Contacts of the strand formed by residues 146 - 156 (chain H) in PDB entry 2YMX
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 MET 146 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144H ASN* 3.3 36.3 + - - +
145H SER* 1.3 89.9 - - - +
147H VAL* 1.3 61.8 + - - +
193H THR* 3.8 34.5 - - + +
194H VAL* 3.4 13.2 - - - -
195H PRO* 3.9 22.0 - - + -
196H SER* 4.4 2.2 - - - -
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Residues in contact with VAL 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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137H PRO* 3.7 31.6 - - + -
140H ALA 5.8 3.8 - - - +
146H MET* 1.3 76.3 - - - +
148H THR* 1.3 68.0 + - - +
149H LEU* 4.0 3.3 + - + -
192H VAL 3.8 1.0 - - - +
193H THR* 3.4 2.9 - - - -
194H VAL* 2.8 53.8 + - + +
196H SER* 4.2 17.2 - - - +
199H TRP* 4.1 29.8 - - + +
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Residues in contact with THR 148 (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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137H PRO* 4.1 6.6 - - - +
147H VAL* 1.3 76.0 - - - +
149H LEU* 1.3 78.2 + - - +
191H SER* 4.1 15.9 - - - +
192H VAL 3.4 4.7 - - - +
193H THR* 2.8 26.8 + - - +
114L THR* 5.2 7.4 - - - +
116L SER* 3.7 26.5 + - - +
118L PHE* 3.3 27.1 - - + -
135L PHE* 4.4 3.1 - - + -
137L ASN* 4.7 6.6 + - - +
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Residues in contact with LEU 149 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135H LEU 3.5 6.7 - - - +
137H PRO* 3.5 29.4 - - + -
147H VAL* 4.5 7.9 - - + +
148H THR* 1.3 78.6 - - - +
150H GLY* 1.3 58.5 + - - +
165H TRP* 4.9 0.2 - - + -
191H SER* 3.3 7.1 - - - -
192H VAL* 2.8 40.4 + - + +
194H VAL* 4.5 7.0 - - + -
199H TRP* 3.7 56.3 - - + +
204H VAL* 3.8 24.2 - - + -
221H ILE* 4.0 16.6 - - + -
118L PHE* 4.5 3.4 - - - -
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Residues in contact with GLY 150 (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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135H LEU* 2.8 49.0 + - - +
149H LEU* 1.3 77.5 - - - +
151H CYS* 1.3 56.6 + - - -
165H TRP* 3.4 9.6 - - - -
190H SER 3.1 12.3 - - - -
191H SER* 4.2 1.1 - - - -
221H ILE* 3.5 12.0 - - - +
135L PHE* 4.3 2.0 - - - -
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Residues in contact with CYS 151 (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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132H VAL* 4.2 9.0 - - + -
133H TYR 3.4 10.1 - - - +
135H LEU* 3.9 3.9 - - - +
150H GLY* 1.3 79.4 - - - -
152H LEU* 1.3 59.3 + - - +
153H VAL* 4.0 8.3 + - + +
163H VAL* 5.3 1.6 - - + -
165H TRP* 3.6 6.0 - - + -
189H SER* 3.4 5.0 - - - -
190H SER* 2.9 34.8 + - - +
206H CYS* 2.0 53.4 - - + -
208H VAL* 5.2 0.7 - - + -
219H LYS* 4.4 2.9 - - - -
221H ILE* 3.9 11.7 - - - -
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Residues in contact with LEU 152 (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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131H SER 3.5 3.3 - - - +
132H VAL* 3.5 0.7 - - - -
133H TYR* 2.8 64.2 + - + +
135H LEU* 4.1 16.3 - - + +
151H CYS* 1.3 71.5 - - - +
153H VAL* 1.3 59.5 + - - +
154H LYS* 3.9 8.4 + - + -
187H THR* 3.6 30.1 - - + -
188H LEU 3.8 7.6 - - - +
189H SER* 4.4 6.3 - - - +
124L GLN* 4.6 2.5 - - - +
131L SER* 3.6 34.3 - - - +
133L VAL* 4.1 12.1 - - + -
178L THR* 4.0 17.9 - - + +
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Residues in contact with VAL 153 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130H PRO* 3.6 28.9 - - + -
131H SER 3.4 4.0 - - - +
132H VAL* 4.4 5.8 - - + -
151H CYS* 4.7 6.1 - - + +
152H LEU* 1.3 77.8 - - - +
154H LYS* 1.3 57.6 + - - +
156H TYR* 3.9 16.6 - - + -
161H VAL* 4.2 4.9 - - + -
163H VAL* 4.5 2.5 - - + -
187H THR* 3.3 3.2 - - - +
188H LEU* 2.8 62.6 + - + +
190H SER* 6.5 0.2 - - - -
208H VAL* 3.7 38.8 - - + -
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Residues in contact with LYS 154 (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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130H PRO* 3.8 0.9 - - - +
131H SER* 2.9 36.8 + - - -
133H TYR* 4.3 19.7 - - + -
152H LEU* 3.9 9.4 + - + -
153H VAL* 1.3 76.7 - - - +
155H GLY* 1.3 67.9 + - - +
156H TYR* 3.5 3.7 + - - -
186H TYR 3.6 2.0 - - - -
187H THR* 3.6 26.7 + - + +
124L GLN* 3.9 17.0 - - - +
131L SER* 4.0 6.5 - - - +
160L LEU* 5.4 4.2 - - - +
178L THR* 5.8 0.6 - - + +
180L THR* 3.5 36.3 + - - +
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Residues in contact with GLY 155 (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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128H THR* 3.2 24.8 - - - +
129H PRO 3.4 4.9 - - - +
154H LYS* 1.3 82.3 - - - +
156H TYR* 1.3 59.3 + - - +
185H LEU* 3.5 27.4 - - - +
186H TYR 2.9 10.7 + - - -
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Residues in contact with TYR 156 (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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128H THR 3.2 12.8 - - - +
130H PRO* 3.7 20.6 - - + -
153H VAL* 3.9 33.2 - - + -
155H GLY* 1.3 78.4 - - - +
157H PHE* 1.3 63.5 + - - +
158H PRO 3.5 21.8 - - - -
159H GLU* 2.5 29.7 + - - -
161H VAL* 3.6 26.6 - - + +
179H ALA* 3.2 17.3 - - - +
185H LEU* 3.5 2.7 - - - -
186H TYR* 2.8 64.6 + + + -
188H LEU* 3.9 15.2 - - + +
210H HIS* 3.7 3.1 - - + -
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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