Contacts of the helix formed by residues 184 - 196 (chain A) in PDB entry 3DC6
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 184 (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* 6.3 0.8 - - - +
79A THR 3.2 16.5 + - - +
80A ASN 2.8 28.1 + - - +
81A LEU 3.6 16.8 + - - -
82A ALA* 3.8 11.8 - - + +
85A GLY* 3.7 10.6 - - - +
155A PHE* 4.6 0.8 - - - -
182A ILE 3.2 1.2 + - - -
183A ALA* 1.3 69.1 - - - +
185A TRP* 1.3 63.1 + - - +
186A LYS* 3.2 24.4 + - - +
187A ASN* 3.0 21.0 + - - +
188A VAL* 3.0 17.0 + - - +
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Residues in contact with TRP 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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85A GLY 2.9 9.3 + - - +
86A GLY 3.4 17.9 - - - -
87A GLU* 3.3 24.5 - - + -
88A PRO* 3.5 23.5 - - + +
92A LEU* 3.8 25.1 - - + -
96A ILE* 4.1 11.9 - - + -
103A LEU* 3.7 32.4 - - + +
106A LEU* 4.6 5.6 - - + -
107A GLN* 4.2 5.3 - - - +
125A LEU* 4.8 5.6 - - + -
155A PHE* 5.7 2.0 - + + -
180A TRP* 3.7 36.4 + + - -
183A ALA* 3.2 25.0 + - + +
184A ASN* 1.3 69.4 - - - +
186A LYS* 1.3 59.5 + - - +
188A VAL* 3.9 19.9 - - + +
189A SER* 2.8 36.1 + - - -
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Residues in contact with LYS 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A GLY 3.3 9.0 + - - +
86A GLY* 6.1 0.2 - - - -
87A GLU 4.6 2.8 + - - -
184A ASN* 3.1 13.7 + - - +
185A TRP* 1.3 78.7 - - - +
187A ASN* 1.3 57.4 + - - +
189A SER* 3.6 4.7 - - - -
190A GLU* 3.0 53.9 + - + +
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Residues in contact with ASN 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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79A THR* 3.1 40.1 + - - +
80A ASN* 2.9 18.6 + - - -
184A ASN* 3.0 16.7 + - - +
186A LYS* 1.3 78.5 - - - +
188A VAL* 1.3 59.5 + - - +
190A GLU* 3.2 18.2 + - - +
191A ARG* 2.9 64.2 + - - +
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Residues in contact with VAL 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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80A ASN* 4.5 4.0 - - - +
92A LEU* 3.8 16.6 - - + -
125A LEU* 4.3 5.4 - - + -
154A LEU* 3.5 42.0 - - + +
155A PHE* 3.7 29.2 - - + -
184A ASN 3.0 18.2 + - - +
185A TRP* 3.4 25.1 + - + +
187A ASN* 1.3 73.9 - - - +
189A SER* 1.3 56.9 + - - +
191A ARG* 3.2 3.8 + - - +
192A PHE* 2.8 27.9 + - - +
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Residues in contact with SER 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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87A GLU 4.4 0.3 + - - -
88A PRO* 3.7 0.5 - - - +
89A SER* 2.9 44.7 + - - -
92A LEU* 3.5 15.1 - - - +
185A TRP 2.8 24.2 + - - -
186A LYS* 3.6 6.1 - - - -
188A VAL* 1.3 77.0 - - - +
190A GLU* 1.3 56.1 + - - +
192A PHE* 3.3 6.5 + - - +
193A ALA* 3.0 27.9 + - - +
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Residues in contact with GLU 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 LYS* 3.0 48.7 + - + +
187A ASN* 3.2 20.8 + - - +
189A SER* 1.3 75.0 - - - +
191A ARG* 1.3 59.3 + - + +
193A ALA* 3.3 7.3 + - - +
194A LYS* 3.0 28.6 + - - +
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Residues in contact with ARG 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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75A SER 4.7 0.4 + - - -
76A ILE* 3.7 35.9 - - - +
79A THR* 2.9 25.9 + - - +
80A ASN* 3.6 5.4 - - - +
152A VAL* 5.0 2.2 - - + +
153A PRO* 3.8 15.0 + - - +
154A LEU* 3.5 32.5 - - + +
187A ASN* 2.9 41.9 + - - +
188A VAL 3.6 4.7 - - - +
190A GLU* 1.3 73.4 - - + +
192A PHE* 1.3 60.8 + - - +
194A LYS* 3.4 5.7 + - - +
195A ALA* 2.8 31.0 + - - +
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Residues in contact with PHE 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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89A SER* 5.1 0.7 - - - -
91A GLU* 3.8 29.4 - - + -
92A LEU* 3.9 27.6 - - + -
95A ALA* 3.6 21.1 - - + -
127A TYR* 3.8 27.8 - + - -
134A LEU* 3.9 23.8 - - + -
154A LEU* 3.6 14.1 - - + +
188A VAL 2.8 16.9 + - - +
189A SER 3.5 6.5 - - - +
190A GLU 3.3 0.2 - - - -
191A ARG* 1.3 74.6 - - - +
193A ALA* 1.3 67.1 + - + +
195A ALA* 3.3 3.8 + - - +
196A GLN* 3.3 58.3 + - - +
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Residues in contact with ALA 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 SER 3.0 14.2 + - - +
190A GLU* 3.3 10.5 + - - +
192A PHE* 1.3 80.9 - - + +
194A LYS* 1.3 62.5 + - - +
196A GLN* 3.2 20.2 + - - +
197A GLN* 3.6 13.6 + - - +
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Residues in contact with LYS 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 GLU 3.0 16.7 + - - +
191A ARG* 3.8 6.3 - - - +
193A ALA* 1.3 78.2 - - - +
195A ALA* 1.3 61.3 + - - +
197A GLN* 2.8 55.9 + - - +
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Residues in contact with ALA 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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127A TYR* 3.5 41.4 - - + -
129A PRO* 5.2 4.2 - - - +
152A VAL* 3.9 28.2 - - + +
154A LEU* 4.3 2.2 - - + -
191A ARG 2.8 18.8 + - - +
192A PHE 3.6 6.3 - - - +
194A LYS* 1.3 75.8 - - - +
196A GLN* 1.3 59.2 + - - +
197A GLN 3.6 6.0 + - - +
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Residues in contact with GLN 196 (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* 5.4 3.6 - - - +
127A TYR* 3.7 30.4 + - + +
132A LYS* 5.6 1.4 + - - +
192A PHE* 3.3 49.6 - - + +
193A ALA* 3.2 11.4 + - - +
194A LYS 3.1 1.0 - - - -
195A ALA* 1.3 76.5 - - - +
197A GLN* 1.3 62.3 + - - +
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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