Contacts of the helix formed by residues 155 - 172 (chain X) in PDB entry 5OOM
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 SER 155 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75X SER 3.0 17.7 + - - -
76X GLN* 4.4 4.3 - - - +
78X GLY 3.2 20.0 + - - -
79X LEU* 4.0 3.4 - - - +
80X TRP* 3.9 11.3 + - - +
150X LYS 5.1 0.2 + - - -
153X LEU* 3.4 14.2 + - - +
154X CYS* 1.3 80.9 + - - +
156X LYS* 1.3 64.2 + - - +
157X PHE 4.0 1.1 - - - -
158X GLY* 3.7 14.4 - - - -
159X MET* 3.2 26.2 + - - +
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Residues in contact with LYS 156 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495 VAL* 5.7 4.5 - - - -
695 TRP* 4.3 16.8 + - - +
705 LEU* 5.5 3.4 - - - +
1713A A 5.8 2.6 - - - +
76X GLN* 3.8 39.9 - - + +
155X SER* 1.3 72.7 - - - +
157X PHE* 1.3 57.8 + - - +
159X MET* 3.4 6.8 + - - +
160X ASP* 2.9 43.6 + - - +
205X GLY 5.4 5.4 - - - +
207X THR* 4.4 19.0 - - + +
210X GLU* 3.9 25.5 + - - -
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Residues in contact with PHE 157 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485 ARG* 3.5 51.1 - - + -
515 GLU* 4.5 1.3 - - - -
525 ILE* 3.9 22.7 - - + -
76X GLN 3.3 19.6 + - - +
77X ARG* 3.3 20.2 - - - +
78X GLY 4.3 3.1 - - - +
79X LEU* 3.5 22.7 - - + -
123X PHE* 4.2 13.9 - + - -
125X VAL* 3.8 25.4 - - + -
155X SER* 3.2 0.6 - - - -
156X LYS* 1.3 76.9 - - - +
158X GLY* 1.3 60.0 + - - +
160X ASP* 3.2 7.0 + - + +
161X LEU* 2.9 41.6 + - + +
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Residues in contact with GLY 158 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79X LEU* 3.8 19.8 - - - +
145X ILE* 3.7 8.9 - - - +
153X LEU* 3.6 24.1 - - - +
155X SER* 3.6 8.7 + - - -
156X LYS 3.4 0.4 - - - -
157X PHE* 1.3 78.5 - - - +
159X MET* 1.3 58.6 + - - +
161X LEU* 3.5 8.2 + - - +
162X LYS* 3.0 24.6 + - - +
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Residues in contact with MET 159 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149X PRO 5.2 0.2 - - - -
150X LYS* 3.2 57.7 - - + +
153X LEU* 4.2 11.4 - - + -
155X SER 3.2 18.7 + - - +
156X LYS* 3.7 7.0 - - - +
157X PHE 3.2 0.2 - - - -
158X GLY* 1.3 75.5 - - - +
160X ASP* 1.3 60.9 + - - +
162X LYS* 3.2 27.4 + - + +
163X ARG* 2.9 26.2 + - - +
204X VAL* 4.2 11.7 - - + +
205X GLY* 3.7 35.9 - - - +
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Residues in contact with ASP 160 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495 VAL* 3.3 23.5 - - + +
525 ILE* 4.0 19.3 - - + +
555 LEU* 3.5 10.0 - - + +
156X LYS* 2.9 37.2 + - - +
157X PHE* 3.2 8.6 + - + +
159X MET* 1.3 75.3 - - - +
161X LEU* 1.3 59.8 + - - +
163X ARG* 2.7 41.1 + - - +
164X GLY* 2.9 23.4 + - - -
205X GLY 4.6 5.2 - - - +
210X GLU* 5.4 1.0 - - - +
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Residues in contact with LEU 161 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525 ILE* 3.8 9.6 - - + -
79X LEU* 4.2 11.7 - - + -
119X LEU* 3.7 15.1 - - + +
123X PHE* 3.7 37.9 - - + -
125X VAL* 5.6 2.2 - - + -
141X LEU* 5.0 6.5 - - + -
145X ILE* 3.7 30.3 - - + -
157X PHE* 2.9 41.8 + - + +
158X GLY* 3.6 7.6 - - - +
160X ASP* 1.3 75.7 - - - +
162X LYS* 1.3 57.6 + - - +
164X GLY* 3.3 0.7 + - - +
165X MET* 2.9 38.9 + - + +
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Residues in contact with LYS 162 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145X ILE* 3.5 32.5 - - + +
146X LEU* 4.3 16.6 + - + +
147X LYS 5.5 0.2 + - - -
148X THR* 3.2 21.6 + - - +
149X PRO* 4.5 1.4 - - - +
150X LYS* 4.3 12.7 - - - +
153X LEU* 6.2 0.9 - - + -
158X GLY 3.0 14.3 + - - +
159X MET* 3.2 32.4 + - + +
161X LEU* 1.3 78.3 - - - +
163X ARG* 1.3 57.6 + - - +
165X MET* 3.9 2.9 - - - +
166X LEU* 2.9 55.1 + - + +
204X VAL* 4.4 7.4 - - + +
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Residues in contact with ARG 163 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495 VAL* 4.4 7.3 - - - +
555 LEU* 3.4 32.7 - - + +
565 GLU 5.3 3.0 + - - -
575 PRO* 5.9 0.8 - - - +
585 ILE* 6.1 1.3 - - - +
159X MET 2.9 10.9 + - - +
160X ASP* 2.7 36.9 + - - +
161X LEU 3.4 0.2 - - - -
162X LYS* 1.3 74.5 - - - +
164X GLY* 1.3 60.8 + - - +
166X LEU* 4.2 4.2 - - - +
167X LEU* 2.9 36.1 + - + +
201X ALA 3.4 19.1 - - - +
202X GLU* 3.3 19.1 - - - +
204X VAL* 3.3 32.6 + - + +
205X GLY 4.1 5.5 + - - -
206X LEU* 3.3 28.3 - - - +
210X GLU* 4.8 9.3 + - - -
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Residues in contact with GLY 164 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525 ILE* 3.8 13.7 - - - -
545 GLY* 4.9 6.3 - - - -
555 LEU* 3.5 18.3 - - - +
119X LEU* 3.6 8.9 - - - +
160X ASP 2.9 12.8 + - - -
161X LEU 3.7 2.5 - - - -
162X LYS 3.3 0.2 - - - -
163X ARG* 1.3 75.5 - - - +
165X MET* 1.3 58.9 + - - +
167X LEU* 3.9 3.1 - - - +
168X ARG* 3.0 28.4 + - - +
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Residues in contact with MET 165 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116X SER* 3.7 19.7 - - - -
118X ILE* 4.0 22.4 - - + +
119X LEU* 4.1 17.3 - - + -
141X LEU* 4.1 13.7 - - + -
142X ASP* 3.3 42.4 - - - +
145X ILE* 4.1 23.6 - - + -
146X LEU* 4.1 13.2 - - + -
161X LEU* 2.9 24.4 + - + +
162X LYS 4.1 2.9 - - - +
164X GLY* 1.3 74.5 - - - +
166X LEU* 1.3 59.0 + - - +
168X ARG* 3.2 2.8 + - - +
169X LEU* 2.9 34.2 + - - +
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Residues in contact with LEU 166 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146X LEU* 3.7 19.3 - - + -
162X LYS* 2.9 44.1 + - + +
163X ARG* 4.2 3.1 - - - +
165X MET* 1.3 77.6 - - - +
167X LEU* 1.3 58.9 + - - +
169X LEU* 4.1 5.9 - - + +
170X ALA* 2.9 29.6 + - - +
194X PHE* 3.4 28.5 - - + +
196X ILE* 3.7 30.5 + - + +
201X ALA* 3.8 13.2 - - + +
204X VAL* 4.2 20.4 - - + -
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Residues in contact with LEU 167 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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545 GLY* 5.6 3.6 - - - +
555 LEU* 4.3 19.3 - - + -
163X ARG* 2.9 31.2 + - + +
164X GLY* 4.1 2.9 - - - +
166X LEU* 1.3 75.2 - - - +
168X ARG* 1.3 65.8 + - - +
169X LEU 3.3 0.2 - - - -
170X ALA* 4.2 1.1 - - + -
171X ARG* 3.2 56.5 + - - +
173X ASP* 4.0 1.0 - - - +
198X GLU* 4.1 17.7 - - + -
201X ALA* 3.5 35.0 - - + +
202X GLU* 4.0 20.0 - - + +
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Residues in contact with ARG 168 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535 PRO* 3.4 32.9 - - - +
545 GLY* 3.8 17.4 - - - +
118X ILE* 2.8 44.8 + - + +
119X LEU* 3.7 17.9 + - + +
164X GLY 3.0 16.9 + - - +
165X MET* 3.5 5.8 - - - +
167X LEU* 1.3 78.6 - - - +
169X LEU* 1.3 58.9 + - - +
172X GLN 3.4 15.2 + - - -
173X ASP* 3.5 33.5 + - - +
175X GLN* 4.4 9.7 + - - +
176X LEU* 3.6 22.4 + - - +
188X TYR* 3.3 28.6 + - + +
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Residues in contact with LEU 169 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118X ILE* 4.2 12.1 - - + -
146X LEU* 4.0 19.1 - - + -
165X MET 2.9 19.9 + - - +
166X LEU* 4.1 7.4 - - + +
168X ARG* 1.3 74.9 - - - +
170X ALA* 1.3 64.2 + - - +
171X ARG 3.2 1.2 + - - -
172X GLN* 3.3 25.5 + - - +
188X TYR* 3.6 36.3 - - + +
191X TYR* 3.7 41.5 - - + +
194X PHE* 4.3 18.2 - - + +
195X ALA* 5.5 7.7 - - - +
196X ILE 6.0 1.6 - - - +
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Residues in contact with ALA 170 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166X LEU 2.9 20.9 + - - +
167X LEU* 4.1 5.6 - - - +
168X ARG 3.4 0.4 - - - -
169X LEU* 1.3 77.5 - - - +
171X ARG* 1.3 60.3 + - - +
172X GLN* 5.3 1.2 - - - +
195X ALA* 6.3 0.2 - - - +
196X ILE 3.3 27.0 - - - +
198X GLU* 4.0 31.6 + - + +
201X ALA* 4.1 6.1 - - + -
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Residues in contact with ARG 171 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545 GLY* 4.0 18.4 + - - -
167X LEU* 3.2 51.0 + - - +
169X LEU 3.2 0.4 - - - -
170X ALA* 1.3 80.0 - - - +
172X GLN* 1.3 69.4 + - - +
173X ASP* 3.3 30.9 + - - +
174X PRO* 5.3 0.7 - - - +
198X GLU* 2.6 39.6 + - + +
202X GLU* 4.6 10.1 + - - +
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Residues in contact with GLN 172 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168X ARG 3.4 6.4 + - - -
169X LEU* 3.3 21.7 + - - +
170X ALA 3.6 1.7 - - - +
171X ARG* 1.3 78.6 - - - +
173X ASP* 1.3 64.3 + - - +
174X PRO* 3.4 6.8 - - - +
188X TYR* 3.1 49.1 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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