Contacts of the helix formed by residues 175 - 195 (chain A) in PDB entry 3H44
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 ASP 175 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A MET* 4.2 3.2 - - - +
116A LEU 5.3 5.9 + - - +
124A GLU* 5.7 1.1 - - + +
173A LEU* 3.1 22.4 - - + +
174A PHE* 1.3 75.1 - - - +
176A GLU* 1.3 61.7 + - - +
177A SER* 2.9 35.7 + - - -
178A ALA* 3.2 15.7 + - + +
179A LYS* 2.8 28.4 + - - +
181A ARG* 4.8 1.3 + - - -
238A ARG* 4.8 1.3 - - - +
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Residues in contact with GLU 176 (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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174A PHE 3.2 3.5 + - - -
175A ASP* 1.3 76.9 + - - +
177A SER* 1.3 59.0 + - - +
179A LYS* 2.9 34.6 + - - +
180A ASP* 3.3 27.5 + - - +
236A ASP* 4.0 10.6 - - - +
238A ARG* 3.2 35.6 - - - +
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Residues in contact with SER 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ASP* 2.9 18.1 + - - -
176A GLU* 1.3 71.8 - - - +
178A ALA* 1.3 66.0 + - - +
179A LYS 3.2 1.3 - - - -
180A ASP* 3.3 14.1 + - - +
181A ARG* 3.1 41.2 + - - +
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Residues in contact with ALA 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A MET* 3.9 14.8 - - + -
116A LEU* 4.1 16.3 - - + +
124A GLU* 3.5 19.7 - - + +
175A ASP* 3.1 26.3 + - + +
177A SER* 1.3 74.8 + - - +
179A LYS* 1.3 58.0 + - - +
181A ARG* 3.1 12.6 + - - +
182A GLU* 2.8 36.4 + - - +
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Residues in contact with LYS 179 (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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109A PHE* 3.5 18.3 - - + -
113A MET* 3.5 19.8 - - + +
174A PHE 5.0 2.7 - - - +
175A ASP 2.8 12.4 + - - +
176A GLU* 2.9 43.3 + - - +
178A ALA* 1.3 76.2 - - - +
180A ASP* 1.3 87.3 + - - +
183A VAL* 3.2 22.3 + - + +
226A LEU 5.7 1.1 - - - +
227A GLU* 5.8 4.2 - - - +
237A VAL* 3.7 33.8 - - + +
238A ARG* 4.0 15.9 - - - +
241A LEU* 4.7 4.3 - - + -
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Residues in contact with ASP 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A GLU* 3.3 17.5 + - - +
177A SER* 3.3 17.0 + - - +
178A ALA 3.2 0.8 - - - -
179A LYS* 1.3 102.1 + - - +
181A ARG* 1.3 64.8 + - + +
183A VAL* 3.6 11.8 - - - +
184A ASN* 3.5 9.9 - - - +
227A GLU* 3.9 19.0 - - - +
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Residues in contact with ARG 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 6.3 0.2 - - - +
124A GLU* 2.6 44.0 + - - -
175A ASP* 4.8 1.0 + - - -
177A SER* 3.1 22.6 + - - +
178A ALA* 3.1 21.6 + - - +
180A ASP* 1.3 76.6 - - + +
182A GLU* 1.3 59.4 + - - +
183A VAL 2.8 10.7 + - - -
184A ASN* 2.8 24.4 + - - +
825A THR* 3.5 17.2 + - - +
826A LYS* 3.1 35.5 - - - +
828A GLN* 3.1 21.2 - - + -
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Residues in contact with GLU 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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109A PHE* 4.0 3.4 - - + -
112A HIS* 3.0 44.4 + - + +
113A MET* 4.0 10.5 - - - -
116A LEU* 3.6 29.2 - - + +
178A ALA 2.8 20.5 + - - +
181A ARG* 1.3 72.1 - - - +
183A VAL* 1.3 61.7 + - - +
184A ASN 3.1 0.4 - - - -
185A ALA* 3.1 26.2 + - - +
186A VAL* 3.4 7.3 + - - +
824A ARG* 3.8 14.4 + - - -
825A THR* 4.6 10.3 - - + +
828A GLN* 3.2 15.5 + - - +
20C GLN* 5.5 0.5 + - - +
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Residues in contact with VAL 183 (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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109A PHE* 3.7 20.2 - - + -
179A LYS* 3.2 16.7 + - + +
180A ASP* 3.6 13.2 - - - +
181A ARG 2.8 1.8 + - - -
182A GLU* 1.3 76.6 - - - +
184A ASN* 1.3 64.1 + - - +
186A VAL* 3.3 6.1 + - + +
187A ASP* 3.1 19.8 + - - +
222A ASN 4.7 3.5 - - - +
223A LYS* 3.8 32.3 + - + -
226A LEU* 3.6 39.3 - - + +
227A GLU* 3.8 12.6 - - + +
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Residues in contact with ASN 184 (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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180A ASP 3.5 10.0 - - - +
181A ARG* 2.8 23.1 + - - +
183A VAL* 1.3 73.6 - - - +
185A ALA* 1.3 69.2 + - - +
187A ASP* 3.1 8.4 + - + +
188A SER* 2.9 25.1 + - - -
223A LYS* 2.8 39.2 - - - +
828A GLN* 3.7 24.3 - - + +
830A GLY* 6.2 0.7 - - - -
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Residues in contact with ALA 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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112A HIS* 4.6 2.7 - - - +
182A GLU* 3.4 33.9 - - - +
184A ASN* 1.3 78.2 - - - +
186A VAL* 1.3 57.1 + - - +
188A SER* 3.2 6.3 + - - -
189A GLU* 2.9 26.7 + - - +
824A ARG* 4.0 21.3 - - - +
828A GLN* 3.0 20.7 - - - +
830A GLY 5.1 0.7 - - - -
831A TYR* 3.8 11.5 - - + +
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Residues in contact with VAL 186 (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 HIS* 3.6 13.5 - - + +
109A PHE* 4.1 21.1 - - + -
112A HIS* 3.9 33.7 - - + +
182A GLU 3.4 9.1 + - - +
183A VAL* 3.3 8.8 + - + +
184A ASN 3.1 0.6 - - - -
185A ALA* 1.3 74.3 - - - +
187A ASP* 1.3 65.9 + - - +
189A GLU* 3.0 8.7 + - - +
190A HIS* 2.9 21.8 + - - +
220A THR* 3.5 24.9 - - + +
221A GLY 3.8 12.1 - - - +
222A ASN* 4.7 1.1 - - - +
226A LEU* 4.7 8.7 - - + -
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Residues in contact with ASP 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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183A VAL 3.1 8.5 + - - +
184A ASN* 3.1 13.1 + - + +
186A VAL* 1.3 75.4 - - - +
188A SER* 1.3 57.4 + - - +
190A HIS* 3.3 3.6 + - - +
191A GLU* 2.9 46.8 + - - +
222A ASN* 3.1 17.7 - - - +
223A LYS* 2.8 47.7 + - + +
224A TYR 4.6 0.3 + - - -
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Residues in contact with SER 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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184A ASN 2.9 12.7 + - - -
185A ALA 3.5 3.8 - - - -
187A ASP* 1.3 72.5 - - - +
189A GLU* 1.3 66.8 + - - +
190A HIS 3.1 1.8 - - - -
191A GLU* 3.0 16.7 + - - +
192A LYS* 3.0 16.8 + - - +
788A ASN* 4.2 17.0 + - - -
830A GLY* 4.0 9.4 - - - -
831A TYR* 3.4 34.1 + - - +
851A GLN* 4.8 0.9 + - - -
852A SER* 5.3 1.9 - - - -
853A GLU* 5.5 1.9 + - - +
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Residues in contact with GLU 189 (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 HIS* 2.3 16.5 + - + -
112A HIS* 2.1 19.1 + - - -
185A ALA 2.9 11.0 + - - +
186A VAL* 3.2 12.1 - - - +
188A SER* 1.3 74.8 - - - +
190A HIS* 1.3 62.4 + - - +
192A LYS* 3.2 25.0 - - - +
193A ASN* 3.5 13.9 + - - +
220A THR* 4.8 2.8 - - + +
831A TYR* 3.1 35.5 - - + +
18C SER* 3.5 5.5 - - - -
19C ARG 2.4 21.9 + - - +
42C ZN 1.7 39.4 - - - -
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Residues in contact with HIS 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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186A VAL 2.9 7.2 + - - +
187A ASP 3.5 7.4 - - - +
189A GLU* 1.3 76.9 - - - +
191A GLU* 1.3 66.5 - - - +
193A ASN* 2.8 28.8 + - - +
194A VAL* 3.1 36.2 + - + +
218A PHE* 3.5 35.0 - + - -
220A THR* 3.7 10.5 - - + +
221A GLY 3.7 16.8 - - - +
222A ASN* 4.0 22.8 + - + -
495A TRP 3.8 14.4 + - - -
496A TYR* 4.0 20.1 + + - -
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Residues in contact with GLU 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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187A ASP* 2.9 36.4 + - - +
188A SER* 3.0 13.6 + - - +
190A HIS* 1.3 87.3 - - - +
192A LYS* 1.3 64.7 + - - +
194A VAL* 3.0 28.5 + - - +
195A MET* 4.2 2.3 + - - +
786A HIS* 5.1 3.3 + - - -
787A ASN* 5.1 9.4 - - - +
788A ASN* 4.3 19.8 - - - +
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Residues in contact with LYS 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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188A SER 3.0 6.7 + - - +
189A GLU* 3.2 20.0 - - - +
191A GLU* 1.3 77.4 - - - +
193A ASN* 1.3 80.0 + - - +
194A VAL 3.6 0.2 + - - -
195A MET 4.3 0.7 + - - -
196A ASN* 4.3 4.2 - - - +
199A TRP* 5.4 2.0 - - - +
677A GLN* 2.9 50.5 + - - +
786A HIS* 4.1 7.6 - - - -
788A ASN* 4.9 0.8 - - - +
831A TYR* 3.7 31.0 - - + -
832A ILE* 3.8 24.5 - - + -
851A GLN* 3.8 15.7 - - - +
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Residues in contact with ASN 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 GLU* 3.5 18.5 + - - +
190A HIS* 2.8 19.0 + - - +
192A LYS* 1.3 95.0 + - - +
194A VAL* 1.3 62.9 + - - +
195A MET 3.3 1.3 - - - -
196A ASN* 3.1 22.1 + - - +
199A TRP* 3.3 57.2 + - + +
220A THR* 4.6 8.5 + - - +
496A TYR* 3.5 16.9 + - + +
18C SER* 5.5 0.4 + - - -
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Residues in contact with VAL 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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190A HIS* 3.1 43.9 + - + +
191A GLU* 3.0 23.1 + - - +
193A ASN* 1.3 80.4 - - - +
195A MET* 1.3 84.3 + - + +
196A ASN 3.3 1.6 + - - -
200A ARG* 2.7 29.1 + - - +
495A TRP 4.5 5.4 - - - +
496A TYR* 3.7 22.2 - - + +
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Residues in contact with MET 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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191A GLU 4.2 3.5 + - - +
192A LYS 4.3 1.8 + - - -
193A ASN 3.3 0.4 - - - -
194A VAL* 1.3 97.0 - - + +
196A ASN* 1.3 59.2 + - - +
197A ASP* 3.6 1.2 + - - +
200A ARG* 4.1 14.1 - - - +
307A ILE* 3.5 35.3 - - - +
496A TYR 5.1 2.2 - - - +
675A ALA* 5.3 2.1 - - - +
785A VAL* 3.8 30.0 - - + +
786A HIS* 3.6 34.9 + - + +
787A ASN 5.3 1.1 - - - +
961A ARG* 3.6 23.8 - - - +
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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