Contacts of the helix formed by residues 169 - 185 (chain A) in PDB entry 3C5C
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 PHE 169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A LYS* 3.4 36.6 - - + +
40A PHE* 3.3 35.2 - + - -
43A LYS* 3.6 49.6 - - + +
167A LEU 4.0 0.2 + - - -
168A ASP* 1.3 73.0 - - - +
170A GLU* 1.3 80.9 + - - +
171A HIS 3.3 0.7 - - - -
172A VAL* 3.1 3.9 + - + +
173A GLN* 2.9 66.2 + - + -
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Residues in contact with GLU 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ASP* 3.4 15.7 + - - +
169A PHE* 1.3 100.7 + - + +
171A HIS* 1.3 56.7 + - - +
173A GLN* 3.5 17.8 + - - +
174A HIS* 2.9 27.5 + - - +
69D HIS* 6.0 7.9 - - + +
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Residues in contact with HIS 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LEU* 5.5 3.9 - - + +
162A GLU 4.3 3.8 - - - -
163A VAL* 3.5 24.1 - - + +
164A SER 2.9 40.1 + - - -
167A LEU* 4.0 18.5 - - + +
168A ASP* 3.0 49.9 + - - +
170A GLU* 1.3 74.5 - - - +
172A VAL* 1.3 66.2 + - + +
174A HIS* 3.5 8.1 + - - +
175A VAL* 3.4 27.2 + - - +
67D PRO* 6.2 3.1 - - + -
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Residues in contact with VAL 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 3.8 28.5 - - + +
39A LYS* 4.1 14.1 - - + -
40A PHE* 4.0 12.3 - - + +
163A VAL* 5.1 1.3 - - + -
164A SER 3.3 26.5 - - - +
168A ASP 3.9 6.5 - - - +
169A PHE* 3.1 7.5 + - + +
171A HIS* 1.3 86.8 - - + +
173A GLN* 1.3 67.3 + - - +
175A VAL* 3.0 26.0 - - + +
176A PHE* 3.2 33.3 - - + -
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Residues in contact with GLN 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A PHE* 4.1 15.0 - - + -
61A GLU* 4.5 4.7 - - - +
169A PHE* 2.9 46.0 + - + +
170A GLU* 3.6 17.1 + - - +
172A VAL* 1.3 75.6 - - - +
174A HIS* 1.3 64.7 + - - +
176A PHE* 3.4 1.0 + - - +
177A HIS* 2.9 57.9 + - + +
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Residues in contact with HIS 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A PHE* 3.8 17.4 - + - -
170A GLU 2.9 17.4 + - - +
171A HIS* 3.6 9.4 - - - +
172A VAL 3.2 0.4 - - - -
173A GLN* 1.3 76.3 - - - +
175A VAL* 1.3 58.4 + - + +
177A HIS* 3.2 5.3 + - - +
178A GLU* 2.7 40.8 + - - +
181A ARG* 3.7 25.7 + - - -
62D THR* 3.9 9.1 + - + -
65D HIS 2.6 30.4 + - - -
67D PRO* 3.6 42.3 - - + +
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Residues in contact with VAL 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU* 6.1 0.9 - - + -
95A LEU* 4.9 2.7 - - + -
130A LEU* 3.3 15.9 - - + +
132A LEU* 4.2 26.0 - - + -
161A PHE* 3.7 28.7 - - + -
163A VAL* 3.6 23.3 - - + -
171A HIS 3.4 11.6 + - - +
172A VAL* 3.0 28.0 + - + +
174A HIS* 1.3 81.5 - - + +
176A PHE* 1.3 66.9 + - + +
178A GLU* 3.3 4.3 + - - -
179A ALA* 2.9 25.6 + - - +
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Residues in contact with PHE 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 3.8 20.6 - - + +
25A ILE* 4.3 2.7 - - + -
36A LEU* 3.9 23.1 - - + -
37A THR* 4.2 7.4 - - - -
40A PHE* 3.6 60.3 - + + -
70A LEU* 5.0 0.4 - - + -
72A VAL* 4.0 25.6 - - + -
95A LEU* 3.7 27.6 - - + -
132A LEU* 5.7 0.4 - - + -
172A VAL* 3.2 32.7 + - + -
173A GLN 3.8 1.6 - - - +
175A VAL* 1.3 86.3 - - + +
177A HIS* 1.3 64.2 + - - +
179A ALA* 3.3 9.2 + - - +
180A VAL* 3.1 23.8 + - - +
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Residues in contact with HIS 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PHE* 4.1 9.8 - + - -
61A GLU* 3.0 28.0 + - + +
62A THR 3.5 23.6 + - - -
63A VAL* 3.6 26.6 - - + +
70A LEU* 5.5 0.7 - - + -
173A GLN* 2.9 51.4 + - + +
174A HIS* 3.8 4.5 - - - +
176A PHE* 1.3 77.6 - - - +
178A GLU* 1.3 58.3 + - - +
180A VAL* 3.2 10.3 + - + +
181A ARG* 2.9 45.5 + - - +
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Residues in contact with GLU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A LEU* 4.3 4.5 - - + -
159A LEU* 4.0 19.1 - - + -
161A PHE* 4.1 4.9 - - + -
174A HIS* 2.7 27.5 + - - +
175A VAL* 3.6 7.2 - - - +
177A HIS* 1.3 71.5 - - - +
179A ALA* 1.3 53.7 + - - +
181A ARG* 2.8 31.3 + - - +
182A GLU* 2.8 33.6 + - - +
185A ARG* 2.7 19.0 + - - -
62D THR* 3.6 11.9 - - - +
65D HIS* 2.7 44.0 + - - +
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Residues in contact with ALA 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 3.7 21.5 - - + -
93A ALA* 3.7 8.1 - - + +
94A PHE 5.3 0.7 - - - +
95A LEU* 3.8 22.7 - - + -
130A LEU* 3.8 18.2 - - + +
175A VAL 2.9 13.8 + - - +
176A PHE 3.3 9.4 + - - +
178A GLU* 1.3 71.7 - - - +
180A VAL* 1.3 60.8 + - - +
182A GLU* 3.3 2.9 + - - +
183A ALA* 2.8 30.3 + - - +
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Residues in contact with VAL 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A VAL* 4.1 16.2 - - + +
23A LEU* 4.4 1.3 - - + -
61A GLU* 6.2 0.4 - - + -
63A VAL* 3.8 33.9 - - + -
68A VAL* 4.1 16.4 - - + -
70A LEU* 3.5 34.8 - - + -
176A PHE 3.1 14.7 + - - +
177A HIS* 3.2 10.0 + - + +
179A ALA* 1.3 76.5 - - - +
181A ARG* 1.3 63.6 + - - +
183A ALA* 3.1 9.6 + - - +
184A ARG* 2.9 24.8 + - + +
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Residues in contact with ARG 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A VAL* 3.9 10.9 - - + +
64A ASP* 3.1 43.2 + - - +
174A HIS* 3.7 13.9 + - - -
177A HIS* 2.9 33.4 + - - +
178A GLU* 2.8 52.5 + - - +
180A VAL* 1.3 74.5 - - - +
182A GLU* 1.3 57.6 + - - +
184A ARG* 3.1 8.3 + - - +
185A ARG* 3.0 56.0 + - + +
62D THR* 3.7 24.4 + - - -
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Residues in contact with GLU 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A PRO* 3.4 38.4 - - + +
129A ALA 5.3 1.7 - - - +
130A LEU* 4.3 7.6 - - + -
159A LEU* 3.8 31.5 - - + +
178A GLU 2.8 22.7 + - - +
179A ALA* 3.6 7.9 - - - +
180A VAL 3.2 0.2 - - - -
181A ARG* 1.3 73.2 - - - +
183A ALA* 1.3 61.1 + - - +
184A ARG 3.5 0.5 + - - -
185A ARG* 2.9 51.9 + - - +
65D HIS* 3.5 9.1 - - - -
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Residues in contact with ALA 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A VAL* 4.0 19.1 - - + -
92A HIS* 3.6 43.0 - - + +
93A ALA* 4.1 0.9 - - + -
128A PRO* 3.8 2.4 - - - +
179A ALA 2.8 20.3 + - - +
180A VAL 3.1 5.8 + - - +
182A GLU* 1.3 73.4 - - - +
184A ARG* 1.3 57.3 + - - +
185A ARG 4.5 2.8 - - - -
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Residues in contact with ARG 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A VAL* 6.1 0.2 - - - +
180A VAL* 2.9 15.9 + - + +
181A ARG* 3.6 10.3 - - - +
183A ALA* 1.3 74.3 - - - +
185A ARG* 1.3 65.2 + - + +
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Residues in contact with ARG 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A GLU* 2.7 29.1 + - - -
181A ARG* 3.0 38.8 + - - +
182A GLU* 2.9 45.9 + - - +
183A ALA 3.5 3.5 - - - -
184A ARG* 1.3 82.2 - - + +
65D HIS* 3.4 12.8 + - - -
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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