Contacts of the helix formed by residues 181 - 194 (chain A) in PDB entry 3DC5
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 ASN 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A PRO* 6.2 0.8 - - - +
79A THR 3.1 17.7 + - - +
80A ASN 2.7 28.8 + - - +
81A LEU 3.9 3.6 + - - -
82A ALA* 3.6 26.5 - - + +
84A ASP 5.0 0.3 - - - +
85A GLY* 3.7 9.7 - - - +
179A ILE 3.2 0.6 + - - -
180A ALA* 1.3 71.2 - - - +
182A TRP* 1.3 55.0 + - - +
183A LYS* 3.3 23.6 + - - +
184A ASN* 2.9 13.7 + - - +
185A ILE* 2.9 29.5 + - - +
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Residues in contact with TRP 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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85A GLY 3.1 7.7 + - - +
86A GLY 3.5 17.5 - - - -
87A GLU* 3.3 21.5 - - - +
88A PRO* 3.6 28.1 - - + +
92A LEU* 3.7 27.8 - - + -
96A ILE* 4.2 8.5 - - + -
103A LEU* 3.7 36.5 - - + +
106A LEU* 4.9 4.7 - - + -
107A GLN* 4.6 3.0 - - - +
125A LEU* 4.9 5.4 - - + -
152A PHE* 5.8 0.2 - + - -
177A TRP* 3.9 30.2 + + - -
180A ALA* 3.1 27.3 + - + +
181A ASN* 1.3 68.5 - - - +
183A LYS* 1.3 60.6 + - - +
185A ILE* 3.7 23.1 - - + -
186A SER* 2.7 37.1 + - - -
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Residues in contact with LYS 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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85A GLY 3.2 11.0 + - - +
87A GLU 4.8 1.5 + - - -
181A ASN* 3.2 13.4 - - - +
182A TRP* 1.3 76.6 - - - +
184A ASN* 1.3 60.5 + - - +
186A SER* 4.0 3.8 - - - -
187A GLU* 3.1 51.7 + - + +
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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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79A THR* 3.0 40.0 + - - +
80A ASN* 2.9 28.4 + - - -
181A ASN* 2.9 16.4 + - + +
183A LYS* 1.3 76.6 - - - +
185A ILE* 1.3 65.7 + - - +
187A GLU* 3.2 17.7 + - - +
188A ARG* 2.9 41.7 + - - +
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Residues in contact with ILE 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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80A ASN* 4.4 5.6 - - - +
92A LEU* 3.9 7.4 - - + -
125A LEU* 4.5 4.0 - - + -
151A LEU* 3.7 40.1 - - + +
152A PHE* 3.5 36.6 - - + -
180A ALA* 4.1 4.3 - - + -
181A ASN 2.9 30.3 + - - +
182A TRP* 3.7 42.0 - - + +
184A ASN* 1.3 75.9 - - - +
186A SER* 1.3 57.1 + - - +
188A ARG* 3.2 4.5 + - - +
189A PHE* 2.9 26.9 + - - +
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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
----------------------------------------------------------
87A GLU 4.4 0.5 + - - -
88A PRO* 3.6 2.3 - - - +
89A SER* 3.1 44.0 + - - -
91A GLU* 4.7 2.6 - - - +
92A LEU* 3.6 16.8 - - - +
182A TRP 2.7 24.5 + - - -
183A LYS* 4.0 3.8 - - - -
185A ILE* 1.3 77.3 - - - +
187A GLU* 1.3 56.4 + - - +
189A PHE* 3.4 5.5 + - - +
190A ALA* 3.0 28.1 + - - +
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Residues in contact with GLU 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 LYS* 3.1 49.3 + - + +
184A ASN* 3.2 20.6 + - - +
186A SER* 1.3 75.4 - - - +
188A ARG* 1.3 59.0 + - + +
190A ALA* 3.4 6.6 + - - +
191A ASN* 3.0 41.3 + - - +
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Residues in contact with ARG 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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75A SER 4.7 0.6 + - - -
76A ILE* 3.8 36.1 - - - +
79A THR* 2.8 29.0 + - - +
80A ASN* 3.7 2.4 - - - +
149A VAL* 4.6 3.2 - - + +
150A PRO* 3.9 15.4 + - - +
151A LEU* 3.5 32.4 - - + +
184A ASN* 2.9 39.7 + - - +
185A ILE 3.2 7.6 + - - +
187A GLU* 1.3 73.3 - - + +
189A PHE* 1.3 59.8 + - - +
191A ASN* 3.4 8.3 + - - +
192A ALA* 2.9 31.4 + - - +
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Residues in contact with PHE 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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91A GLU* 3.8 12.1 - - + -
92A LEU* 3.6 43.3 - - + -
95A THR* 3.2 28.5 - - + -
127A TYR* 3.8 28.5 - + - -
134A LEU* 3.9 18.4 - - + -
151A LEU* 3.5 14.3 - - + +
185A ILE 2.9 13.6 + - - +
186A SER* 3.4 10.3 - - - +
188A ARG* 1.3 73.4 - - - +
190A ALA* 1.3 66.0 + - - +
192A ALA* 3.1 4.4 + - - +
193A ARG* 3.0 65.4 + - - +
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Residues in contact with ALA 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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91A GLU* 3.8 21.1 - - - +
186A SER 3.0 16.5 + - - +
187A GLU* 3.6 8.1 - - - +
188A ARG 3.4 0.2 - - - -
189A PHE* 1.3 79.2 - - - +
191A ASN* 1.3 67.0 + - - +
193A ARG* 3.2 16.8 + - - +
194A GLN* 3.3 20.4 + - - +
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Residues in contact with ASN 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 GLU* 3.0 23.3 + - - +
188A ARG* 3.9 7.7 - - - +
189A PHE 3.3 0.2 - - - -
190A ALA* 1.3 80.4 - - - +
192A ALA* 1.3 61.4 + - - +
193A ARG 3.5 0.2 + - - -
194A GLN* 3.5 30.2 + - - +
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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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127A TYR* 3.9 20.4 - - + -
129A LYS* 2.7 40.7 + - - +
149A VAL* 3.6 38.6 - - + +
151A LEU* 4.5 0.4 - - + -
188A ARG 2.9 18.4 + - - +
189A PHE* 3.1 6.3 + - - +
191A ASN* 1.3 76.3 - - - +
193A ARG* 1.3 53.6 + - - +
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Residues in contact with ARG 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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91A GLU* 3.3 34.5 + - - +
95A THR* 3.1 23.0 + - - +
98A ARG* 4.1 15.0 - - - +
127A TYR* 4.1 27.7 + - + +
129A LYS* 3.8 6.4 + - - -
189A PHE* 3.0 41.8 + - + +
190A ALA* 3.2 9.4 + - - +
192A ALA* 1.3 78.2 - - - +
194A GLN* 1.3 64.3 + - + +
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Residues in contact with GLN 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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129A LYS* 4.5 9.9 - - - -
190A ALA* 3.3 11.5 + - - +
191A ASN* 3.5 32.9 + - - +
192A ALA 3.5 1.4 - - - -
193A ARG* 1.3 84.3 - - + +
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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