASP* 3.0 35.0 + - - +
149C ALA* 1.4 72.0 - - - +
151C THR* 1.4 65.4 + - - +
209C PHE* 3.5 15.5 - - - +
45D MET* 4.5 0.8 - - - +
48D LYS* 3.6 45.7 - - - +
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Residues in contact with THR 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ASP* 4.1 18.8 - - - +
53C LYS* 5.9 3.6 - - - -
121C ASP* 2.9 23.4 + - - +
122C THR* 5.1 1.1 - - - -
150C ARG* 1.4 82.3 - - - +
152C ALA* 1.3 58.9 + - - +
206C ARG* 4.4 1.8 - - - +
208C SER* 3.6 10.4 - - - -
209C PHE* 3.4 18.0 - - - -
211C HIS* 6.3 0.9 - - + -
303C SO4 3.5 34.1 + - - +
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Residues in contact with ALA 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ASP* 3.4 26.2 - - - +
121C ASP 3.4 2.4 + - - -
122C THR* 3.4 5.3 - - + -
123C VAL 3.1 21.8 + - - -
149C ALA* 3.3 8.3 - - - +
151C THR* 1.3 80.5 - - - +
153C VAL* 1.3 63.3 + - - +
154C TYR* 3.7 14.4 - - + -
206C ARG* 3.5 15.9 - - + +
207C PHE 3.2 11.0 - - - +
208C SER* 4.6 0.2 - - - +
209C PHE* 4.3 1.7 - - - -
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Residues in contact with VAL 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C VAL* 3.3 11.9 - - + +
125C MET* 4.4 6.3 - - + -
142C LEU* 4.2 8.1 - - + -
145C ALA* 3.4 50.7 - - + +
146C LEU* 3.8 13.9 - - + +
149C ALA* 3.5 15.5 - - + -
152C ALA* 1.3 71.1 - - - +
154C TYR* 1.3 69.5 + - - +
205C ILE 3.4 1.0 - - - +
206C ARG* 3.5 2.1 - - - -
207C PHE* 2.8 57.2 + - + -
209C PHE* 5.0 0.4 - - + -
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Residues in contact with TYR 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C MET* 3.8 9.1 - - + +
43C ILE* 3.5 52.7 - - + -
47C TYR* 3.1 23.7 - + - +
49C ASP* 2.6 21.8 + - - +
122C THR* 3.7 20.2 - - + -
123C VAL 2.9 10.0 + - - +
124C ILE* 3.4 4.5 - - + -
125C MET* 3.0 26.3 + - - +
152C ALA* 3.7 16.6 - - + -
153C VAL* 1.3 72.6 - - - +
155C SER* 1.3 59.9 + - - +
179C ILE* 3.8 20.6 - - + -
204C LEU* 4.5 4.7 - - + -
205C ILE 3.3 4.0 - - - +
206C ARG* 2.9 37.2 + - + -
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Residues in contact with SER 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C MET* 4.5 0.4 - - - +
125C MET* 3.2 31.8 - - - +
127C PRO* 3.3 12.6 - - - +
153C VAL* 4.1 0.6 - - - -
154C TYR* 1.3 75.2 - - - +
156C LEU* 1.3 65.5 + - - +
157C HIS* 3.0 30.8 + - - -
203C ASP 3.4 1.6 - - - +
204C LEU* 3.6 5.0 - - - +
205C ILE* 2.9 33.8 + - - +
207C PHE* 4.0 9.0 - - - -
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Residues in contact with LEU 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C THR* 4.6 1.8 - - + -
35C ILE* 3.7 30.1 - - + -
39C MET* 3.9 18.6 - - - -
125C MET 3.5 4.0 + - - +
126C ASN* 3.4 40.3 - - + +
127C PRO* 3.5 14.9 - - - +
129C PHE* 3.5 14.9 - - - -
155C SER* 1.3 73.4 + - - +
157C HIS* 1.3 61.7 + - - +
182C LEU* 4.6 5.2 - - + -
184C TYR* 5.1 2.7 - - + +
202C VAL* 3.7 31.6 - - + -
203C ASP 3.3 2.7 - - - -
204C LEU* 4.0 29.6 - - + +
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Residues in contact with HIS 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C MET* 4.7 0.2 - - + -
127C PRO* 4.3 1.3 - - + -
129C PHE* 3.9 2.9 - - - -
138C ASP* 2.9 52.7 + - + +
139C MET* 4.5 5.3 - - - -
142C LEU* 4.1 14.5 - - + +
155C SER* 3.0 35.0 + - - -
156C LEU* 1.3 72.3 + - - +
158C LYS* 1.3 67.2 + - - +
161C THR* 4.2 0.4 - - - +
165C VAL* 4.2 13.9 - - + +
202C VAL* 3.3 5.1 - - - +
203C ASP* 2.8 31.5 + - - +
205C ILE* 3.7 28.7 - - + -
207C PHE* 3.9 16.3 - + - -
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Residues in contact with LYS 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C PHE* 3.7 54.9 - - + +
138C ASP* 4.7 1.0 + - - +
157C HIS* 1.3 76.0 - - - +
159C SER* 1.3 62.4 + - - +
160C SER* 3.2 12.1 - - - +
161C THR* 2.7 43.4 + - + -
162C ARG* 3.9 1.2 + - - -
165C VAL* 5.2 0.2 - - - +
200C ILE* 4.4 19.3 - - + -
201C GLU 3.7 6.7 - - - +
202C VAL* 4.0 1.8 - - - -
203C ASP* 3.7 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