Contacts of the helix formed by residues 178 - 195 (chain A) in PDB entry 4N78
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 LYS 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A LEU* 3.2 27.8 - - + +
84A TYR 3.7 13.8 + - - -
86A TRP 2.6 31.5 + - - +
87A ARG* 4.5 3.2 - - - +
174A LEU 3.1 12.2 + - - +
175A LYS* 3.6 12.7 + - - +
176A ASN 3.5 2.5 - - - -
177A MET* 1.3 96.5 - - + +
179A CYS* 1.3 64.6 + - - +
180A SER* 3.1 4.7 - - - -
181A VAL* 3.3 31.2 + - + +
182A LYS* 3.6 5.4 + - - +
625A GLU* 4.5 12.0 + - - -
629A GLU* 3.2 30.2 + - - +
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Residues in contact with CYS 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ARG* 6.3 0.9 - - - +
176A ASN 5.0 6.1 - - - -
177A MET 2.9 16.9 + - - -
178A LYS* 1.3 69.4 - - - +
180A SER* 1.3 61.0 + - - +
182A LYS* 3.2 10.7 + - + +
183A ASN* 2.8 46.9 + - - +
629A GLU* 3.0 8.8 + - - +
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Residues in contact with SER 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A TRP* 4.0 14.4 - - - -
87A ARG* 4.9 0.2 - - - -
88A SER* 3.8 37.8 + - - -
91A ARG* 5.3 3.1 + - - -
178A LYS* 4.4 1.8 - - - -
179A CYS* 1.3 77.0 - - - +
181A VAL* 1.3 55.8 + - - +
183A ASN* 3.9 6.3 - - - +
184A ASP* 2.8 36.2 + - - +
629A GLU* 2.6 32.0 + - - -
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Residues in contact with VAL 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 4.4 15.3 - - + -
86A TRP* 3.6 37.2 - - + +
122A LEU* 3.5 33.1 - - + +
178A LYS* 3.5 29.4 - - + +
179A CYS 3.1 0.6 - - - -
180A SER* 1.3 76.8 - - - +
182A LYS* 1.3 64.5 + - - +
184A ASP* 3.2 3.6 + - - +
185A HIS* 3.1 21.7 + - - +
214A LEU* 3.9 18.6 - - + -
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Residues in contact with LYS 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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178A LYS 3.6 5.2 + - - +
179A CYS* 3.2 14.7 + - + +
181A VAL* 1.3 79.3 - - - +
183A ASN* 1.3 71.2 + - - +
185A HIS* 3.5 3.8 + - - +
186A SER* 3.1 35.0 + - - +
214A LEU* 3.6 38.1 - - + +
215A ALA* 4.0 25.8 - - - +
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Residues in contact with ASN 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A SER* 5.6 0.2 - - - +
90A SER* 4.3 13.0 + - - +
91A ARG* 5.1 11.1 - - - +
179A CYS* 2.8 37.8 + - - +
180A SER* 3.9 6.1 - - - +
182A LYS* 1.3 85.7 + - - +
184A ASP* 1.3 59.0 + - - +
186A SER* 3.3 8.0 + - - -
187A ALA* 2.9 28.9 + - - +
190A ARG* 5.6 0.2 + - - -
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Residues in contact with ASP 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A TRP* 2.7 38.4 + - + -
87A ARG 3.6 1.4 - - - +
88A SER* 3.7 1.8 + - - -
89A CYS* 3.1 27.0 + - - +
90A SER* 2.8 35.1 + - - -
115A LEU* 3.4 16.7 - - + +
119A VAL* 5.7 0.7 - - - -
180A SER 2.8 22.9 + - - +
181A VAL 3.6 4.3 - - - +
183A ASN* 1.3 72.2 - - - +
185A HIS* 1.3 61.7 + - - +
187A ALA* 3.1 8.5 + - - +
188A TYR* 3.0 18.9 + - - +
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Residues in contact with HIS 185 (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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119A VAL* 3.9 23.4 - - + +
122A LEU* 4.2 7.8 - - + +
123A MET* 5.1 0.6 - - - +
181A VAL 3.1 8.2 + - - +
182A LYS 3.7 5.1 + - - +
184A ASP* 1.3 76.3 - - - +
186A SER* 1.3 57.2 + - - +
188A TYR* 2.9 11.5 + + - +
189A LYS* 2.6 48.6 + - + +
207A SER* 4.0 12.4 + - - -
210A LEU* 3.3 38.5 - - + +
211A SER* 3.2 31.0 + - - -
214A LEU* 3.7 28.2 - - + +
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Residues in contact with SER 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A LYS* 3.1 25.4 + - - +
183A ASN* 3.6 10.9 - - - -
185A HIS* 1.3 80.9 + - - +
187A ALA* 1.3 54.8 + - - +
189A LYS* 3.7 9.5 - - - +
190A ARG* 2.8 53.8 + - - +
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Residues in contact with ALA 187 (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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90A SER* 4.1 18.6 - - - -
93A ILE* 5.4 1.8 - - + -
111A THR* 3.7 7.3 - - + +
115A LEU* 4.0 12.6 - - + -
183A ASN 2.9 13.6 + - - +
184A ASP 3.3 9.6 - - - +
185A HIS 3.1 0.2 - - - -
186A SER* 1.3 76.7 - - - +
188A TYR* 1.3 61.5 + - - +
190A ARG* 3.6 17.9 + - - +
191A ALA* 3.3 23.0 + - - +
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Residues in contact with TYR 188 (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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111A THR* 4.5 3.6 - - - -
112A VAL* 3.6 25.8 - - + -
115A LEU* 3.8 15.0 - - + +
116A GLU* 3.4 59.2 + - + +
119A VAL* 3.6 35.4 - - + -
184A ASP 3.0 10.3 + - - +
185A HIS* 2.9 12.0 + + - +
187A ALA* 1.3 76.5 - - - +
189A LYS* 1.3 65.2 + - + +
191A ALA* 3.1 2.3 + - - +
192A ALA* 2.8 40.8 + - + +
197A LYS* 4.0 13.3 + - - +
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Residues in contact with LYS 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A HIS* 2.6 30.0 + - + +
186A SER* 3.7 8.5 - - - +
188A TYR* 1.3 79.7 - - + +
190A ARG* 1.3 60.1 + - - +
192A ALA* 4.3 3.3 - - - +
193A GLN* 3.1 57.3 + - + +
204A ILE* 5.1 0.8 + - - +
207A SER* 2.4 49.1 + - - +
208A GLN* 4.0 11.5 + - - +
211A SER* 3.3 26.7 - - - +
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Residues in contact with ARG 190 (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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108A TYR* 4.9 16.6 - - + +
183A ASN 5.6 0.2 + - - -
186A SER* 2.8 38.2 + - - +
187A ALA* 3.6 22.8 + - - +
188A TYR 3.2 0.2 - - - -
189A LYS* 1.3 76.6 - - - +
191A ALA* 1.3 60.1 + - - +
193A GLN* 4.3 6.4 - - - +
194A PHE* 3.6 21.1 + - - +
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Residues in contact with ALA 191 (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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108A TYR* 3.7 39.6 - - + +
111A THR* 3.9 17.5 - - + -
112A VAL* 4.1 5.6 - - + -
187A ALA 3.3 16.4 + - - +
188A TYR 3.1 3.6 + - - +
190A ARG* 1.3 77.8 - - - +
192A ALA* 1.3 64.5 + - - +
193A GLN 3.1 1.3 - - - -
194A PHE* 3.4 2.3 + - - +
195A LEU* 3.2 28.8 + - - +
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Residues in contact with ALA 192 (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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112A VAL* 3.9 12.5 - - + +
188A TYR* 2.8 37.0 + - + +
189A LYS* 4.3 4.3 - - - +
191A ALA* 1.3 73.5 - - - +
193A GLN* 1.3 60.9 + - + +
195A LEU* 3.6 1.6 + - - -
196A ARG 3.4 1.7 + - - -
197A LYS* 3.0 52.3 + - + +
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Residues in contact with GLN 193 (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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189A LYS* 3.1 51.9 + - + +
190A ARG* 4.3 7.3 - - - +
191A ALA 3.1 0.6 - - - -
192A ALA* 1.3 75.6 - - + +
194A PHE* 1.3 60.6 + - - +
195A LEU 3.1 1.6 - - - -
196A ARG* 2.8 28.7 + - - +
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Residues in contact with PHE 194 (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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104A ARG* 3.2 39.3 - - + -
105A VAL* 4.4 14.6 - - + -
108A TYR* 3.3 35.0 - + + -
190A ARG 3.6 16.3 + - - +
191A ALA 3.4 4.6 + - - +
193A GLN* 1.3 78.9 - - - +
195A LEU* 1.3 65.0 + - + +
196A ARG* 3.2 7.9 + - - +
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Residues in contact with LEU 195 (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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105A VAL* 4.1 26.0 - - + +
108A TYR* 3.5 46.2 - - + +
109A GLU* 3.5 15.7 - - + +
112A VAL* 4.0 11.2 - - + -
191A ALA 3.2 15.3 + - - +
192A ALA* 4.0 5.2 - - - +
193A GLN 3.1 1.2 - - - -
194A PHE* 1.3 86.4 - - + +
196A ARG* 1.3 71.5 + - - +
197A LYS* 3.1 6.7 + - + +
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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