Contacts of the strand formed by residues 178 - 187 (chain H) in PDB entry 3KTM
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 178 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51G LYS* 6.1 3.0 - - - +
66H LYS* 6.5 0.2 - - + -
144H CYS* 3.0 45.8 + - - +
145H GLU* 3.2 16.4 - - - +
146H THR* 4.0 17.7 - - + +
173H PRO* 3.5 2.3 - - - +
174H CYS* 2.8 24.8 + - - -
175H GLY* 3.2 17.7 + - - +
176H ILE 3.5 13.0 - - - +
177H ASP* 1.3 86.4 - - - +
179H PHE* 1.3 66.5 + - - +
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Residues in contact with PHE 179 (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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84H ASN* 4.9 4.7 - - - -
85H VAL 4.1 2.2 - - - -
86H VAL* 3.9 15.9 - - + -
118H LEU* 5.0 2.2 - - + -
122H PHE* 4.3 13.7 - + - -
144H CYS* 3.8 0.2 - - - -
145H GLU 2.8 29.1 + - - -
147H HIS* 4.6 5.8 - - + -
150H TRP* 2.7 30.5 + + + +
170H MET* 3.4 45.8 - - + -
171H LEU 3.2 13.7 - - - +
172H LEU 3.6 2.9 - - - -
173H PRO* 3.8 25.6 - - + -
174H CYS* 3.7 5.4 - - - -
177H ASP* 3.2 44.0 - - - -
178H LYS* 1.3 78.4 - - - +
180H ARG* 1.3 56.9 + - - +
181H GLY 4.2 4.5 - - - +
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Residues in contact with ARG 180 (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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52G TRP* 6.0 3.0 - - - -
92G VAL* 5.8 2.0 - - - +
93G THR* 3.0 44.8 + - - +
94G ILE* 5.7 0.2 - - - +
95G GLN* 4.6 12.8 - - - +
139H GLU* 3.5 3.0 - - - +
140H ARG 2.9 30.7 + - - +
141H MET* 3.6 21.5 + - - +
142H ASP 5.4 0.2 - - - -
143H VAL 2.9 25.0 + - - +
144H CYS* 3.2 11.5 - - - +
150H TRP* 3.3 10.8 - - - -
171H LEU 4.1 0.4 - - - -
172H LEU* 2.9 37.6 + - + +
173H PRO 5.2 0.6 + - - +
174H CYS* 3.1 28.5 - - + +
179H PHE* 1.3 71.2 - - - +
181H GLY* 1.3 56.3 + - - +
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Residues in contact with GLY 181 (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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138H GLN 3.1 13.5 - - - -
139H GLU* 3.9 2.9 - - - -
150H TRP* 3.4 26.2 - - - -
170H MET* 4.0 3.1 - - - -
171H LEU* 3.2 30.8 + - - +
179H PHE* 3.5 0.7 - - - +
180H ARG* 1.3 81.0 - - - +
182H VAL* 1.3 63.7 + - - +
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Residues in contact with VAL 182 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137H HIS* 3.1 3.1 - - - +
138H GLN* 2.7 49.3 + - + +
150H TRP* 3.7 45.8 - - + +
153H VAL* 4.6 5.6 - - + -
154H ALA* 4.1 7.9 - - + -
168H TYR* 4.2 12.6 - - + -
169H GLY 3.5 13.9 - - - +
170H MET* 4.4 1.1 - - + -
171H LEU* 3.8 7.4 - - - +
181H GLY* 1.3 74.3 - - - +
183H GLU* 1.3 71.1 + - - +
184H PHE* 4.0 21.7 - - + -
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Residues in contact with GLU 183 (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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198G ALA* 3.4 5.0 - - - -
199G ALA* 3.2 25.1 + - + -
124H SER* 4.0 2.2 - - - -
125H ASP* 2.6 43.2 + - - +
127H LEU* 3.8 14.1 - - + +
135H PHE* 3.6 14.2 - - + -
136H LEU 3.3 5.4 - - - +
137H HIS* 3.9 6.1 - - + +
168H TYR* 3.1 4.0 - - - +
169H GLY* 2.9 45.5 + - - +
171H LEU* 3.7 20.6 - - + +
182H VAL* 1.3 74.3 - - - +
184H PHE* 1.3 62.3 + - - +
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Residues in contact with PHE 184 (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 LEU* 3.9 4.6 - - - +
135H PHE* 3.6 4.2 - - - -
136H LEU* 2.6 84.5 + - + +
137H HIS* 4.1 6.3 - - - -
138H GLN* 4.4 6.3 - - + -
153H VAL 5.4 0.2 - - - -
154H ALA* 3.8 16.4 - - + -
157H THR* 3.6 33.2 - - + -
158H CYS* 3.8 6.7 - - - -
165H LEU* 3.5 13.2 - - + -
167H ASP 3.3 13.7 - - - +
168H TYR* 3.6 4.7 - - + -
182H VAL* 4.0 22.9 - - + -
183H GLU* 1.3 79.5 - - - +
185H VAL* 1.3 63.5 + - - +
186H CYS* 3.7 21.3 - - - -
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Residues in contact with VAL 185 (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 LEU* 4.1 12.1 - - + -
128H LEU 3.8 23.8 - - - +
129H VAL* 3.9 13.2 - - + -
130H PRO* 4.3 4.5 - - + -
133H CYS* 3.6 24.0 - - + -
134H LYS 3.2 13.5 - - - +
135H PHE* 3.9 19.3 - - + -
158H CYS* 4.5 0.7 - - - -
165H LEU* 3.8 1.7 - - - -
166H HIS* 2.8 30.9 + - + +
167H ASP* 2.9 16.8 + - + +
184H PHE* 1.3 79.3 - - - +
186H CYS* 1.3 61.3 + - - +
187H CYS* 4.3 3.8 - - - -
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Residues in contact with CYS 186 (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 CYS* 2.9 21.8 - - - +
134H LYS* 3.0 26.2 + - + +
136H LEU* 3.5 29.2 - - + -
158H CYS* 2.0 50.0 - - - -
161H LYS* 4.4 1.3 - - - -
163H THR* 3.4 17.7 - - - +
164H ASN 3.2 5.2 - - - +
184H PHE* 3.7 7.4 - - - -
185H VAL* 1.3 74.5 - - - +
187H CYS* 1.3 60.0 + - - +
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Residues in contact with CYS 187 (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* 3.9 4.5 - - - -
133H CYS* 2.1 43.5 - - - +
163H THR* 3.2 10.6 - - - -
164H ASN* 2.7 44.7 + - + +
166H HIS* 3.6 33.9 - - + +
185H VAL* 4.3 0.4 - - - -
186H CYS* 1.3 74.0 - - - +
188H PRO* 1.3 73.2 - - + +
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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