Contacts of the helix formed by residues 174 - 187 (chain A) in PDB entry 1H3F
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 LEU 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A VAL* 4.3 12.3 - - + -
144A THR* 3.7 27.8 - - + -
170A LEU* 4.3 4.0 - - + +
171A HIS* 3.0 13.8 + - - +
173A LEU* 1.3 80.7 - - + +
175A TYR* 1.3 67.2 + - + +
176A PRO 3.3 1.1 - - - -
177A PHE* 3.0 19.9 + - + +
178A ALA* 3.3 9.5 + - - +
137B PHE* 4.4 15.2 - - + -
140B VAL* 4.1 20.6 - - + -
141B VAL* 4.3 17.3 - - + -
144B THR* 3.4 27.6 - - + +
170B LEU* 5.6 2.2 - - + -
174B LEU* 4.3 13.0 - - + -
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Residues in contact with TYR 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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79A PHE* 5.3 18.3 + + - -
155A ARG* 6.0 0.4 - - - +
171A HIS* 3.6 37.2 + + - -
172A GLU* 3.4 12.5 + - + +
174A LEU* 1.3 80.0 - - + +
176A PRO* 1.3 68.4 - - + +
178A ALA* 3.0 22.9 + - + +
179A GLN* 3.0 14.4 + - - +
200A ASN* 5.8 1.3 - - - +
137B PHE* 5.5 1.3 - + - -
141B VAL* 3.8 31.8 - - + +
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Residues in contact with PRO 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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152A MET* 4.3 14.8 - - + -
155A ARG* 3.4 27.8 - - - +
158A PHE* 5.1 0.9 - - + -
172A GLU 3.4 14.8 - - - +
173A LEU* 3.5 9.4 - - - +
174A LEU 3.4 4.9 - - - -
175A TYR* 1.3 91.0 - - + +
177A PHE* 1.3 57.2 + - + +
179A GLN* 3.6 3.5 + - + +
180A ALA* 2.9 27.7 + - - +
199A PHE* 4.3 12.8 - - + -
200A ASN* 3.4 22.5 - - - +
203A VAL* 3.9 15.8 - - + +
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Residues in contact with PHE 177 (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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143A LEU* 3.3 52.8 - - + +
144A THR* 4.0 17.9 - - + -
146A LEU* 4.8 2.5 - - + -
147A MET* 3.5 34.1 - - + -
152A MET* 4.0 9.6 - - + -
173A LEU 3.3 27.8 - - - -
174A LEU* 3.0 10.0 + - + +
176A PRO* 1.3 78.2 - - + +
178A ALA* 1.3 60.1 + - - +
180A ALA* 3.7 4.0 - - - +
181A TYR* 2.9 28.4 + - - +
203A VAL* 4.1 15.9 - - + -
207A VAL* 4.4 7.4 - - + -
137B PHE* 5.7 2.0 - - + -
170B LEU* 3.4 24.5 - - + -
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Residues in contact with ALA 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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79A PHE* 5.3 2.2 - - + -
132A LEU* 4.2 20.6 - - + +
135A LEU* 5.8 1.3 - - - -
174A LEU 3.3 3.0 + - - +
175A TYR* 3.0 20.2 + - + +
177A PHE* 1.3 77.9 - - - +
179A GLN* 1.3 64.0 + - - +
181A TYR* 3.2 4.0 + - - +
182A ASP* 3.1 29.1 + - - +
137B PHE* 3.8 30.4 - - + -
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Residues in contact with GLN 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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41A LYS* 2.7 32.2 + - - +
175A TYR 3.0 14.3 + - - +
176A PRO* 3.8 5.6 - - + +
178A ALA* 1.3 77.9 - - - +
180A ALA* 1.3 59.3 + - - +
182A ASP* 3.2 15.2 + - - +
191A GLU* 3.0 21.2 + - - +
197A GLN* 3.2 13.9 - - - +
200A ASN* 2.8 25.3 + - + +
201A LEU* 3.6 13.7 - - - +
1433A TYE 2.4 58.9 + - + +
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Residues in contact with ALA 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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41A LYS* 4.8 0.2 - - - +
176A PRO 2.9 19.0 + - - +
177A PHE* 3.7 3.4 - - - +
178A ALA 3.2 0.2 - - - -
179A GLN* 1.3 73.5 - - - +
181A TYR* 1.3 67.3 + - - +
183A SER* 3.0 20.4 + - - -
184A VAL* 3.4 8.3 + - - +
191A GLU* 5.9 0.2 - - - -
200A ASN 5.2 0.7 - - - -
203A VAL* 3.7 5.2 - - + +
204A GLY* 3.6 26.9 - - - +
207A VAL* 3.5 31.8 - - + +
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Residues in contact with TYR 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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131A TRP* 3.6 38.8 - + + +
132A LEU* 4.0 9.4 - - + -
135A LEU* 4.0 26.7 - - + +
139A GLU* 4.6 5.6 + - - -
143A LEU* 4.5 13.9 - - + -
177A PHE 2.9 19.1 + - - +
178A ALA* 3.2 7.4 + - - +
180A ALA* 1.3 77.3 - - - +
182A ASP* 1.3 56.9 + - - +
184A VAL* 3.0 20.2 + - + +
185A ALA* 2.9 31.0 + - + -
207A VAL* 4.4 3.6 - - - +
211A TYR* 3.7 39.5 - + - -
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Residues in contact with ASP 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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41A LYS* 3.7 7.4 - - - +
75A ILE* 3.9 7.0 - - + +
128A ASN* 3.2 29.2 + - - +
131A TRP* 2.6 35.7 + - + +
132A LEU* 3.7 5.1 - - - +
178A ALA 3.1 20.1 + - - +
179A GLN* 3.2 10.4 - - - +
180A ALA 3.1 0.2 - - - -
181A TYR* 1.3 77.8 - - - +
183A SER* 1.3 61.1 + - - +
185A ALA* 3.2 3.3 + - - +
186A ILE* 3.1 27.4 + - - +
1433A TYE 2.4 28.0 + - - +
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Residues in contact with SER 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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41A LYS* 2.7 30.8 + - - +
180A ALA* 3.0 14.4 + - - -
182A ASP* 1.3 78.9 - - - +
184A VAL* 1.3 56.5 + - - +
186A ILE* 4.4 0.4 - - - -
187A ARG* 3.0 23.0 + - - -
188A ALA* 3.0 14.5 + - - -
191A GLU* 3.5 1.2 + - - -
204A GLY 4.8 1.3 - - - -
208A GLN* 3.5 15.9 - - - +
216A GLN* 2.5 35.9 + - - -
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Residues in contact with VAL 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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180A ALA 3.4 1.5 + - - +
181A TYR* 3.0 21.6 + - + +
183A SER* 1.3 76.2 - - - +
185A ALA* 1.3 67.1 + - - +
187A ARG* 3.3 7.8 + - - +
207A VAL* 3.7 29.6 - - + -
208A GLN* 4.0 22.2 - - + -
211A TYR* 3.9 33.0 - - + -
213A GLN* 3.1 36.3 + - - +
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Residues in contact with ALA 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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126A ARG* 5.2 5.5 + - - -
131A TRP* 3.5 45.8 - - + +
181A TYR* 2.9 17.5 + - + +
182A ASP 3.2 8.9 + - - +
184A VAL* 1.3 80.2 - - - +
186A ILE* 1.3 59.8 + - - +
187A ARG* 3.9 3.3 + - - +
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Residues in contact with ILE 186 (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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39A THR* 3.8 16.1 + - + +
41A LYS* 3.7 35.0 - - + -
73A VAL* 3.8 35.8 - - + +
75A ILE* 4.0 4.5 - - + -
126A ARG* 4.1 19.1 - - + +
131A TRP* 3.9 23.1 - - + -
182A ASP 3.1 17.2 + - - +
183A SER* 4.0 0.9 - - - +
185A ALA* 1.3 79.7 - - - +
187A ARG* 1.3 71.8 + - - +
188A ALA* 3.9 12.3 - - + +
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Residues in contact with ARG 187 (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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39A THR* 3.9 9.0 + - - -
183A SER 3.0 8.7 + - - -
184A VAL 3.3 4.3 + - - +
185A ALA 4.8 2.5 - - - +
186A ILE* 1.3 81.5 - - - +
188A ALA* 1.3 65.4 + - - +
189A ASP* 3.5 7.3 + - - +
208A GLN* 4.3 0.4 - - - -
213A GLN* 3.5 45.8 - - - +
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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