Contacts of the helix formed by residues 160 - 169 (chain A) in PDB entry 5IFM
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 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A TYR 4.0 0.8 + - - -
159A VAL* 1.3 73.3 - - - +
161A ASN* 1.3 63.7 + - - +
162A GLU* 3.6 4.2 + - - -
163A LEU* 3.1 21.0 + - - +
164A LEU* 3.0 24.3 + - - +
179A VAL* 3.5 6.5 - - - +
236B LEU 3.2 15.9 - - - -
238B GLU* 2.8 42.9 + - - +
241B VAL* 3.9 8.5 - - - -
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Residues in contact with ASN 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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160A SER* 1.3 71.1 - - - +
162A GLU* 1.3 66.9 + - + +
164A LEU* 3.6 1.5 + - - -
165A GLU* 3.1 27.6 + - - +
177A ALA* 3.6 25.4 - - - +
178A VAL* 3.6 3.8 - - - +
179A VAL* 2.8 29.8 + - - +
233B GLU 5.5 0.2 + - - -
234B GLU 2.8 28.9 + - - -
235B GLY* 3.9 0.2 - - - -
236B LEU 2.9 32.2 + - - +
237B PRO* 3.5 6.9 - - - +
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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
----------------------------------------------------------
160A SER* 3.2 4.1 + - - +
161A ASN* 1.3 79.1 + - + +
163A LEU* 1.4 59.3 + - - +
165A GLU* 3.3 11.0 + - - +
166A GLU* 3.0 44.0 + - - +
237B PRO* 3.4 16.3 - - - +
238B GLU* 2.9 42.3 + - + +
239B LYS* 4.9 2.4 + - - +
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Residues in contact with LEU 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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158A TYR 4.0 0.9 - - - +
159A VAL* 3.9 28.7 - - + -
160A SER* 3.1 24.2 + - - +
162A GLU* 1.4 74.6 - - - +
164A LEU* 1.4 56.0 + - - +
166A GLU* 3.3 19.3 + - - +
167A ALA* 2.9 28.6 + - - +
215A LEU* 3.9 19.5 - - + +
216A THR* 4.2 3.8 - - + -
238B GLU* 4.9 0.4 + - - +
251B ARG* 3.8 38.8 - - - +
255B PRO* 3.8 26.9 - - + -
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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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152A VAL* 4.6 3.1 - - + -
155A LEU* 4.0 13.7 - - + -
159A VAL* 4.3 5.3 - - + +
160A SER 3.0 15.8 + - - +
161A ASN 3.7 5.2 - - - +
163A LEU* 1.4 74.2 - - - +
165A GLU* 1.3 57.8 + - - +
167A ALA* 3.4 2.9 + - - -
168A PHE* 3.0 61.0 + - + +
177A ALA* 3.9 2.6 - - + +
178A VAL 3.4 34.3 - - - +
179A VAL* 4.1 8.1 - - + -
191A GLY* 4.4 5.6 - - - -
192A ILE 3.9 16.4 - - - +
193A VAL* 3.8 11.9 - - + -
215A LEU* 3.9 19.3 - - + -
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Residues in contact with GLU 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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68A LYS* 2.8 37.4 + - - -
161A ASN 3.1 17.8 + - - +
162A GLU* 3.5 10.5 - - - +
163A LEU 3.3 0.2 - - - -
164A LEU* 1.3 77.8 - - - +
166A GLU* 1.3 61.6 + - + +
168A PHE 3.5 0.2 + - - -
169A SER* 3.1 27.7 + - - -
174A VAL* 3.7 24.7 - - + +
176A ARG* 4.9 1.0 - - - -
177A ALA* 3.6 19.0 + - + +
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Residues in contact with GLU 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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162A GLU* 3.0 35.1 + - - +
163A LEU* 3.7 21.4 - - + +
165A GLU* 1.3 74.0 - - + +
167A ALA* 1.3 62.8 + - - +
169A SER* 2.7 23.5 + - - -
170A VAL* 4.1 3.1 + - - +
255B PRO* 5.2 4.1 - - + +
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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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163A LEU 2.9 17.8 + - - +
164A LEU* 3.6 6.7 - - - +
166A GLU* 1.3 78.9 - - - +
168A PHE* 1.4 62.6 + - + +
170A VAL* 3.4 13.2 - - - +
213A PHE* 3.3 20.0 - - + -
215A LEU* 3.6 31.2 - - + -
255B PRO* 3.6 23.3 - - + +
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Residues in contact with PHE 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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150A LEU* 5.1 0.9 - - + -
152A VAL* 3.9 15.5 - - + -
164A LEU* 3.0 41.0 + - + +
167A ALA* 1.4 74.4 - - + +
169A SER* 1.4 55.6 + - - +
170A VAL 3.0 5.4 - - - -
171A PHE* 3.0 45.7 + + - -
174A VAL* 3.7 6.5 - - + -
193A VAL* 3.6 35.0 - - + -
195A PHE* 3.3 24.2 - + + -
204A ALA* 4.2 7.6 - - + -
208A CYS* 4.2 2.7 - - - -
213A PHE* 3.9 21.8 - + - -
215A LEU* 4.4 6.3 - - + -
222A VAL* 4.2 4.5 - - + -
224A VAL* 3.8 32.8 - - + -
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Residues in contact with SER 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 GLU* 3.1 16.9 + - - -
166A GLU* 2.7 24.4 + - - -
168A PHE* 1.4 73.9 - - - +
170A VAL* 1.4 60.0 + - - +
171A PHE 3.2 0.2 - - - -
172A GLY* 3.0 26.3 + - - +
173A GLN* 5.8 0.4 - - - -
174A VAL* 3.5 9.6 - - - +
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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