Contacts of the helix formed by residues 154 - 173 (chain A) in PDB entry 4GL5
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 GLY 154 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A SER* 1.3 74.8 - - - +
155A PRO* 1.3 66.1 - - - +
157A LEU* 3.7 6.5 + - - +
158A VAL* 3.5 24.3 + - - +
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Residues in contact with PRO 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A LYS* 5.1 10.3 - - - +
153A SER 3.1 10.5 - - - +
154A GLY* 1.3 82.8 - - - +
156A GLY* 1.3 58.5 + - - +
158A VAL* 3.3 9.2 + - + +
159A ARG* 3.0 31.9 + - + +
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Residues in contact with GLY 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ALA 4.3 12.8 - - - -
153A SER 3.3 5.1 + - - -
155A PRO* 1.3 83.2 - - - +
157A LEU* 1.3 60.1 + - - +
159A ARG* 3.5 7.3 + - - +
160A MET* 3.0 27.7 + - - +
202A LEU* 3.4 17.5 - - - +
442A ILE* 4.2 3.3 - - - +
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Residues in contact with LEU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A LEU 4.4 5.2 - - - +
153A SER* 3.9 16.9 + - - +
154A GLY 3.7 10.4 + - - +
155A PRO 3.3 0.2 - - - -
156A GLY* 1.3 76.5 - - - +
158A VAL* 1.3 62.9 + - + +
160A MET* 3.7 12.0 + - - +
161A VAL* 3.7 8.5 + - - +
347A ILE* 3.8 24.9 - - + +
350A ILE* 6.3 0.4 - - + -
441A TYR* 3.7 17.9 - - + +
442A ILE* 3.5 40.3 - - + +
445A VAL* 3.8 22.4 - - + +
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Residues in contact with VAL 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A GLY 3.5 15.4 + - - +
155A PRO* 3.3 10.7 + - + +
156A GLY 3.2 0.4 - - - -
157A LEU* 1.3 78.0 - - + +
159A ARG* 1.3 65.6 + - - +
160A MET 3.3 0.7 + - - -
161A VAL* 3.5 19.9 - - - +
162A THR* 3.7 6.3 - - + +
347A ILE* 3.9 42.2 - - + -
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Residues in contact with ARG 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 PRO* 3.0 20.2 + - + +
156A GLY* 3.7 9.4 - - - +
158A VAL* 1.3 75.9 - - - +
160A MET* 1.3 58.7 + - - +
162A THR* 3.4 9.2 + - - +
163A VAL* 3.0 55.9 + - - +
201A THR* 3.6 23.6 + - - -
202A LEU* 3.9 16.7 + - + +
205A ARG* 5.7 8.1 - - - +
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Residues in contact with MET 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 GLY 3.0 18.5 + - - +
157A LEU 3.8 7.0 - - - +
158A VAL 3.2 0.8 - - - -
159A ARG* 1.3 74.3 - - - +
161A VAL* 1.3 60.8 + - - +
163A VAL* 2.9 3.8 + - - -
164A CYS* 2.7 40.3 + - - +
198A THR* 3.4 31.4 - - + +
199A SER* 5.8 0.2 - - - +
202A LEU* 3.5 42.0 - - + -
203A PHE* 4.1 11.0 - - + -
442A ILE* 3.8 19.3 - - + -
445A VAL* 4.9 3.6 - - + -
446A MET* 3.6 38.4 - - + +
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Residues in contact with VAL 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 LEU 3.7 5.1 + - - +
158A VAL 3.5 16.3 + - - +
160A MET* 1.3 78.2 - - - +
162A THR* 1.3 69.1 + - + +
164A CYS* 4.7 0.2 - - - -
165A ALA* 3.6 17.2 + - - +
345A ILE* 4.2 17.1 - - + +
346A LYS* 4.1 4.7 - - + -
347A ILE* 3.6 31.2 - - + +
350A ILE* 3.9 22.0 - - + -
445A VAL* 3.8 26.0 - - + +
449A ALA* 3.9 21.4 - - + +
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Residues in contact with THR 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 VAL* 3.7 7.9 - - + +
159A ARG* 3.6 13.8 + - - +
161A VAL* 1.3 86.1 - - + +
163A VAL* 1.3 63.2 + - - +
164A CYS 3.2 1.3 - - - -
165A ALA* 3.5 5.7 - - - +
166A GLU* 3.0 43.8 + - - +
345A ILE 4.8 9.9 - - - +
346A LYS* 5.4 9.9 - - + -
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Residues in contact with VAL 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 ARG* 3.0 57.1 + - - +
160A MET* 2.9 5.5 + - - +
162A THR* 1.3 78.7 - - - +
164A CYS* 1.3 57.6 + - - +
166A GLU* 4.0 3.6 - - - +
167A SER* 3.0 33.9 + - - -
198A THR* 4.1 11.0 - - - +
201A THR* 3.4 31.4 - - - +
202A LEU* 3.7 18.4 - - + -
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Residues in contact with CYS 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 MET* 2.7 30.7 + - - +
161A VAL 3.9 5.6 - - - +
163A VAL* 1.3 71.7 - - - +
165A ALA* 1.3 63.3 + - - +
167A SER* 3.8 1.0 - - - -
168A LEU* 3.1 25.6 + - - +
195A MET* 4.5 2.9 - - - -
198A THR* 3.7 20.7 + - - -
446A MET* 3.7 33.9 - - - -
449A ALA* 4.1 8.5 - - + -
450A ILE* 3.8 26.3 - - + +
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Residues in contact with ALA 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 VAL 3.6 6.7 + - - +
162A THR* 3.3 10.0 + - - +
164A CYS* 1.3 78.6 - - - +
166A GLU* 1.3 70.6 + - - +
168A LEU* 3.0 4.0 + - - +
169A LYS* 2.9 34.0 + - - +
344A ASP* 4.5 2.9 - - - +
345A ILE* 3.7 30.3 - - + +
449A ALA* 5.1 1.9 - - + +
453A THR* 4.4 18.7 + - + +
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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 THR* 3.0 33.4 + - - +
163A VAL* 4.4 3.1 - - - +
165A ALA* 1.3 79.4 - - - +
167A SER* 1.3 56.9 + - - +
169A LYS* 3.1 28.8 + - - +
170A THR* 3.2 28.4 + - - +
344A ASP* 3.7 22.8 - - - +
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Residues in contact with SER 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 VAL* 3.0 23.3 + - - -
164A CYS 3.8 0.7 - - - -
166A GLU* 1.3 76.6 - - - +
168A LEU* 1.3 58.3 + - - +
170A THR* 3.5 7.9 - - - -
171A HIS* 2.9 23.4 + - - -
194A VAL* 3.6 14.1 + - - +
197A ASP* 2.7 35.6 + - - +
198A THR* 3.6 14.7 + - - -
201A THR* 5.0 2.2 - - - -
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Residues in contact with LEU 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 CYS 3.1 15.9 + - - +
165A ALA 3.0 4.1 + - - +
167A SER* 1.3 77.6 - - - +
169A LYS* 1.3 64.6 + - - +
170A THR 3.3 1.6 - - - -
171A HIS* 3.2 2.8 + - + -
172A LEU* 3.0 44.3 + - + +
190A LEU* 5.0 8.7 - - + -
191A LEU* 5.5 3.4 - - + -
194A VAL* 4.2 27.8 - - + -
450A ILE* 3.5 37.2 - - + +
453A THR* 3.4 29.4 - - - +
454A LEU* 4.0 12.3 - - + +
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Residues in contact with LYS 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 ALA* 2.9 17.9 + - - +
166A GLU* 3.1 30.6 + - - +
168A LEU* 1.3 77.0 - - - +
170A THR* 1.3 64.0 + - - +
172A LEU* 3.0 19.9 + - + +
173A ASP* 3.2 20.7 + - - +
344A ASP* 3.1 35.6 + - - -
453A THR* 4.7 21.3 - - + -
456A ARG* 6.1 2.9 - - - +
457A ARG* 5.3 5.2 - - - +
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Residues in contact with THR 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 GLU 3.2 18.2 + - - +
167A SER* 3.3 20.9 - - - +
169A LYS* 1.3 81.6 - - - +
171A HIS* 1.3 75.3 + - + +
172A LEU 3.4 0.3 + - - -
173A ASP* 3.4 10.8 + - - +
174A ARG* 2.9 42.4 + - - +
197A ASP* 4.3 4.3 - - - +
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Residues in contact with HIS 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 SER 2.9 18.6 + - - -
168A LEU 3.2 5.2 + - - +
169A LYS 3.2 0.6 - - - -
170A THR* 1.3 84.1 - - + +
172A LEU* 1.3 59.7 + - - +
173A ASP 3.4 0.4 - - - -
174A ARG* 3.4 34.7 - - + +
175A LEU* 3.9 1.9 + - - +
177A GLU* 6.1 1.1 - - + -
190A LEU* 3.9 21.3 - - + +
193A ARG* 4.3 14.3 - - + +
194A VAL* 3.4 28.1 - - + +
197A ASP* 3.4 26.9 - - + -
210A GLU* 2.6 34.7 + - - -
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Residues in contact with LEU 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 LEU* 3.0 43.7 + - + +
169A LYS* 3.0 7.8 + - + +
171A HIS* 1.3 75.1 - - - +
173A ASP* 1.3 60.5 + - - +
174A ARG 3.2 5.2 - - - -
175A LEU* 2.9 45.4 - - + +
190A LEU* 4.4 16.8 - - + -
453A THR* 4.4 12.8 - - - +
454A LEU* 4.6 8.7 - - + -
457A ARG* 3.3 30.8 + - - +
458A PHE* 4.0 20.4 - - + -
492A PHE* 4.4 9.0 - - + -
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Residues in contact with ASP 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 LYS* 3.2 15.3 + - - +
170A THR* 3.4 7.5 + - - +
171A HIS 3.4 0.4 - - - -
172A LEU* 1.3 75.5 - - - +
174A ARG* 1.3 74.6 + - - +
176A GLU* 4.0 7.8 - - - +
457A ARG* 2.9 32.6 + - - +
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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