Contacts of the helix formed by residues 189 - 196 (chain A) in PDB entry 4D87
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 SER 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A ILE* 3.5 3.1 - - - +
176A GLN 3.5 3.8 - - - -
177A TYR 2.9 7.6 + - - -
178A ASP* 2.4 48.6 + - - +
179A THR* 3.7 9.6 - - - -
186A SER* 4.0 10.0 + - - -
187A GLN 3.1 1.8 - - - -
188A ASN* 1.3 78.1 - - - +
190A PHE* 1.3 64.6 + - - +
191A ARG 3.3 3.5 + - - -
192A ASN* 3.5 7.9 + - - +
193A GLN* 3.1 25.5 + - - +
198A ILE* 5.2 1.7 - - - +
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Residues in contact with PHE 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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66A LEU* 3.9 17.3 - - + -
171A ALA* 3.2 23.3 - - + -
172A LEU* 4.5 5.6 - - + -
174A ILE* 3.1 13.4 - - + +
176A GLN 2.7 21.0 + - - +
177A TYR* 3.7 10.8 - + - +
189A SER* 1.3 71.1 - - - +
191A ARG* 1.3 59.6 + - - +
193A GLN* 3.9 0.5 - - - +
194A LEU* 2.9 56.6 + - + +
237A ILE* 4.3 5.6 - - + -
238A TRP* 3.6 29.6 - + - -
241A TRP* 3.0 58.6 - + + +
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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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61A MET 4.2 7.9 - - - -
62A SER 3.3 27.3 + - - +
63A SER* 4.1 1.1 - - - +
65A PHE* 4.4 6.7 - - + -
66A LEU* 4.2 13.0 - - + +
177A TYR* 2.7 53.1 + - + +
178A ASP* 2.6 39.0 + - - +
182A TRP 4.0 0.4 - - - -
183A ASP 3.2 17.4 + - - +
186A SER* 3.0 21.2 + - - -
190A PHE* 1.3 79.7 - - - +
192A ASN* 1.3 88.6 + - - +
194A LEU* 4.2 2.7 - - - +
195A GLU* 3.0 39.0 + - - +
197A PHE* 4.5 1.0 - - - -
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Residues in contact with ASN 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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183A ASP 3.7 4.5 - - - +
184A MET 2.7 25.9 + - - +
186A SER* 3.1 27.2 + - - +
189A SER* 3.4 9.3 + - - +
190A PHE 3.2 0.4 - - - -
191A ARG* 1.3 106.8 + - - +
193A GLN* 1.3 67.4 + - - +
195A GLU* 3.2 0.9 + - - +
196A GLY 2.9 18.9 + - - -
197A PHE* 3.1 31.6 + - - +
198A ILE* 3.5 15.7 - - + +
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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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170A ASN* 4.7 5.6 + - - +
171A ALA* 4.1 21.9 + - + +
174A ILE* 2.8 38.9 - - + +
188A ASN* 5.5 4.4 - - - +
189A SER 3.1 15.6 + - - +
190A PHE* 3.9 3.6 - - - +
192A ASN* 1.3 76.2 - - - +
194A LEU* 1.3 65.9 + - - +
195A GLU 2.8 2.1 + - - -
196A GLY* 2.8 16.5 + - - -
198A ILE* 3.2 38.7 - - + +
202A GLN* 4.9 1.6 - - - +
203A LEU* 3.6 14.0 - - + +
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Residues in contact with LEU 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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65A PHE* 5.0 1.6 - - + -
66A LEU* 3.3 33.2 - - + -
94A TRP* 5.2 5.2 - - + -
171A ALA* 4.7 4.1 - - + +
190A PHE* 2.9 46.6 + - + +
191A ARG* 4.2 3.6 - - - +
193A GLN* 1.3 73.1 - - - +
195A GLU* 1.3 57.5 + - - +
203A LEU* 3.6 22.1 - - + +
204A HIS* 3.1 22.8 + - + +
234A VAL* 3.7 32.5 - - + +
237A ILE* 4.2 19.5 - - + -
238A TRP 4.6 0.7 - - - +
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Residues in contact with GLU 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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60A HIS* 3.3 18.0 - - - +
61A MET 3.0 23.6 + - - -
65A PHE* 3.6 20.1 - - + +
191A ARG* 3.0 44.8 + - - +
192A ASN 3.2 5.1 + - - +
193A GLN 2.8 2.2 + - - -
194A LEU* 1.3 78.0 - - - +
196A GLY* 1.3 53.8 + - - +
197A PHE* 3.4 23.4 - - + -
204A HIS* 3.2 12.2 + - - +
205A ASN* 2.7 49.8 + - - +
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Residues in contact with GLY 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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192A ASN 2.9 1.8 + - - -
193A GLN 2.8 12.6 + - - -
195A GLU* 1.3 79.9 - - - +
197A PHE* 1.3 60.2 + - - +
198A ILE* 3.6 2.2 - - - -
200A GLY* 3.0 12.5 - - - -
201A PRO* 3.5 1.9 - - - +
202A GLN* 2.7 46.9 + - - +
205A ASN* 3.5 7.6 - - - +
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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