Contacts of the helix formed by residues 154 - 171 (chain B) in PDB entry 4F4I
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 GLN 154 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153B ASP* 1.3 72.1 - - - +
155B GLU* 1.3 66.1 + - + +
157B LEU* 4.1 19.3 - - + +
158B LYS* 3.5 47.9 + - - +
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Residues in contact with GLU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ASP* 3.2 25.9 - - - +
154B GLN* 1.3 79.1 + - + +
156B ASP* 1.3 68.2 + - - +
157B LEU 3.0 1.9 + - - -
158B LYS* 4.1 1.7 - - - +
159B PHE* 3.2 24.1 + - - +
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Residues in contact with ASP 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B ASP* 2.9 27.7 + - - +
155B GLU* 1.3 78.4 - - - +
157B LEU* 1.3 60.6 + - + +
159B PHE* 3.8 9.6 - - - +
160B HIS* 3.0 30.4 + - - +
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Residues in contact with LEU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B ARG* 4.0 37.7 - - + +
143B ILE* 6.2 1.1 - - + -
153B ASP 3.9 13.9 + - - +
154B GLN* 3.9 22.0 + - - +
155B GLU 3.0 1.4 + - - -
156B ASP* 1.3 81.8 - - + +
158B LYS* 1.3 63.0 + - + +
160B HIS* 3.2 7.6 + - - +
161B GLU* 2.8 38.8 + - + +
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Residues in contact with LYS 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B GLN* 3.5 42.3 + - - +
155B GLU 3.4 3.4 + - - +
157B LEU* 1.3 78.9 - - + +
159B PHE* 1.3 58.5 + - - +
161B GLU* 3.3 16.5 + - - +
162B LYS* 2.9 30.1 + - - +
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Residues in contact with PHE 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B TYR* 4.5 15.7 - + - -
104B ALA* 4.0 28.7 - - + -
105B ARG* 4.0 30.7 - - + -
155B GLU 3.2 17.9 + - - +
156B ASP* 3.8 9.4 - - - +
158B LYS* 1.3 74.2 - - - +
160B HIS* 1.3 61.7 + - + +
162B LYS* 3.0 14.0 + - + +
163B VAL* 2.9 44.9 + - + +
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Residues in contact with HIS 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B PRO* 3.9 5.0 - - + +
11B GLU* 2.8 51.7 + - + -
135B ALA* 4.2 10.2 + - - +
138B GLY* 4.0 6.3 - - - -
139B ARG* 3.9 26.1 + - - +
142B ILE* 4.4 10.4 - - + +
156B ASP 3.0 20.6 + - - +
157B LEU* 3.4 7.2 + - - +
159B PHE* 1.3 73.8 - - + +
161B GLU* 1.3 64.8 + - - +
162B LYS 3.0 2.5 + - - -
163B VAL* 3.4 11.0 + - + +
164B ILE* 3.1 49.8 + - + +
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Residues in contact with GLU 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B ALA* 3.8 27.1 - - + +
136B GLU* 4.9 5.2 - - - +
139B ARG* 5.8 2.1 + - - -
157B LEU* 2.8 27.2 + - + +
158B LYS* 3.5 18.6 - - - +
160B HIS* 1.3 73.1 - - - +
162B LYS* 1.3 61.5 + - - +
164B ILE* 3.9 9.6 + - - +
165B GLU* 3.3 29.2 + - - +
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Residues in contact with LYS 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B TYR* 3.7 31.1 - - + -
104B ALA* 3.2 35.7 + - + +
105B ARG 5.7 0.2 - - - -
106B GLY* 6.1 0.6 - - - -
158B LYS 2.9 13.2 + - - +
159B PHE* 3.0 17.0 + - + +
161B GLU* 1.3 76.6 - - - +
163B VAL* 1.3 68.8 + - - +
165B GLU* 3.0 14.5 + - - +
166B GLY 2.9 18.7 + - - -
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Residues in contact with VAL 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B PRO* 3.8 16.4 - - + -
99B ALA* 4.1 13.0 - - + +
100B TYR* 3.7 40.2 - - + -
104B ALA* 4.2 7.4 - - + +
159B PHE* 2.9 32.0 + - + +
160B HIS* 3.6 12.8 - - + +
162B LYS* 1.3 76.7 - - - +
164B ILE* 1.3 62.8 + - - +
166B GLY* 3.1 2.4 + - - -
167B TYR* 3.0 46.1 + - + -
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Residues in contact with ILE 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B PRO* 3.9 20.2 - - + -
130B TYR* 4.5 4.7 - - - +
133B VAL* 4.0 17.0 - - + +
134B SER* 4.7 1.3 - - - -
135B ALA* 4.0 26.0 - - + +
160B HIS* 3.1 55.2 + - + +
161B GLU* 4.0 5.2 - - - +
162B LYS 3.2 0.6 - - - -
163B VAL* 1.3 75.4 - - - +
165B GLU* 1.3 67.9 + - - +
167B TYR* 2.9 11.5 + - - +
168B GLN* 2.8 40.3 + - + +
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Residues in contact with GLU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B TYR* 2.7 36.2 + - + +
161B GLU* 3.3 18.8 + - - +
162B LYS* 3.0 19.6 + - - +
164B ILE* 1.3 79.0 - - - +
166B GLY* 1.3 54.1 + - - +
168B GLN* 3.0 27.4 - - + +
169B GLU* 3.1 10.9 + - - +
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Residues in contact with GLY 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ALA* 4.5 3.8 - - - -
103B TYR* 3.6 34.7 - - - -
162B LYS 2.9 11.7 + - - -
163B VAL 3.1 3.8 + - - -
164B ILE 3.0 0.2 + - - -
165B GLU* 1.3 71.5 - - - +
167B TYR* 1.3 60.5 + - - +
169B GLU* 3.2 3.1 + - - +
170B ILE* 2.9 39.4 + - - +
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Residues in contact with TYR 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B GLU* 3.0 36.5 + - + -
9B GLY 3.4 30.3 + - - -
10B PRO* 4.3 4.0 - - + -
15B LYS* 5.3 0.3 - - - -
95B ASP* 3.9 19.7 - - + -
96B SER* 3.5 13.6 + - - -
99B ALA* 3.9 14.2 - - + +
100B TYR* 4.1 4.8 - + - -
130B TYR* 2.9 42.0 - + + +
163B VAL* 3.0 41.3 + - + -
164B ILE* 2.9 5.3 + - - +
166B GLY* 1.3 75.3 - - - +
168B GLN* 1.3 62.0 + - - +
170B ILE* 3.5 6.5 + - + -
171B ILE* 3.2 36.3 + - + +
178B PHE* 6.3 0.7 - + - -
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Residues in contact with GLN 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ARG* 5.3 2.6 + - - -
52A LEU* 4.4 12.5 - - - +
130B TYR* 4.4 7.9 + - - -
132B ASN* 3.3 33.5 + - - +
164B ILE* 2.8 30.6 + - + +
165B GLU* 3.0 17.3 - - + +
167B TYR* 1.3 77.0 - - - +
169B GLU* 1.3 59.2 + - - +
171B ILE* 3.7 15.9 - - - +
172B HIS* 4.2 6.1 + - - +
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Residues in contact with GLU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A ARG* 3.1 31.5 + - - +
103B TYR* 3.5 26.3 - - + -
165B GLU 3.1 11.9 + - - +
166B GLY* 3.2 8.5 + - - +
168B GLN* 1.3 73.3 - - - +
170B ILE* 1.3 69.1 + - + +
171B ILE 3.0 3.5 + - - -
172B HIS* 3.2 20.0 + - - +
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Residues in contact with ILE 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ASP* 3.4 27.8 - - + +
98B LEU* 3.3 46.4 - - + -
99B ALA* 3.8 13.7 - - + +
109B VAL* 5.3 9.0 - - + -
113B ARG* 5.0 8.9 + - - +
166B GLY 2.9 20.4 + - - +
167B TYR* 3.9 8.7 - - + +
169B GLU* 1.3 75.9 - - + +
171B ILE* 1.3 60.6 + - + +
172B HIS 3.1 15.8 - - - +
174B GLU* 3.7 13.3 - - + +
177B ARG* 5.0 0.7 - - - +
178B PHE* 3.9 25.6 - - + -
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Residues in contact with ILE 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LEU* 4.0 37.4 - - + +
130B TYR* 4.0 35.4 - - + -
167B TYR* 3.2 24.7 - - + +
168B GLN* 3.7 16.8 - - - +
169B GLU 3.0 0.4 + - - -
170B ILE* 1.3 78.5 - - + +
172B HIS* 1.3 65.3 + - - +
173B ASN 3.5 0.5 + - - -
174B GLU 3.4 19.2 + - - +
175B SER* 4.4 3.6 + - - -
178B PHE* 4.1 38.5 - - + +
180B SER* 4.1 3.8 - - - +
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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