Contacts of the strand formed by residues 145 - 155 (chain H) in PDB entry 1J5O
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 145 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143H ASN* 2.9 35.4 + - - +
144H SER* 1.3 91.0 - - - +
146H VAL* 1.3 67.7 + - - +
192H THR* 4.3 14.4 - - + +
193H VAL 3.9 2.2 - - - -
194H PRO* 3.4 32.8 - - + -
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Residues in contact with VAL 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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136H PRO* 4.0 20.0 - - + -
141H GLN* 4.8 19.7 - - + -
142H THR 5.2 1.1 - - - +
143H ASN 4.0 12.3 - - - +
145H MET* 1.3 82.1 - - - +
147H THR* 1.3 74.6 + - - +
148H LEU* 3.4 15.2 - - + +
192H THR* 2.8 8.9 - - - +
193H VAL* 2.7 46.6 + - + +
195H SER* 4.7 10.5 - - - -
198H TRP* 4.5 11.2 - - + -
199H PRO* 5.8 0.7 - - + -
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Residues in contact with THR 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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136H PRO* 4.0 2.4 - - - +
146H VAL* 1.3 81.1 - - - +
148H LEU* 1.3 83.0 + - - +
190H SER* 3.9 13.9 - - - +
191H VAL 2.9 10.8 - - - +
192H THR* 2.6 18.7 + - - +
114L THR* 5.8 4.2 - - - +
116L SER* 3.7 21.7 + - - +
118L PHE* 3.6 28.9 - - + -
135L PHE* 4.5 4.3 - - + -
137L ASN* 5.2 6.5 + - - +
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Residues in contact with LEU 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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134H LEU 3.7 7.6 - - - +
136H PRO* 3.8 28.3 - - + -
146H VAL* 3.4 22.4 - - + +
147H THR* 1.3 82.3 - - - +
149H GLY* 1.3 56.7 + - - +
164H TRP* 4.4 7.0 - - + -
190H SER* 2.9 7.6 - - - -
191H VAL* 2.4 66.4 + - + +
193H VAL* 4.2 18.6 - - + +
198H TRP* 4.0 26.2 - - + -
203H VAL* 5.2 5.4 - - + -
220H ILE* 4.0 14.8 - - - +
118L PHE* 4.2 3.1 - - - -
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Residues in contact with GLY 149 (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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133H PRO* 3.6 2.4 - - - +
134H LEU* 2.6 50.5 + - - +
148H LEU* 1.3 77.6 - - - +
150H CYS* 1.3 59.1 + - - +
164H TRP* 3.4 14.3 - - - -
189H SER 3.1 13.0 - - - -
190H SER* 3.8 3.1 - - - -
220H ILE* 5.3 1.9 - - - +
135L PHE* 4.2 0.2 - - - -
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Residues in contact with CYS 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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131H VAL* 3.5 14.6 - - + -
132H TYR 3.3 19.3 - - - -
133H PRO* 4.1 4.9 - - - -
134H LEU* 3.2 6.6 - - - +
149H GLY* 1.3 77.7 - - - -
151H LEU* 1.3 58.7 + - - +
152H VAL* 3.7 7.3 + - + +
162H VAL* 5.4 3.8 - - + -
164H TRP* 4.2 2.7 - - + -
188H SER* 2.9 28.1 - - - -
189H SER* 2.9 13.1 + - - +
205H CYS* 2.0 53.2 - - + -
218H LYS* 4.3 3.1 - - - -
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Residues in contact with LEU 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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130H SER 3.1 4.0 - - - +
131H VAL* 3.0 5.3 - - - -
132H TYR* 2.4 83.0 + - + +
134H LEU* 3.8 15.3 - - + +
150H CYS* 1.3 66.4 - - - +
152H VAL* 1.3 66.3 + - - +
153H LYS* 4.1 7.6 - - + +
186H THR* 3.9 22.4 - - + -
187H LEU 3.6 8.5 - - - +
188H SER* 4.3 9.0 - - - -
124L GLN* 4.1 2.9 - - - +
131L SER* 3.8 30.1 - - - +
133L VAL* 6.4 1.1 - - + -
178L THR* 5.2 11.2 - - + +
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Residues in contact with VAL 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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129H PRO* 3.8 27.8 - - + -
130H SER 3.9 1.6 - - - -
131H VAL* 4.4 5.6 - - + +
150H CYS* 4.2 9.9 - - + +
151H LEU* 1.3 73.8 - - - +
153H LYS* 1.3 57.4 + - - +
155H TYR* 4.2 13.9 - - + -
160H VAL* 4.6 1.8 - - + -
162H VAL* 4.9 4.3 - - + -
185H TYR 3.9 1.9 - - - +
186H THR* 3.2 2.3 - - - -
187H LEU* 2.4 76.2 + - + +
207H VAL* 4.0 37.9 - - + -
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Residues in contact with LYS 153 (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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129H PRO* 5.0 0.4 - - - -
130H SER* 2.7 52.2 + - - +
132H TYR* 3.4 22.2 + - + -
151H LEU* 4.1 9.6 - - + -
152H VAL* 1.3 76.4 - - - +
154H GLY* 1.3 60.1 + - - +
155H TYR 3.8 0.7 - - - -
181H GLN* 5.3 2.7 - - - +
186H THR* 3.6 26.2 - - + +
124L GLN* 2.9 34.8 - - - +
129L GLY* 3.9 14.1 - - - +
131L SER* 4.4 5.1 + - - +
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Residues in contact with GLY 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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127H THR* 3.3 8.5 + - - -
128H PRO 2.5 26.4 - - - +
129H PRO* 4.2 0.4 - - - -
130H SER* 4.6 3.5 - - - -
153H LYS* 1.3 80.8 - - - +
155H TYR* 1.3 55.8 + - - +
184H LEU* 3.8 19.9 - - - +
185H TYR 3.4 7.4 + - - -
186H THR* 3.8 3.2 + - - -
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Residues in contact with TYR 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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127H THR* 3.1 16.6 - - - +
129H PRO* 3.9 14.6 - - + -
152H VAL* 4.2 20.4 - - + -
153H LYS 3.8 0.2 - - - -
154H GLY* 1.3 77.6 - - - +
156H PHE* 1.3 56.7 + - - +
157H PRO 3.3 14.8 - - - -
158H GLU* 2.9 40.9 + - - -
160H VAL* 3.3 25.7 - - + +
178H ALA* 3.5 9.2 - - - +
184H LEU* 3.7 2.5 - - - -
185H TYR* 2.7 79.7 + + + +
187H LEU* 4.2 15.9 - - + +
209H HIS* 4.0 11.7 - + + -
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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