Contacts of the helix formed by residues 174 - 184 (chain A) in PDB entry 1D0L
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 ILE 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A THR 3.2 1.9 + - - +
173A ARG* 1.3 71.6 - - - +
175A LEU* 1.3 57.2 + - - +
177A ALA* 3.4 5.2 + - - +
178A LEU* 2.9 52.5 + - + +
199A PHE* 3.6 27.4 - - + -
213A LEU* 3.0 24.2 + - + +
214A LYS 3.9 0.7 - - - -
215A GLY* 3.4 28.9 - - - +
216A SER 4.7 0.2 - - - +
219A GLY* 3.6 24.2 - - - +
221A MET* 3.5 32.5 - - + -
228A PRO* 5.0 0.2 - - + -
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Residues in contact with LEU 175 (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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81A ILE* 3.6 30.3 - - + +
82A LEU* 4.2 9.6 - - + -
85A ALA* 4.1 14.1 - - + -
173A ARG* 3.1 3.2 - - + +
174A ILE* 1.3 79.8 - - - +
176A ASP* 1.3 58.1 + - - +
178A LEU* 4.8 1.8 - - - -
179A ALA* 2.9 33.8 + - - +
196A LEU* 4.0 20.6 - - + -
199A PHE* 4.1 10.5 - - + -
200A LEU* 4.1 19.5 - - + -
210A PRO* 3.8 16.9 + - + +
211A LEU* 3.3 35.4 - - + -
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Residues in contact with ASP 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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85A ALA* 3.4 4.2 - - - -
86A LYS* 2.7 63.1 + - - +
88A LEU* 3.6 19.8 - - + +
173A ARG* 2.9 41.0 + - - +
175A LEU* 1.3 76.8 - - - +
177A ALA* 1.3 60.2 + - - +
179A ALA* 4.7 1.3 - - - -
180A THR* 2.7 34.6 + - - -
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Residues in contact with ALA 177 (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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88A LEU* 4.3 6.0 - - - +
91A VAL* 4.6 2.9 - - + -
172A THR* 4.1 7.4 - - + -
173A ARG 3.2 9.1 + - - +
174A ILE 3.7 6.7 - - - +
176A ASP* 1.3 80.3 - - - +
178A LEU* 1.3 57.7 + - - +
180A THR* 3.6 4.3 - - - -
181A LEU* 3.0 36.3 + - - +
216A SER 3.9 15.5 - - - +
217A PHE* 3.5 24.2 - - - +
218A ALA 4.5 0.2 - - - -
219A GLY* 4.0 8.5 - - - +
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Residues in contact with LEU 178 (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 ILE* 2.9 40.5 + - + +
177A ALA* 1.3 73.1 - - - +
179A ALA* 1.3 58.2 + - - +
181A LEU* 3.9 2.2 - - - +
182A SER* 2.6 37.5 + - - -
192A PHE* 3.9 21.5 - - + +
195A GLU* 3.8 24.0 - - + +
196A LEU* 3.8 21.1 - - + -
199A PHE* 3.8 24.9 - - + -
218A ALA 3.7 23.6 - - - +
219A GLY* 4.2 3.4 - - - -
227A MET* 4.8 1.6 - - + -
228A PRO* 3.9 7.4 - - + -
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Residues in contact with ALA 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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54A PHE* 3.7 24.6 - - + -
82A LEU* 4.6 5.8 - - + -
85A ALA* 4.1 11.0 - - + -
175A LEU 2.9 19.9 + - - +
176A ASP 4.0 1.3 - - - +
178A LEU* 1.3 73.0 - - - +
180A THR* 1.3 62.2 + - - +
182A SER* 4.4 0.2 - - - -
183A PHE* 2.9 54.9 + - + +
196A LEU* 4.2 6.0 - - + +
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Residues in contact with THR 180 (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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54A PHE* 3.7 9.1 - - - -
86A LYS 3.0 6.1 + - - -
87A ARG* 3.2 6.0 - - + -
88A LEU* 2.9 47.0 + - - +
91A VAL* 4.4 8.3 - - + -
92A LEU* 3.6 24.4 - - + +
176A ASP 2.7 22.7 + - - -
177A ALA* 3.6 5.8 - - - -
179A ALA* 1.3 77.3 - - - +
181A LEU* 1.3 57.3 + - - +
184A ASN* 2.9 31.4 + - - +
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Residues in contact with LEU 181 (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 VAL* 3.7 18.8 - - + +
92A LEU* 4.5 4.5 - - + -
95A MET* 3.9 31.6 - - + -
177A ALA 3.0 22.6 + - - +
178A LEU 4.2 1.1 - - - +
180A THR* 1.3 75.8 - - - +
182A SER* 1.3 61.1 + - - +
185A TYR* 3.4 41.9 - - + +
188A ARG 4.3 0.7 - - - +
189A ALA* 3.6 7.8 + - - -
192A PHE* 3.5 48.3 - - + +
217A PHE 3.7 20.0 - - - +
218A ALA* 4.1 4.5 - - - -
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Residues in contact with SER 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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59A ASN* 4.5 6.1 - - - +
178A LEU 2.6 25.9 + - - -
179A ALA 3.8 0.9 - - - -
181A LEU* 1.3 77.2 - - - +
183A PHE* 1.3 82.9 + - - +
189A ALA* 3.5 28.8 - - - +
192A PHE* 3.0 25.0 + - - -
193A SER* 3.2 14.8 + - - -
196A LEU* 3.7 7.2 - - - +
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Residues in contact with PHE 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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54A PHE* 3.8 19.1 - + + -
57A ASN* 3.0 34.4 + - - +
59A ASN* 3.1 24.8 + - + -
60A ALA* 3.7 33.7 - - + -
63A PHE* 3.5 37.0 - + + -
82A LEU* 4.2 14.1 - - + -
179A ALA* 2.9 35.7 + - + +
182A SER* 1.3 94.5 - - - +
184A ASN* 1.3 56.3 + - - +
185A TYR 3.8 1.3 - - - -
189A ALA* 6.0 0.2 - - - -
193A SER* 5.1 1.3 - - - -
196A LEU* 3.5 20.4 - - + -
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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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53A ASP 5.3 0.5 - - - +
54A PHE* 3.2 29.6 - - - -
57A ASN* 3.4 18.5 + - - +
87A ARG* 3.5 28.0 - - + +
92A LEU* 3.4 23.4 - - + +
180A THR 2.9 13.8 + - - +
183A PHE* 1.3 77.8 + - - +
185A TYR* 1.3 62.5 + - - +
186A PRO* 3.7 8.5 - - - +
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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