Contacts of the strand formed by residues 137 - 147 (chain H) in PDB entry 1A3L
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 137 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134H THR* 3.4 29.5 - - + +
135H ASN 3.8 1.2 + - - +
136H SER* 1.3 85.9 - - - +
138H VAL* 1.3 58.9 + - - +
192H THR* 3.7 30.7 - - + +
193H VAL* 3.4 16.2 - - - -
194H PRO* 3.8 24.2 - - + -
195H SER* 3.2 12.3 + - - -
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Residues in contact with VAL 138 (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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126H PRO* 4.2 18.4 - - + -
133H GLN* 4.7 14.4 - - + +
134H THR* 4.9 2.0 - - - -
137H MET* 1.3 76.1 - - - +
139H THR* 1.3 71.2 + - - +
140H LEU* 4.1 9.3 + - + -
191H VAL 3.8 0.9 - - - +
192H THR* 3.3 2.3 - - - -
193H VAL* 2.6 56.2 + - + +
195H SER* 3.8 14.6 + - - +
199H TRP* 4.2 28.3 - - + -
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Residues in contact with THR 139 (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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126H PRO* 4.0 5.9 - - - +
133H GLN* 4.8 5.7 + - - +
134H THR* 5.3 3.0 + - - -
138H VAL* 1.3 74.8 - - - +
140H LEU* 1.3 79.3 + - - +
190H SER* 4.3 6.7 - - - -
191H VAL 3.3 3.6 - - - +
192H THR* 2.6 28.5 + - - +
114L THR* 5.4 6.4 - - - +
116L SER* 3.6 28.1 + - - +
118L PHE* 3.2 25.4 - - + -
135L PHE* 4.3 11.4 - - + -
137L ASN* 4.7 6.9 + - - +
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Residues in contact with LEU 140 (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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124H LEU 3.6 7.0 - - - +
126H PRO* 3.7 25.4 - - + -
138H VAL* 4.5 8.1 - - + +
139H THR* 1.3 89.2 - - - +
141H GLY* 1.3 60.5 + - - +
190H SER* 3.3 5.2 - - - -
191H VAL* 2.8 38.6 + - + +
193H VAL* 5.0 4.0 - - + -
199H TRP* 3.4 53.8 - - + +
205H VAL* 3.8 23.8 - - + -
223H ILE* 4.1 15.9 - - + -
118L PHE* 4.2 4.9 - - - -
135L PHE* 4.3 0.2 - - - -
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Residues in contact with GLY 141 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H LEU* 2.8 48.3 + - - +
140H LEU* 1.3 78.6 - - - +
142H CYS* 1.3 63.1 + - - -
157H TRP* 3.5 11.4 - - - -
189H SER 2.9 13.9 - - - -
190H SER* 4.1 0.7 - - - -
223H ILE* 3.6 5.4 - - - +
135L PHE* 4.4 0.7 - - - -
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Residues in contact with CYS 142 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121H VAL* 4.4 7.0 - - + -
122H TYR 3.3 10.1 - - - +
124H LEU* 3.9 5.1 - - - +
141H GLY* 1.3 82.6 - - - -
143H LEU* 1.3 60.6 - - - +
144H VAL* 4.0 7.2 + - + +
154H VAL* 5.8 0.9 - - + -
157H TRP* 3.8 3.3 - - + -
188H SER* 3.3 4.7 + - - -
189H SER* 2.9 34.6 + - - +
208H CYS* 2.0 53.6 - - + -
210H VAL* 5.4 0.4 - - + -
221H LYS* 4.1 4.5 - - - -
223H ILE* 3.7 17.7 - - - -
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Residues in contact with LEU 143 (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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120H SER 3.5 1.6 - - - +
121H VAL* 3.3 4.0 - - - +
122H TYR* 2.7 57.6 + - + +
124H LEU* 4.0 14.9 - - + +
142H CYS* 1.3 72.2 - - - +
144H VAL* 1.3 58.9 + - - +
145H LYS* 3.9 18.3 + - + -
186H THR* 3.8 20.0 - - + -
187H LEU 3.8 7.6 - - - +
188H SER* 3.3 20.2 - - - +
124L GLN* 4.2 4.3 - - - +
131L SER* 3.6 30.1 - - - +
133L VAL* 4.4 12.8 - - + -
178L THR* 4.7 9.4 - - + +
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Residues in contact with VAL 144 (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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119H PRO* 3.6 27.6 - - + -
120H SER 3.3 4.3 - - - +
121H VAL* 4.4 4.7 - - + -
142H CYS* 4.5 8.1 - - + +
143H LEU* 1.3 74.0 - - - +
145H LYS* 1.3 59.6 + - - +
147H TYR* 4.0 13.5 - - + -
152H VAL* 4.5 3.4 - - + -
154H VAL* 4.5 2.9 - - + -
185H TYR 4.1 0.7 - - - +
186H THR* 3.3 5.5 - - - +
187H LEU* 2.7 61.3 + - + +
189H SER* 6.0 0.4 - - - -
210H VAL* 3.7 39.0 - - + -
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Residues in contact with LYS 145 (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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119H PRO* 3.6 0.2 - - - +
120H SER* 2.7 46.8 + - - +
122H TYR* 4.0 17.7 - - + +
143H LEU* 3.9 21.8 - - + -
144H VAL* 1.3 75.8 - - - +
146H GLY* 1.3 65.5 + - - +
147H TYR* 3.6 2.9 - - - -
179H GLN* 5.8 1.8 + - - -
185H TYR 3.8 0.4 - - - -
186H THR* 3.6 30.5 + - + +
124L GLN* 4.2 12.9 - - - +
131L SER* 3.8 15.5 - - - -
178L THR* 5.8 1.1 - - - -
180L THR* 4.1 20.1 - - - +
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Residues in contact with GLY 146 (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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117H THR* 3.5 15.4 - - - +
118H PRO 3.5 4.5 - - - +
145H LYS* 1.3 79.5 - - - +
147H TYR* 1.3 59.4 + - - +
184H LEU* 3.5 33.4 - - - +
185H TYR 3.0 11.0 + - - -
186H THR* 3.7 2.6 + - - -
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Residues in contact with TYR 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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117H THR 3.1 14.8 - - - +
119H PRO* 3.7 32.1 - - + -
144H VAL* 4.0 20.9 - - + -
146H GLY* 1.3 78.4 - - - +
148H PHE* 1.3 65.6 + - - +
149H PRO 3.8 17.3 - - - -
150H GLU* 3.0 30.1 + - - -
152H VAL* 3.5 36.4 - - + +
176H ALA* 3.4 16.5 - - - +
184H LEU* 3.6 3.5 - - - -
185H TYR* 2.8 67.1 + - + +
186H THR* 4.3 1.6 - - - -
187H LEU* 3.9 5.6 - - + +
212H HIS* 3.9 3.4 - - + -
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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