Contacts of the strand formed by residues 141 - 151 (chain H) in PDB entry 5U2V
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 LYS 141 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136G ASP* 5.7 0.6 + - - -
161G MET* 4.2 10.1 - - - -
164G MET* 4.0 21.3 - - + -
166G PHE* 3.6 49.1 - - + -
135H GLU* 3.2 25.8 - - - +
136H ILE* 3.6 8.8 + - - -
139H THR* 2.9 32.0 + - - +
140H GLN* 1.3 83.1 - - - +
142H ALA* 1.3 60.8 + - - +
196H ARG* 3.7 20.4 - - + +
197H VAL 3.7 9.4 - - - +
198H SER 4.6 0.2 - - - -
199H ALA 4.0 2.0 - - - +
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Residues in contact with ALA 142 (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 PRO* 3.6 25.1 - - + -
135H GLU* 3.8 2.5 - - - -
136H ILE* 4.2 8.1 - - + -
141H LYS* 1.3 74.5 - - - +
143H THR* 1.3 61.9 + - - +
144H LEU* 4.0 0.5 + - - +
195H LEU 3.7 1.9 - - - +
196H ARG* 3.1 3.1 - - - -
197H VAL* 2.7 47.2 + - + +
198H SER 4.4 2.5 - - - +
199H ALA* 4.3 1.5 - - - +
202H TRP* 3.7 24.9 - - + -
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Residues in contact with THR 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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121G LEU* 3.3 10.2 - - - +
133G LEU* 3.6 29.2 - - + +
135G THR* 5.3 0.5 + - - -
159G LEU* 5.2 3.7 - - + +
131H PRO* 3.3 24.0 - - - +
135H GLU* 2.8 33.9 + - - +
142H ALA* 1.3 72.7 - - - +
144H LEU* 1.3 71.7 + - - +
145H VAL* 4.3 3.8 - - + -
194H ARG* 4.1 17.7 - - + -
195H LEU 3.6 5.8 - - - +
196H ARG* 3.0 21.5 + - + +
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Residues in contact with LEU 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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128H VAL* 4.4 15.5 - - + -
129H PHE 3.5 7.0 - - - +
131H PRO* 3.8 25.4 - - + -
142H ALA 4.1 6.3 - - - +
143H THR* 1.3 73.8 - - - +
145H VAL* 1.3 62.5 + - - +
160H TRP* 3.8 16.8 - - + -
194H ARG* 3.1 5.7 - - - +
195H LEU* 2.7 48.0 + - + +
197H VAL* 4.4 11.0 - - + -
202H TRP* 3.9 21.5 - - + -
209H PHE* 3.8 40.8 - - + -
240H ALA* 4.9 1.8 - - + -
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Residues in contact with VAL 145 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121G LEU* 3.8 21.1 - - + -
131G VAL* 4.3 9.6 - - + -
133G LEU* 4.1 25.4 - - + -
172G VAL* 4.0 19.7 - - + -
128H VAL* 3.5 2.1 - - - -
129H PHE* 2.8 45.4 + - + -
143H THR* 4.3 6.1 - - + -
144H LEU* 1.3 78.2 - - - +
146H CYS* 1.3 61.4 + - - +
147H LEU* 3.7 25.4 - - + -
160H TRP* 4.2 2.7 - - - -
193H SER 3.2 12.3 - - - +
194H ARG* 4.6 1.8 - - + -
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Residues in contact with CYS 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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126H VAL* 3.8 16.2 - - - -
127H ALA 3.6 4.7 - - - -
128H VAL* 4.6 0.7 - - - +
145H VAL* 1.3 74.3 - - - +
147H LEU* 1.3 68.9 + - - +
148H ALA 4.2 0.4 - - - -
158H LEU* 4.1 7.6 - - + +
160H TRP* 3.5 19.3 - - + -
191H LEU 3.7 0.7 - - - +
192H SER* 3.2 6.4 - - - -
193H SER* 2.7 39.5 + - - +
211H CYS* 2.0 51.8 - - + -
213H VAL* 5.0 0.4 - - - -
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Residues in contact with LEU 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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131G VAL* 3.6 24.0 - - + -
172G VAL* 4.3 8.3 - - + -
174G TRP* 3.8 36.1 - - + +
125H GLU 3.2 2.1 - - - +
126H VAL* 3.2 5.4 - - - -
127H ALA* 2.9 41.5 + - + +
129H PHE* 3.9 15.3 - - + -
145H VAL* 3.7 20.2 + - + -
146H CYS* 1.3 87.7 - - - +
148H ALA* 1.3 59.7 + - - +
149H THR* 4.0 12.6 + - + +
191H LEU 3.5 3.1 - - - +
192H SER* 3.8 15.9 - - - -
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Residues in contact with ALA 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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124H PRO* 3.9 18.6 - - + -
125H GLU 3.2 5.2 - - - +
126H VAL* 4.5 0.7 - - + +
146H CYS* 4.2 0.8 - - - -
147H LEU* 1.3 71.4 - - - +
149H THR* 1.3 62.4 + - - +
151H PHE* 3.5 12.9 - - + -
158H LEU* 4.8 3.3 - - + +
190H ALA* 3.2 3.1 - - - -
191H LEU* 2.8 45.5 + - + +
213H VAL* 4.0 26.7 - - + -
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Residues in contact with THR 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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174G TRP* 4.3 19.3 - - + +
123H PRO 4.1 0.2 - - - +
124H PRO* 3.3 1.4 - - - +
125H GLU* 2.9 49.3 + - - +
147H LEU* 4.5 13.6 + - + -
148H ALA* 1.3 82.7 - - - +
150H GLY* 1.3 66.6 + - - +
151H PHE* 3.2 4.6 + - - -
180H GLU* 3.3 14.8 - - - +
189H TYR 3.7 2.0 - - - -
190H ALA* 4.0 10.5 - - + -
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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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122H PHE* 3.3 22.7 - - - +
123H PRO 3.8 3.8 - - - +
149H THR* 1.3 72.0 - - - +
151H PHE* 1.3 60.0 + - - +
180H GLU* 3.0 29.0 + - - -
188H ARG* 3.6 17.3 + - - -
189H TYR 3.1 2.9 + - - -
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Residues in contact with PHE 151 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122H PHE 3.1 12.1 - - - +
123H PRO 3.9 0.7 - - - -
124H PRO* 3.6 35.2 - - + -
148H ALA* 3.5 24.2 - - + -
149H THR 3.2 0.8 - - - -
150H GLY* 1.3 79.0 - - - +
152H TYR* 1.3 64.2 + - - +
153H PRO 3.4 13.5 - - - -
154H ASP* 3.9 14.4 - - - -
156H VAL* 3.7 37.2 - - + -
177H PRO* 3.9 13.0 - - + -
188H ARG* 3.4 1.0 - - - -
189H TYR* 2.8 68.3 + - + -
190H ALA* 4.0 1.6 - - - -
191H LEU* 4.0 9.0 - - + -
215H PHE* 4.4 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