Contacts of the helix formed by residues 158 - 169 (chain A) in PDB entry 5FV7
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 GLU 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A ASP* 3.6 8.3 - - - +
89A PRO* 6.3 0.4 - - + -
90A PRO* 3.7 15.5 - - + +
93A LYS* 3.0 27.7 + - - -
155A ALA* 4.6 1.6 - - - -
157A SER* 1.3 78.9 - - - +
159A ALA* 1.3 66.7 + - - +
160A GLU* 3.1 34.0 - - - +
161A ALA* 2.9 26.7 + - + +
162A SER* 3.5 5.0 + - - -
185A PHE* 4.9 2.9 - - + -
233A ASP* 5.1 1.0 - - - +
234A TYR* 2.6 28.2 + - - +
287A GLU 4.8 2.2 + - - +
1339A MG 3.9 4.7 - - - -
1340A MG 3.2 9.0 - - - -
1341A R3Z 3.3 6.3 + - - +
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Residues in contact with ALA 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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34A ASP* 3.4 15.3 - - - +
36A SER 5.4 0.4 - - - +
84A VAL* 3.3 40.8 - - + +
86A ASP* 2.6 30.6 + - - +
155A ALA* 4.0 5.4 - - - -
157A SER 3.7 2.2 + - - -
158A GLU* 1.3 69.8 - - - +
160A GLU* 1.3 52.6 + - - +
162A SER 3.2 2.8 + - - -
163A CYS* 2.7 37.4 + - - -
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Residues in contact with GLU 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASP* 3.9 14.3 + - - +
158A GLU* 3.1 19.5 - - - +
159A ALA* 1.3 71.0 - - - +
161A ALA* 1.3 59.3 + - - +
163A CYS* 3.8 9.9 - - - -
164A ALA* 3.2 20.3 + - - +
177A THR* 4.8 2.5 - - + -
179A ASP* 3.2 3.8 - - - +
181A ASP* 3.1 17.0 - - - +
182A CYS* 3.3 29.2 - - + +
185A PHE* 3.4 20.8 - - + -
1339A MG 2.2 27.1 - - - -
1340A MG 2.1 30.8 - - - -
1341A R3Z 2.9 3.9 + - - -
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Residues in contact with ALA 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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158A GLU* 2.9 14.6 + - + +
160A GLU* 1.3 79.6 - - - +
162A SER* 1.3 58.6 + - - +
164A ALA* 3.3 5.5 + - - +
165A ALA* 3.0 26.0 + - - +
185A PHE* 3.8 37.9 - - + +
286A PRO* 4.0 17.4 - - + +
287A GLU 4.7 4.7 - - - +
288A VAL* 4.2 9.8 - - + +
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Residues in contact with SER 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A VAL* 4.0 7.2 - - - -
155A ALA* 3.3 29.4 - - - +
156A PRO* 3.8 3.6 - - - +
157A SER 5.2 0.3 + - - -
158A GLU 3.5 3.0 + - - -
159A ALA 3.2 7.1 + - - -
161A ALA* 1.3 74.5 - - - +
163A CYS* 1.3 66.9 + - - +
165A ALA* 3.3 10.4 + - - +
166A LEU* 3.2 25.9 + - - +
287A GLU 4.5 1.9 + - - -
288A VAL* 4.0 7.7 - - - +
289A LEU* 3.8 31.3 + - - +
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Residues in contact with CYS 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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32A ALA* 3.9 25.8 - - + +
33A ILE 4.1 0.2 - - - -
34A ASP* 3.9 22.7 - - - -
84A VAL* 3.9 23.1 - - - +
159A ALA 2.7 27.3 + - - +
160A GLU* 3.8 10.5 - - - +
162A SER* 1.3 70.5 - - - +
164A ALA* 1.3 63.7 - - - +
166A LEU* 2.9 19.3 + - - +
167A VAL* 3.3 16.0 + - - +
175A ALA* 3.7 15.9 - - + -
177A THR* 6.3 0.2 - - + -
182A CYS* 4.6 0.9 - - - -
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Residues in contact with ALA 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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160A GLU 3.2 12.7 + - - +
161A ALA 3.4 9.6 - - - +
163A CYS* 1.3 77.7 - - - +
165A ALA* 1.3 51.4 + - - +
167A VAL* 3.0 5.4 + - - +
168A LYS* 2.8 38.3 + - - +
182A CYS* 3.9 6.2 - - - +
185A PHE* 4.0 13.7 - - + +
186A GLY 4.5 0.2 - - - -
187A SER* 3.3 42.1 - - - +
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Residues in contact with ALA 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 ALA 3.0 13.8 + - - +
162A SER* 3.4 14.8 - - - +
163A CYS 3.1 0.4 + - - -
164A ALA* 1.3 75.4 - - - +
166A LEU* 1.3 58.1 + - - +
168A LYS* 3.6 13.9 - - + +
169A ALA* 2.9 32.2 + - - +
288A VAL* 4.3 22.4 - - + -
289A LEU* 4.6 2.2 - - + +
291A PRO* 3.7 15.6 - - + +
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Residues in contact with LEU 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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32A ALA* 3.8 22.0 - - + -
82A VAL* 5.1 2.9 - - + -
84A VAL* 3.9 9.0 - - + -
153A LEU* 3.8 31.4 - - + -
162A SER 3.2 16.4 + - - +
163A CYS* 2.9 6.5 + - - +
165A ALA* 1.3 75.6 - - - +
167A VAL* 1.3 55.5 + - - +
169A ALA 3.8 0.2 - - - -
170A GLY 3.1 4.7 + - - -
171A LYS* 2.8 44.3 + - + +
172A VAL* 3.5 18.6 + - + +
289A LEU* 4.6 4.9 - - + -
291A PRO* 4.0 24.0 - - + -
294A VAL* 4.4 11.2 - - + -
296A LEU* 4.6 9.0 - - + -
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Residues in contact with VAL 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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163A CYS 3.3 15.0 - - - +
164A ALA 3.0 5.3 + - - +
166A LEU* 1.3 75.5 - - - +
168A LYS* 1.3 65.0 + - - +
170A GLY* 3.1 12.0 + - - -
172A VAL* 3.7 11.7 - - + +
173A TYR 3.6 24.0 - - - +
174A ALA* 3.7 7.0 - - - -
175A ALA* 3.7 22.9 - - + +
187A SER* 3.4 17.0 - - - +
188A PRO* 3.6 24.6 - - + +
189A VAL* 3.9 13.2 - - + +
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Residues in contact with LYS 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 ALA* 2.8 16.0 + - - +
165A ALA* 3.6 15.4 - - + +
167A VAL* 1.3 73.6 - - - +
169A ALA* 1.3 58.7 - - - +
170A GLY* 2.9 9.5 + - - -
185A PHE 2.8 24.4 + - - -
186A GLY* 3.4 32.1 - - - +
188A PRO* 3.9 11.3 - - + +
283A PHE 5.9 0.2 + - - -
284A LEU 5.5 4.0 + - - -
286A PRO* 5.7 4.9 - - - +
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Residues in contact with ALA 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 ALA 2.9 20.3 + - - +
166A LEU 4.3 1.8 - - - +
168A LYS* 1.3 71.2 - - - +
170A GLY* 1.3 62.1 + - - +
171A LYS* 3.4 14.3 + - - +
291A PRO* 3.8 22.7 - - + -
292A GLU* 3.5 23.0 - - - +
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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