Contacts of the helix formed by residues 156 - 170 (chain A) in PDB entry 2FV7
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 THR 156 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A ASN 4.2 2.2 + - - -
129A LEU* 2.8 39.0 + - - +
131A LEU 4.8 0.6 + - - -
155A ILE* 1.3 76.1 - - - +
157A PRO* 1.4 67.2 - - + +
158A ALA* 3.8 20.9 - - + +
159A THR* 2.8 36.3 + - - +
160A SER 3.2 8.0 + - - -
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Residues in contact with PRO 157 (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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129A LEU* 6.0 0.7 - - + -
153A LEU* 4.2 20.9 - - + +
155A ILE 3.1 9.3 - - - +
156A THR* 1.4 86.7 - - + +
158A ALA* 1.3 57.7 + - - +
160A SER* 3.2 4.1 + - - -
161A LEU* 2.9 24.9 + - - +
182A ILE* 4.4 17.5 - - + -
185A LEU* 6.3 0.2 - - + -
189A PHE* 3.3 29.4 - - + -
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Residues in contact with ALA 158 (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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133A THR* 5.0 3.8 - - + +
156A THR* 3.2 14.5 - - + +
157A PRO* 1.3 77.2 - - - +
159A THR* 1.3 57.3 + - - +
161A LEU* 3.4 4.9 + - - +
162A GLU* 3.0 29.6 + - - +
260B LYS* 3.8 26.1 + - - +
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Residues in contact with THR 159 (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 LEU* 2.8 43.5 + - + +
132A ASN* 4.2 7.0 - - - +
133A THR* 4.8 5.4 + - - +
136A LEU* 3.3 23.3 - - + +
155A ILE* 3.6 19.7 - - + -
156A THR* 2.8 22.7 + - - +
158A ALA* 1.3 75.8 - - - +
160A SER* 1.3 58.9 + - - -
162A GLU* 3.4 4.6 + - - +
163A ALA* 3.0 25.5 + - - +
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Residues in contact with SER 160 (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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151A CYS* 3.9 14.6 - - - -
152A GLN 3.1 16.1 + - - -
153A LEU* 4.9 0.8 - - - +
155A ILE* 3.3 13.3 - - - +
156A THR 3.2 4.5 + - - -
157A PRO* 3.2 11.3 + - - +
159A THR* 1.3 76.5 - - - +
161A LEU* 1.3 58.3 + - - +
163A ALA* 3.4 2.7 + - - +
164A LEU* 3.0 34.4 + - - +
176A PHE* 5.0 1.3 - - - -
189A PHE* 4.2 11.0 - - - -
501A UNX 2.8 25.7 - - - -
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Residues in contact with LEU 161 (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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157A PRO 2.9 17.0 + - - +
158A ALA* 3.7 5.8 - - - +
160A SER* 1.3 77.9 - - - +
162A GLU* 1.3 57.5 + - - +
164A LEU* 3.5 6.3 + - + +
165A THR* 2.8 32.2 + - - +
186A ASP* 3.4 24.5 - - - +
188A GLN* 3.6 28.3 - - + +
189A PHE* 3.8 49.9 - - + +
192A LEU* 4.0 9.4 - - + -
260B LYS* 3.9 24.7 - - + +
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Residues in contact with GLU 162 (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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133A THR* 3.7 27.6 - - + -
136A LEU* 3.8 5.4 - - + -
158A ALA 3.0 18.5 + - - +
159A THR 3.9 4.5 - - - +
160A SER 3.3 0.2 - - - -
161A LEU* 1.3 73.5 - - - +
163A ALA* 1.3 61.0 + - - +
165A THR* 3.3 16.2 + - - +
166A MET* 3.0 62.3 + - + +
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Residues in contact with ALA 163 (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 17.0 - - + -
136A LEU* 3.5 15.1 - - + +
143A ILE* 4.6 5.7 - - + +
149A MET* 3.8 10.4 - - - +
151A CYS* 3.9 17.3 - - - -
159A THR 3.0 18.3 + - - +
160A SER 3.6 5.2 - - - +
162A GLU* 1.3 74.1 - - - +
164A LEU* 1.3 64.1 + - - +
166A MET* 3.2 7.4 + - - +
167A ALA* 3.0 23.7 + - - +
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Residues in contact with LEU 164 (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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149A MET* 3.5 23.5 - - + +
151A CYS* 4.4 7.0 - - + -
160A SER 3.0 21.4 + - - +
161A LEU* 3.6 9.0 - - + +
163A ALA* 1.3 75.6 - - - +
165A THR* 1.3 57.1 + - - +
168A ARG* 3.0 32.2 + - - +
174A THR* 3.7 25.4 - - - +
175A LEU 5.1 0.4 - - - +
176A PHE* 4.3 29.4 - - + -
189A PHE* 3.9 32.1 - - + +
192A LEU* 4.2 21.6 - - + +
193A SER* 4.5 6.5 - - - +
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Residues in contact with THR 165 (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 LEU* 2.8 23.0 + - - +
162A GLU* 3.5 22.2 + - - +
163A ALA 3.2 0.2 - - - -
164A LEU* 1.3 74.7 - - - +
166A MET* 1.3 59.5 + - + +
168A ARG* 3.9 3.9 - - - +
169A ARG* 3.1 34.3 + - - +
188A GLN* 4.6 2.4 + - - -
192A LEU* 3.3 20.5 - - - +
261B ALA 4.8 3.4 - - - +
262B VAL* 3.9 36.7 - - + +
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Residues in contact with MET 166 (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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133A THR* 4.6 3.8 - - - +
136A LEU* 3.7 36.3 - - + +
137A ARG* 4.1 13.9 - - + +
140A ALA* 5.0 10.3 - - + -
143A ILE* 4.2 22.0 - - + -
162A GLU* 3.0 50.8 + - + +
163A ALA 3.6 6.3 - - - +
165A THR* 1.3 73.9 - - + +
167A ALA* 1.3 64.7 + - - +
169A ARG* 3.5 8.6 + - - +
170A SER* 3.1 28.3 + - - -
115B ASN 6.1 0.9 - - - +
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Residues in contact with ALA 167 (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 ILE* 4.0 8.0 - - + +
149A MET* 3.8 19.3 - - + -
163A ALA 3.0 12.9 + - - +
166A MET* 1.3 78.3 - - - +
168A ARG* 1.3 62.6 + - - +
170A SER* 3.0 8.2 + - - -
172A VAL* 2.8 46.1 + - + +
174A THR* 3.5 23.3 - - + -
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Residues in contact with ARG 168 (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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164A LEU 3.0 20.0 + - - +
165A THR 3.9 3.4 - - - +
166A MET 3.3 0.2 - - - -
167A ALA* 1.3 76.5 - - - +
169A ARG* 1.3 61.1 + - - +
171A GLY* 3.2 12.6 + - - -
172A VAL 4.3 6.0 + - - +
174A THR* 4.1 3.7 + - + +
191A THR 3.0 22.3 + - - -
192A LEU* 3.3 48.3 + - + +
193A SER 3.7 3.8 + - - +
194A ASP* 2.8 37.9 + - - +
230A GLN* 4.8 5.4 - - - +
262B VAL* 5.2 1.3 - - + -
304B ALA* 6.2 2.4 - - - +
305B ALA* 4.3 22.2 - - + +
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Residues in contact with ARG 169 (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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165A THR* 3.1 29.3 + - - +
166A MET* 3.7 8.3 - - - +
167A ALA 3.3 0.2 - - - -
168A ARG* 1.3 76.0 - - - +
170A SER* 1.3 60.2 + - - +
171A GLY 3.3 1.1 + - - -
31B LEU* 4.3 8.7 - - - +
48B PHE* 4.9 9.0 - - - -
113B VAL* 4.4 14.3 - - - +
114B ASN 5.0 1.8 + - - -
115B ASN 5.5 3.0 + - - -
117B GLY* 4.1 31.1 + - - +
262B VAL* 3.3 34.8 + - + +
263B ASP* 4.4 18.1 + - + +
265B THR* 5.7 0.4 + - - -
305B ALA* 4.5 12.3 - - + -
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Residues in contact with SER 170 (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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144A SER* 3.4 40.9 - - - +
166A MET 3.1 14.9 + - - -
167A ALA 3.0 6.1 + - - -
169A ARG* 1.3 78.0 + - - +
171A GLY* 1.3 62.0 + - - +
172A VAL* 3.3 7.2 + - - +
507A UNX 4.5 1.3 - - - -
31B LEU* 3.8 20.0 - - - +
45B HIS* 4.9 1.0 + - - -
46B LYS* 3.6 19.3 - - - +
115B ASN* 5.5 0.5 + - - -
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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