Contacts of the strand formed by residues 140 - 150 (chain H) in PDB entry 5D7I
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 140 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161G MET* 3.9 18.4 - - + -
164G MET* 4.4 17.1 - - + -
166G PHE* 3.6 53.7 - - + -
134H GLU* 3.3 21.1 - - - +
135H ILE* 3.4 11.9 - - - -
138H THR* 3.0 24.5 + - - +
139H GLN* 1.3 84.6 - - - +
141H ALA* 1.3 61.0 + - - +
195H ARG* 3.6 19.3 - - - +
196H VAL 3.5 10.1 - - - +
197H SER* 4.4 1.8 - - - +
198H ALA* 3.9 1.6 - - - +
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Residues in contact with ALA 141 (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* 3.6 26.5 - - + -
134H GLU* 3.8 2.5 - - - -
135H ILE* 4.0 10.3 - - + -
140H LYS* 1.3 74.3 - - - +
142H THR* 1.3 62.9 + - - +
143H LEU* 3.9 1.6 + - - +
194H LEU 3.8 1.4 - - - +
195H ARG* 3.4 1.6 - - - -
196H VAL* 2.7 44.7 + - + +
197H SER 4.4 2.7 - - - +
198H ALA* 4.4 1.6 - - - -
201H TRP* 3.8 22.7 - - + -
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Residues in contact with THR 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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121G LEU* 3.2 19.8 - - - +
133G LEU* 3.7 28.2 - - + +
135G THR* 5.3 0.5 + - - -
159G LEU* 5.0 2.5 - - + -
130H PRO* 3.4 13.3 - - - +
134H GLU* 2.6 36.9 + - - +
141H ALA* 1.3 71.0 - - - +
143H LEU* 1.3 70.7 + - - +
144H VAL* 4.6 1.6 - - + -
193H ARG* 4.0 19.5 - - + -
194H LEU 3.6 5.2 - - - +
195H ARG* 3.1 24.6 + - + +
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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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127H VAL* 4.1 19.5 - - + -
128H PHE 3.5 7.0 - - - +
129H GLU* 5.3 0.4 - - - -
130H PRO* 3.7 23.6 - - + -
141H ALA 4.2 6.5 - - - +
142H THR* 1.3 73.2 - - - +
144H VAL* 1.3 62.4 + - - +
159H TRP* 4.0 15.5 - - + -
193H ARG* 3.2 7.6 - - - +
194H LEU* 2.8 47.5 + - + +
196H VAL* 4.6 5.6 - - + -
201H TRP* 4.0 20.2 - - + -
208H PHE* 3.8 45.5 - - + -
239H ALA* 4.7 2.5 - - + -
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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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121G LEU* 3.7 21.8 - - + -
131G VAL* 4.1 22.9 - - + -
133G LEU* 4.5 13.2 - - + -
172G VAL* 4.2 26.5 - - + -
127H VAL* 3.4 2.3 - - - +
128H PHE* 2.7 46.5 + - + -
142H THR* 4.6 4.7 - - + -
143H LEU* 1.3 79.0 - - - +
145H CYS* 1.3 72.4 + - - +
146H LEU* 4.4 8.1 - - + -
159H TRP* 4.1 2.9 - - - -
191H SER* 4.9 0.4 - - - -
192H SER 3.3 9.2 - - - +
193H ARG* 4.8 2.0 - - + -
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Residues in contact with CYS 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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125H VAL* 3.6 18.6 - - - -
126H ALA 3.4 5.4 - - - -
127H VAL* 4.5 0.4 - - + +
144H VAL* 1.3 78.8 - - - +
146H LEU* 1.3 65.2 + - - +
147H ALA 4.2 0.2 - - - -
157H LEU* 4.0 12.7 - - + +
159H TRP* 3.5 18.2 - - + -
191H SER* 3.3 5.2 - - - -
192H SER* 2.8 31.0 + - - +
210H CYS* 2.0 51.8 - - + -
212H VAL* 4.6 0.2 - - - -
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Residues in contact with LEU 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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131G VAL* 3.5 25.8 - - + -
172G VAL* 4.5 1.6 - - + -
174G TRP* 3.7 49.6 - - + +
124H GLU 3.5 1.6 - - - +
125H VAL* 3.3 4.5 - - - +
126H ALA* 2.9 33.4 + - + +
128H PHE* 3.8 23.3 - - + -
144H VAL* 4.1 6.9 + - + -
145H CYS* 1.3 76.7 - - - +
147H ALA* 1.3 58.8 + - - +
148H THR* 4.0 12.8 + - + +
190H LEU 3.5 2.2 - - - +
191H SER* 3.5 28.3 - - - -
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Residues in contact with ALA 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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123H PRO* 4.1 16.6 - - + -
124H GLU 3.2 4.9 - - - +
125H VAL* 4.4 0.9 - - + +
145H CYS* 4.2 0.6 - - - -
146H LEU* 1.3 73.4 - - - +
148H THR* 1.3 61.8 + - - +
150H PHE* 3.5 13.0 - - + -
157H LEU* 4.9 3.6 - - + +
189H ALA* 3.2 3.6 - - - -
190H LEU* 2.8 47.9 + - + +
212H VAL* 4.1 27.8 - - + -
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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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174G TRP* 4.5 13.9 - - + +
122H PRO 4.3 0.3 - - - +
123H PRO* 3.3 2.6 - - - +
124H GLU* 2.8 54.4 + - - +
146H LEU* 4.2 22.8 + - + -
147H ALA* 1.3 81.1 - - - +
149H GLY* 1.3 65.0 + - - +
150H PHE* 3.3 3.5 - - - -
179H GLU* 3.4 14.8 - - - +
188H TYR 3.6 2.0 - - - -
189H ALA* 4.1 7.9 - - + -
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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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121H PHE* 3.4 21.1 - - - +
122H PRO 3.9 4.1 - - - +
148H THR* 1.3 71.8 - - - +
150H PHE* 1.3 60.7 + - - +
179H GLU* 3.0 29.3 + - - -
187H ARG* 3.6 18.1 + - - -
188H TYR 3.0 3.0 + - - -
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Residues in contact with PHE 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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121H PHE 3.2 12.8 - - - +
122H PRO 4.1 0.7 - - - -
123H PRO* 3.5 34.8 - - + -
147H ALA* 3.5 27.8 - - + -
149H GLY* 1.3 79.8 - - - +
151H TYR* 1.3 63.5 + - - +
152H PRO 3.4 13.0 - - - -
153H ASP* 3.7 15.5 - - - -
155H VAL* 3.6 37.2 - - + -
176H PRO* 3.9 13.7 - - + -
187H ARG* 3.4 1.5 - - - -
188H TYR* 2.7 73.3 + - + -
190H LEU* 3.8 7.4 - - + -
214H PHE* 4.4 2.0 - + + -
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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