Contacts of the helix formed by residues 159 - 175 (chain A) in PDB entry 4I5L
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 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A GLU* 2.8 23.9 + - - -
158A VAL* 1.3 77.0 - - - +
160A SER* 1.3 59.9 - - - +
161A ALA* 3.7 8.1 + - - +
162A VAL* 3.1 21.0 + - - +
163A LYS* 2.8 26.8 + - - +
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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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158A VAL 4.0 0.2 + - - -
159A SER* 1.3 74.0 - - - +
161A ALA* 1.3 62.2 + - - +
163A LYS* 3.4 15.5 + - - +
164A ALA* 3.0 23.9 + - - +
167A ARG* 4.8 1.0 + - - -
197A GLU* 5.7 0.3 + - - -
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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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159A SER* 3.3 8.5 + - - +
160A SER* 1.3 77.8 - - - +
162A VAL* 1.3 64.0 + - + +
164A ALA* 3.3 7.9 + - - +
165A GLU* 3.3 31.1 + - - +
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Residues in contact with VAL 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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125A GLU* 3.8 24.9 - - + +
129A VAL* 4.0 33.0 - - + -
133A LYS* 5.7 0.7 - - - +
158A VAL* 3.7 23.8 - - + -
159A SER* 3.1 20.1 + - - +
161A ALA* 1.3 76.6 - - + +
163A LYS* 1.3 64.6 + - - +
165A GLU* 3.1 18.7 + - - +
166A LEU* 3.0 23.1 + - + +
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Residues in contact with LYS 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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155A TYR* 3.1 60.3 - - + +
156A PRO* 3.6 14.6 + - - +
158A VAL* 3.5 20.4 + - + +
159A SER 2.8 18.3 + - - +
160A SER* 3.5 17.8 + - - +
162A VAL* 1.3 73.8 - - - +
164A ALA* 1.3 56.1 + - - +
166A LEU* 3.4 1.8 + - - +
167A ARG* 3.0 39.9 + - - +
197A GLU* 3.1 28.3 + - - +
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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 SER 3.0 13.4 + - - +
161A ALA* 3.7 10.1 - - - +
162A VAL 3.2 0.4 - - - -
163A LYS* 1.3 73.4 - - - +
165A GLU* 1.3 66.1 + - + +
167A ARG* 3.4 28.0 + - - +
168A GLN* 3.1 21.7 + - - +
171A ARG* 4.8 2.3 + - - -
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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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129A VAL* 6.1 0.2 - - + -
133A LYS* 2.8 34.3 + - - -
161A ALA* 3.3 20.0 + - - +
162A VAL* 3.1 21.2 + - + +
164A ALA* 1.3 76.4 - - + +
166A LEU* 1.3 61.0 + - + +
168A GLN* 3.0 8.1 + - - +
169A TYR* 2.8 44.9 + - + -
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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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129A VAL* 4.2 12.3 - - + -
132A VAL* 4.1 23.1 - - + -
133A LYS* 6.0 2.0 - - + -
151A PHE* 3.2 35.9 - - + +
154A CYS* 4.0 22.7 - - - -
155A TYR* 4.0 31.9 - - + -
158A VAL* 4.1 13.2 - - + -
162A VAL* 3.0 23.5 + - + +
163A LYS 3.6 7.2 - - - +
164A ALA 3.4 0.2 - - - -
165A GLU* 1.3 76.9 - - + +
167A ARG* 1.3 57.7 + - - +
169A TYR* 4.5 4.3 - - + -
170A PHE* 2.9 27.4 + - - +
192A PHE* 4.6 1.3 - - - -
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Residues in contact with ARG 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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155A TYR* 2.8 35.8 + - + -
160A SER 4.8 1.0 + - - -
163A LYS* 3.0 41.4 + - - +
164A ALA* 3.6 28.1 - - - +
165A GLU 3.2 0.2 - - - -
166A LEU* 1.3 76.3 - - - +
168A GLN* 1.3 56.7 + - - +
170A PHE* 3.5 2.2 + - - +
171A ARG* 3.0 36.1 + - - +
192A PHE* 4.4 14.6 - - + -
196A LEU* 4.0 18.2 - - + -
197A GLU* 4.5 0.6 + - - -
200A ASN* 3.7 23.8 + - - +
204A GLU* 2.8 36.9 + - + +
208A MET* 5.2 2.1 - - - +
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Residues in contact with GLN 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 3.1 13.4 + - - +
165A GLU* 3.0 12.2 + - - +
167A ARG* 1.3 75.4 - - - +
169A TYR* 1.3 70.4 + - + +
171A ARG* 2.9 39.6 + - - +
172A ASN* 3.0 53.9 + - - +
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Residues in contact with TYR 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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132A VAL* 6.2 0.2 - - + -
133A LYS* 3.4 62.6 - - + +
136A ALA* 3.9 20.8 - - + +
137A GLY* 5.2 2.7 - - - -
151A PHE* 3.8 15.0 - + + -
165A GLU* 2.8 34.6 + - + +
166A LEU* 3.8 7.4 - - + +
168A GLN* 1.3 81.4 - - + +
170A PHE* 1.3 63.8 + - - +
172A ASN* 3.2 17.4 + - + +
173A LEU* 3.0 27.4 + - - +
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Residues in contact with PHE 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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148A CYS* 4.4 17.7 - - - -
151A PHE* 3.7 29.5 - + + -
166A LEU 2.9 18.1 + - - +
167A ARG 3.8 2.5 - - - +
169A TYR* 1.3 75.1 - - - +
171A ARG* 1.3 64.1 + - - +
173A LEU* 3.1 8.2 + - + +
174A CYS* 3.0 38.9 + - - -
185A ALA* 3.8 27.4 - - + -
188A LYS* 4.5 5.2 - - + -
189A LEU* 3.8 26.0 - - + -
192A PHE* 3.5 44.6 - + + -
208A MET* 3.8 11.7 - - - -
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Residues in contact with ARG 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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164A ALA 4.8 2.0 + - - -
167A ARG* 3.0 24.2 + - - +
168A GLN* 2.9 50.1 + - - +
170A PHE* 1.3 75.3 - - - +
172A ASN* 1.3 62.9 + - - +
174A CYS* 3.3 5.4 + - - +
175A SER* 3.1 23.8 + - - -
204A GLU* 2.9 44.2 + - - +
208A MET* 3.8 31.1 - - + +
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Residues in contact with ASN 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 GLN* 3.0 43.8 + - - +
169A TYR* 3.3 21.2 - - + +
170A PHE 3.2 0.2 - - - -
171A ARG* 1.3 73.4 - - - +
173A LEU* 1.3 69.1 + - + +
175A SER* 3.3 8.4 + - - -
176A ASP* 3.0 21.8 + - - +
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Residues in contact with LEU 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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136A ALA* 3.8 33.2 - - + +
144A ARG* 4.1 15.9 - - + +
147A ALA* 4.6 2.0 - - + -
148A CYS* 3.9 27.6 - - - -
151A PHE* 3.6 32.5 - - + -
169A TYR 3.0 25.3 + - - +
170A PHE* 3.1 8.5 + - + +
172A ASN* 1.3 79.3 - - + +
174A CYS* 1.3 60.9 + - - +
176A ASP* 3.2 22.1 + - - +
181A VAL* 3.9 20.9 - - + +
182A ARG* 4.0 6.4 - - - -
185A ALA* 4.1 6.1 - - + -
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Residues in contact with CYS 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 PHE* 3.0 43.7 + - - -
171A ARG* 3.6 10.1 - - - +
172A ASN 3.3 0.4 - - - -
173A LEU* 1.3 76.4 - - - +
175A SER* 1.3 57.3 + - - +
182A ARG* 3.1 19.6 - - - +
185A ALA* 3.9 15.3 - - - -
189A LEU* 4.9 0.4 - - - -
208A MET* 3.8 20.9 - - + -
211A ASN* 6.6 0.2 - - + -
212A LEU* 3.4 37.4 - - + +
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Residues in contact with SER 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 ARG 3.1 15.8 + - - -
172A ASN* 3.5 9.0 + - - -
173A LEU 3.1 0.6 - - - -
174A CYS* 1.3 78.4 - - - +
176A ASP* 1.3 65.0 + - - +
177A ASP* 3.6 4.7 + - - +
182A ARG* 4.4 4.3 - - - +
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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
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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