Contacts of the helix formed by residues 154 - 173 (chain A) in PDB entry 4R1Z
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 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A CYS 4.9 3.8 + - - -
148A PHE* 3.6 10.6 + - - -
152A SER 3.8 3.4 + - - -
153A VAL* 1.3 77.3 - - - +
155A ILE* 1.3 75.5 + - - +
156A GLU* 3.0 15.0 - - - -
157A LYS* 2.8 34.1 + - - +
158A ILE* 3.5 9.8 + - - +
139B LYS* 4.0 12.1 + - - +
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Residues in contact with ILE 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LEU* 3.8 31.2 - - + +
148A PHE* 3.8 8.9 + - + +
154A SER* 1.3 84.1 + - - +
156A GLU* 1.3 74.1 + - + +
158A ILE* 2.9 19.9 + - + +
159A ILE* 2.9 33.3 + - + +
191A VAL* 4.9 9.6 - - + +
195A LEU* 3.5 33.9 - - + -
355A LEU* 5.9 0.2 - - + -
458A LEU* 4.8 8.3 - - + -
461A MET* 3.9 29.2 - - + -
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Residues in contact with GLU 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A SER* 3.0 10.3 - - - -
155A ILE* 1.3 86.0 - - + +
157A LYS* 1.3 66.2 + - + +
159A ILE* 3.3 8.9 + - - +
160A CYS* 3.0 36.7 + - - -
354A GLN* 3.6 13.0 - - - +
355A LEU* 2.9 55.4 + - + +
356A SER 4.7 1.4 + - - -
461A MET* 5.8 0.2 - - - -
465A LEU* 4.6 4.1 - - + +
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Residues in contact with LYS 157 (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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151A GLY 5.2 0.2 + - - -
152A SER* 4.7 7.3 + - - -
153A VAL* 3.8 40.4 - - + +
154A SER 2.8 23.6 + - - +
156A GLU* 1.3 77.5 - - + +
158A ILE* 1.3 58.7 + - + +
160A CYS* 3.5 5.7 + - - +
161A ARG* 2.8 29.3 + - - +
135B LYS* 6.1 4.6 - - - +
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Residues in contact with ILE 158 (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 PHE* 3.0 43.5 - - + -
153A VAL* 5.4 5.2 - - + -
154A SER 3.9 4.9 - - - +
155A ILE* 2.9 21.0 + - + +
157A LYS* 1.3 77.2 - - + +
159A ILE* 1.3 62.4 + - + +
161A ARG* 3.6 22.7 - - - +
162A GLU* 3.1 27.2 + - + +
190A ASN 4.1 9.0 - - - +
191A VAL* 4.2 11.9 - - + +
194A ALA* 3.9 25.1 - - + -
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Residues in contact with ILE 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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155A ILE* 2.9 25.6 + - + +
156A GLU* 3.7 4.3 - - - +
158A ILE* 1.3 78.6 - - - +
160A CYS* 1.3 56.0 + - - +
162A GLU* 3.1 4.0 + - - +
163A ALA* 3.0 26.9 + - + +
191A VAL* 4.1 24.9 - - + -
458A LEU* 4.3 11.4 - - + -
461A MET* 4.0 25.8 - - + -
462A GLU* 4.0 20.9 - - + -
465A LEU* 3.5 33.0 - - + -
466A PHE* 4.1 20.0 - - + -
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Residues in contact with CYS 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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156A GLU* 3.0 34.4 + - - +
157A LYS* 3.7 5.8 - - - +
159A ILE* 1.3 74.6 - - - +
161A ARG* 1.3 64.3 + - - +
163A ALA* 3.9 2.2 - - - +
164A SER* 3.0 24.8 + - - -
353A PRO 4.2 3.8 - - - -
354A GLN* 5.3 1.3 - - - -
465A LEU* 3.9 17.0 - - - -
469A TRP* 3.8 42.1 - - + +
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Residues in contact with ARG 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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157A LYS 2.8 22.1 + - - +
158A ILE* 3.6 21.9 + - - +
159A ILE 3.2 0.2 - - - -
160A CYS* 1.3 72.0 - - - +
162A GLU* 1.3 92.9 + - - +
164A SER* 3.3 8.4 + - - -
165A SER* 3.2 21.1 + - - -
190A ASN* 4.3 4.9 + - - +
194A ALA* 5.8 1.0 - - - +
199A SER 5.1 0.8 + - - -
200A SER* 3.6 27.4 + - - -
202A LYS* 6.3 0.2 - - - -
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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
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158A ILE* 3.1 19.0 + - + +
159A ILE 3.1 4.7 + - - +
161A ARG* 1.3 111.0 + - - +
163A ALA* 1.3 62.8 + - - +
165A SER* 3.6 11.4 + - - +
166A MET* 3.2 24.1 + - - +
186A ARG* 5.3 2.6 + - - -
187A ALA* 3.5 31.1 - - + +
190A ASN* 3.2 31.4 + - + -
191A VAL* 4.3 6.3 - - + +
466A PHE* 4.1 12.3 - - + -
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Residues in contact with ALA 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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159A ILE 3.0 15.7 + - - +
160A CYS* 3.9 1.8 - - - +
162A GLU* 1.3 74.1 - - - +
164A SER* 1.3 67.2 + - - +
165A SER 3.2 0.4 - - - -
166A MET* 3.2 5.5 + - - +
167A CYS* 3.0 30.6 + - - -
465A LEU* 4.7 3.4 - - + +
466A PHE* 4.0 21.0 - - + -
469A TRP* 3.7 37.0 - - + -
470A ILE* 6.3 0.7 - - + -
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Residues in contact with SER 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 CYS 3.0 17.5 + - - -
161A ARG* 3.3 9.8 + - - -
163A ALA* 1.3 78.2 - - - +
165A SER* 1.3 56.4 + - - +
167A CYS* 3.5 2.4 + - - +
168A GLU* 3.1 27.9 + - - +
352A HIS* 5.5 1.4 + - - -
469A TRP* 3.9 22.3 - - - -
473A ARG* 4.6 8.8 + - - +
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Residues in contact with SER 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 ARG* 3.2 9.6 + - - -
162A GLU* 3.8 17.9 - - - -
163A ALA 3.2 0.4 - - - -
164A SER* 1.3 76.6 - - - +
166A MET* 1.3 60.9 + - - +
168A GLU* 3.1 25.8 + - - +
169A VAL* 2.9 31.4 + - - +
186A ARG* 5.1 9.6 + - - -
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Residues in contact with MET 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 3.2 15.5 + - - +
163A ALA* 3.2 15.0 + - - +
165A SER* 1.3 79.1 - - - +
167A CYS* 1.3 60.3 + - - +
169A VAL* 3.1 6.5 + - - +
170A LEU* 2.8 50.6 + - + +
180A LEU* 5.0 4.5 - - + +
183A GLU* 3.4 46.0 - - + +
184A LEU* 3.4 31.9 - - + +
187A ALA* 3.9 14.6 - - + -
466A PHE* 4.6 5.2 - - + -
470A ILE* 4.8 13.0 - - + -
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Residues in contact with CYS 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 ALA 3.0 20.1 + - - +
164A SER 3.9 0.7 - - - +
166A MET* 1.3 76.7 - - - +
168A GLU* 1.3 58.8 + - - +
170A LEU* 3.5 2.0 + - - -
171A THR* 2.5 35.5 + - - -
469A TRP* 3.7 31.2 - - - -
470A ILE* 4.3 9.9 - - - -
473A ARG* 3.0 33.9 - - - +
474A PHE* 3.5 24.3 - - + -
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Residues in contact with GLU 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 SER 3.1 12.9 + - - +
165A SER* 3.1 33.8 + - - +
166A MET 3.2 0.4 - - - -
167A CYS* 1.3 74.3 - - - +
169A VAL* 1.3 66.4 + - + +
171A THR* 3.1 17.5 + - - -
172A GLU* 3.3 19.3 + - - +
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Residues in contact with VAL 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 SER* 2.9 21.2 + - - +
166A MET* 3.3 9.4 - - + +
168A GLU* 1.3 79.5 - - + +
170A LEU* 1.3 72.4 + - + +
171A THR 3.0 0.3 + - - -
172A GLU* 3.3 9.5 + - - +
173A SER* 3.0 34.6 + - - +
180A LEU* 6.4 0.7 - - + -
183A GLU* 3.7 34.8 - - + +
186A ARG* 5.1 3.6 - - - +
203A ARG* 3.1 30.5 - - - +
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Residues in contact with LEU 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 MET* 2.8 40.4 + - + +
167A CYS* 3.7 7.0 - - - +
168A GLU 3.4 0.2 - - - -
169A VAL* 1.3 78.7 - - + +
171A THR* 1.3 61.4 + - - +
173A SER* 3.4 8.0 - - - +
174A GLN* 3.2 23.2 - - - +
178A VAL* 6.4 0.4 - - + -
180A LEU* 4.1 33.0 - - + -
470A ILE* 4.2 22.0 - - + -
474A PHE* 3.7 35.2 - - + -
476A LEU* 4.7 2.9 - - + -
504A ALA* 3.8 27.6 - - + +
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Residues in contact with THR 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 CYS 2.5 22.3 + - - -
168A GLU* 3.4 10.9 - - - -
169A VAL 3.0 1.0 + - - -
170A LEU* 1.3 74.3 - - - +
172A GLU* 1.3 59.4 + - - +
174A GLN* 2.6 45.5 - - - +
474A PHE* 3.6 12.3 - - - -
506A VAL* 5.0 6.1 - - + -
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Residues in contact with GLU 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 GLU* 3.3 14.0 + - - +
169A VAL* 3.5 13.0 - - - +
171A THR* 1.3 74.5 - - - +
173A SER* 1.3 67.1 + - - +
174A GLN 3.0 10.9 + - - +
176A SER* 5.0 0.2 + - - -
203A ARG* 4.2 18.5 + - - -
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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 VAL* 3.0 32.2 + - - +
170A LEU* 3.4 7.9 - - - +
171A THR 3.2 0.2 - - - -
172A GLU* 1.3 83.4 + - - +
174A GLN* 1.3 55.4 + - - +
176A SER* 3.1 25.7 + - - +
178A VAL* 3.9 26.5 - - - +
504A ALA* 5.4 2.4 + - - +
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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