Contacts of the helix formed by residues 162 - 182 (chain A) in PDB entry 2IVF
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 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A PRO* 4.0 1.8 - - - -
161A VAL* 1.3 78.2 - - - +
163A TRP* 1.3 64.5 + - - +
164A ASP* 3.4 12.4 + - - +
165A GLU* 3.0 25.0 + - - +
166A ALA* 3.0 22.5 + - - +
683A GLU* 4.9 5.2 - - - -
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Residues in contact with TRP 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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146A PRO* 3.6 24.5 - - + +
162A SER* 1.3 73.2 - - - +
164A ASP* 1.3 58.6 + - - +
166A ALA* 4.4 1.8 - - - -
167A ALA* 2.8 40.2 + - + +
650A LEU* 3.6 45.5 - - + -
651A PRO* 3.3 30.7 - - + -
652A CYS* 5.5 0.4 - - - -
683A GLU* 2.7 36.7 + - + +
685A ARG* 3.3 47.9 - - + +
690A ALA* 3.7 31.0 - - + -
693A LEU* 4.0 16.4 - - + -
694A ILE* 5.9 0.2 - - + -
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Residues in contact with ASP 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A SER* 3.1 12.2 + - - +
163A TRP* 1.3 79.9 - - - +
165A GLU* 1.3 61.8 + - - +
168A GLY* 3.0 21.1 + - - -
693A LEU* 5.7 1.7 - - - +
697A LYS* 2.8 37.3 + - - +
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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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148A LYS* 3.1 27.6 + - + +
159A LYS* 4.9 4.6 + - - -
161A VAL* 3.7 27.6 - - + +
162A SER* 3.0 20.7 + - - +
164A ASP* 1.3 77.1 + - - +
166A ALA* 1.3 55.3 + - - +
168A GLY* 3.2 2.1 + - - -
169A ASP* 2.8 45.8 + - - +
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Residues in contact with ALA 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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146A PRO* 4.1 5.8 - - + -
161A VAL* 3.9 15.7 - - + -
162A SER 3.0 16.9 + - - +
163A TRP 4.0 2.0 - - - +
165A GLU* 1.3 74.6 - - - +
167A ALA* 1.3 65.9 + - - +
169A ASP* 3.3 3.6 + - - +
170A ILE* 3.1 30.3 + - - +
648A ILE* 3.8 19.1 - - + +
650A LEU* 3.6 24.0 - - + -
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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 TRP* 2.8 26.4 + - + +
164A ASP 4.4 0.4 - - - +
166A ALA* 1.3 73.6 - - - +
168A GLY* 1.3 57.7 + - - +
170A ILE* 3.4 11.4 + - - +
171A ALA* 2.9 30.1 + - - +
650A LEU* 4.7 2.1 - - + +
693A LEU* 4.1 18.4 - - + -
694A ILE* 4.3 16.7 - - + -
697A LYS* 3.9 21.6 - - + +
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Residues in contact with GLY 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 ASP 3.0 20.6 + - - -
165A GLU* 3.5 1.1 - - - -
166A ALA 3.2 0.2 - - - -
167A ALA* 1.3 73.8 - - - +
169A ASP* 1.3 61.2 + - - +
171A ALA* 3.3 4.5 + - - +
172A ASP* 2.9 36.2 + - - +
697A LYS* 4.3 12.2 - - - +
701A ARG* 4.4 10.5 - - - +
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Residues in contact with ASP 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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148A LYS* 2.5 41.0 + - - +
165A GLU* 2.8 27.2 + - - +
166A ALA 3.3 4.7 + - - +
168A GLY* 1.3 73.0 - - - +
170A ILE* 1.3 63.5 + - - +
172A ASP* 3.4 8.3 + - - +
173A SER* 3.0 23.4 + - - -
631A MET* 3.7 17.1 - - + +
648A ILE* 4.0 9.9 - - + +
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Residues in contact with ILE 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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166A ALA 3.1 18.1 + - - +
167A ALA* 3.6 7.4 - - - +
169A ASP* 1.3 78.3 - - - +
171A ALA* 1.3 62.2 + - - +
173A SER* 2.8 23.4 + - - +
174A ILE* 3.0 20.5 + - + +
631A MET* 4.4 7.9 - - - -
633A PHE* 3.6 64.8 - - + -
648A ILE* 3.9 12.3 - - + -
650A LEU* 3.6 23.3 - - + -
694A ILE* 4.0 14.4 - - + -
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Residues in contact with ALA 171 (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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167A ALA 2.9 17.9 + - - +
168A GLY 3.6 4.3 - - - +
170A ILE* 1.3 76.0 - - - +
172A ASP* 1.3 65.1 + - - +
174A ILE* 3.3 4.0 + - - +
175A ILE* 2.9 29.9 + - - +
694A ILE* 4.2 1.3 - - - +
697A LYS* 3.7 11.2 - - + +
698A VAL* 3.5 44.1 - - + +
701A ARG* 4.1 4.5 - - + -
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Residues in contact with ASP 172 (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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168A GLY 2.9 19.5 + - - +
169A ASP* 3.8 8.8 - - - +
171A ALA* 1.3 77.8 - - - +
173A SER* 1.3 57.6 + - - +
175A ILE* 4.3 0.4 - - - -
176A ASP* 2.8 39.9 + - - +
701A ARG* 3.2 42.9 + - - +
705A ARG* 3.0 27.3 + - - +
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Residues in contact with SER 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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169A ASP 3.0 14.1 + - - -
170A ILE 2.8 17.9 + - - -
172A ASP* 1.3 75.9 - - - +
174A ILE* 1.3 62.2 + - - +
176A ASP* 3.4 11.1 + - - +
177A SER* 3.1 19.1 + - - -
602A VAL* 3.4 19.4 - - - +
630A LYS* 5.2 8.3 - - - +
631A MET* 3.2 42.4 - - - +
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Residues in contact with ILE 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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170A ILE* 3.0 29.4 + - + +
171A ALA* 3.5 6.7 - - - +
173A SER* 1.3 78.6 + - - +
175A ILE* 1.3 60.2 + - - +
177A SER* 3.3 1.3 + - - -
178A PHE* 2.9 67.9 + - + -
186A PHE* 4.2 18.8 - - + -
206A MET* 5.8 0.9 - - - -
210A MET* 4.0 17.0 - - + -
602A VAL* 4.1 21.8 - - + -
633A PHE* 5.0 0.9 - - + -
694A ILE* 4.0 17.0 - - + -
698A VAL* 4.0 19.3 - - + -
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Residues in contact with ILE 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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171A ALA 2.9 21.0 + - - +
174A ILE* 1.3 74.1 - - - +
176A ASP* 1.3 66.0 + - - +
177A SER 3.2 0.2 + - - -
178A PHE* 3.3 0.9 + - - +
179A GLU* 2.9 23.4 + - + +
698A VAL* 3.6 15.3 - - + +
701A ARG* 3.8 14.1 - - + -
702A ALA* 3.4 32.5 - - - +
705A ARG* 3.5 23.6 - - - +
707A LEU* 3.4 32.3 - - + -
720A TYR* 4.0 28.7 - - + +
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Residues in contact with ASP 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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172A ASP* 2.8 32.4 + - - +
173A SER* 3.6 10.1 - - - +
174A ILE 3.3 0.2 - - - -
175A ILE* 1.3 71.8 - - - +
177A SER* 1.3 58.7 + - - +
179A GLU* 3.8 4.9 - - - +
180A ALA* 3.0 29.0 + - - +
601A GLN* 4.8 2.7 - - - +
630A LYS* 5.5 11.3 - - + -
705A ARG* 2.7 37.2 + - - +
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Residues in contact with SER 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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173A SER 3.1 14.5 + - - -
174A ILE 4.0 2.2 - - - -
175A ILE 3.2 0.2 - - - -
176A ASP* 1.3 76.4 - - - +
178A PHE* 1.3 64.9 + - - +
180A ALA* 3.3 1.4 + - - -
181A GLN* 2.9 54.4 + - - +
182A GLY 4.1 0.4 + - - -
185A GLY* 3.4 15.9 - - - -
601A GLN* 3.5 30.4 - - - +
602A VAL* 4.3 6.7 - - - -
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Residues in contact with PHE 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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174A ILE* 2.9 42.1 + - + +
177A SER* 1.3 81.3 - - - +
179A GLU* 1.3 59.8 + - - +
182A GLY* 2.9 36.7 + - - -
183A SER* 3.9 11.9 - - - -
186A PHE* 3.8 28.3 - - + -
210A MET* 3.9 31.9 - - + -
212A GLY* 5.6 0.2 - - - -
602A VAL* 6.5 0.4 - - + -
710A PHE* 3.4 55.5 - + + +
711A ASN 5.0 1.4 + - - -
720A TYR* 3.5 22.4 - + - +
723A LEU* 5.6 1.1 - - + -
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Residues in contact with GLU 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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175A ILE* 2.9 21.9 + - + +
176A ASP* 3.8 5.4 - - - +
178A PHE* 1.3 78.2 - - - +
180A ALA* 1.3 61.7 + - - +
182A GLY 5.0 0.2 + - - -
705A ARG* 5.4 2.2 - - - +
707A LEU* 3.6 40.1 - - + +
709A GLU 3.5 16.6 - - - +
710A PHE* 5.0 0.7 - - - +
720A TYR* 3.0 24.1 + - - +
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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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176A ASP 3.0 18.3 + - - +
177A SER* 3.3 7.2 + - - +
179A GLU* 1.3 78.8 - - - +
181A GLN* 1.3 61.6 + - + +
601A GLN* 4.5 9.2 - - - +
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Residues in contact with GLN 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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177A SER* 2.9 23.3 + - - +
179A GLU 3.4 0.6 - - - -
180A ALA* 1.3 83.0 - - + +
182A GLY* 1.3 66.9 + - - +
184A ASP 4.5 2.4 + - - -
185A GLY* 3.2 22.2 - - - +
598A LYS* 3.1 45.5 + - + +
599A THR* 2.5 50.5 + - - -
601A GLN* 3.5 11.4 - - - +
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Residues in contact with GLY 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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177A SER 3.6 10.2 - - - +
178A PHE* 2.9 27.5 + - - -
181A GLN* 1.3 81.3 - - - +
183A SER* 1.3 64.7 + - - -
184A ASP 3.2 1.8 + - - -
185A GLY 3.6 7.1 + - - -
711A ASN* 3.2 24.9 - - - +
712A ASP 5.2 1.3 - - - -
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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
------------------------------------------------------------
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