Contacts of the helix formed by residues 162 - 172 (chain A) in PDB entry 1D8V
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 PHE 162 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ILE* 5.9 0.2 - - - -
158A GLU 3.2 2.6 + - - -
159A ALA 2.7 20.4 - - - +
160A ALA 4.6 1.3 - - - -
161A ARG* 1.3 89.6 - - + +
163A LYS* 1.3 63.7 + - - +
164A TYR* 4.1 5.4 - + + +
165A ILE* 3.4 22.7 + - + +
166A GLU 3.2 9.4 + - - -
186A LEU* 4.2 19.3 - - + -
190A TRP* 3.6 39.9 - + + -
193A LEU* 5.0 1.1 - - + -
230A VAL* 3.3 29.6 - - + -
234A ASN* 2.8 59.2 - - - -
235A ILE* 3.4 18.2 - - + -
236A LYS* 5.5 1.1 - - - +
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Residues in contact with LYS 163 (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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15A THR* 5.6 9.8 - - - +
19A GLU* 6.1 0.2 - - - -
162A PHE* 1.3 74.1 - - - +
164A TYR* 1.3 52.9 + - - +
166A GLU* 3.1 28.6 + - - +
167A ARG* 2.7 70.3 + - + +
233A GLY 3.9 22.4 + - - +
234A ASN* 3.3 10.3 + - - +
236A LYS* 3.5 36.5 - - + +
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Residues in contact with TYR 164 (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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162A PHE* 3.1 2.9 - + + -
163A LYS* 1.3 73.3 - - - +
165A ILE* 1.3 78.1 + - + +
167A ARG* 3.0 17.7 + - + +
168A HIS* 3.2 44.6 + + - -
180A ASN* 3.3 12.6 + - - -
182A ALA* 3.3 27.2 - - + +
183A ILE* 3.7 25.4 - - + +
186A LEU* 4.4 24.5 - - + -
214A ILE 5.9 0.4 - - - -
216A PRO* 3.7 22.5 - - + +
234A ASN* 2.5 47.6 + - - +
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Residues in contact with ILE 165 (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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125A LEU* 5.9 0.7 - - + -
154A GLN* 4.0 21.3 - - + +
158A GLU* 3.8 33.9 - - + +
159A ALA* 4.0 8.3 - - - -
161A ARG* 5.5 0.4 - - + -
162A PHE* 3.4 20.0 + - + +
163A LYS 3.3 0.2 - - - -
164A TYR* 1.3 94.3 - - + +
166A GLU* 1.3 64.0 + - - +
168A HIS* 3.4 4.6 + - - +
169A VAL* 2.9 31.0 + - + +
183A ILE* 4.1 36.6 - - + -
186A LEU* 4.7 10.3 - - + -
187A GLU* 5.8 1.6 - - + -
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Residues in contact with GLU 166 (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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14A TYR* 3.6 21.9 - - + -
15A THR* 3.2 38.5 + - - +
18A ILE* 3.2 31.1 - - + +
159A ALA* 3.7 17.7 + - - +
162A PHE 3.2 8.8 + - - +
163A LYS* 3.1 31.2 - - - +
165A ILE* 1.3 80.9 - - - +
167A ARG* 1.3 54.6 + - + +
169A VAL* 3.8 1.2 - - - +
170A ALA* 2.6 41.0 + - + +
236A LYS* 4.5 3.0 + - - -
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Residues in contact with ARG 167 (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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163A LYS* 2.7 56.6 + - + +
164A TYR* 3.0 10.7 + - + +
166A GLU* 1.3 73.2 - - + +
168A HIS* 1.3 64.5 + - + +
170A ALA* 3.1 6.0 + - - +
171A LYS* 2.8 51.6 + - - +
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Residues in contact with HIS 168 (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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164A TYR* 3.2 41.4 + + + +
165A ILE* 3.9 7.4 - - - +
167A ARG* 1.3 84.9 - - + +
169A VAL* 1.3 64.2 + - + +
171A LYS* 3.4 30.2 + - + +
172A TYR* 3.1 32.0 - + + -
177A PHE* 5.5 14.8 - + + -
180A ASN* 4.3 15.4 + - - -
183A ILE* 5.4 8.1 - - + -
216A PRO* 3.9 17.9 + - + +
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Residues in contact with VAL 169 (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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14A TYR* 3.5 35.2 - - + +
125A LEU* 4.0 26.9 - - + -
126A GLY* 5.0 4.0 - - - -
127A LEU* 4.2 13.2 + - + +
154A GLN 4.6 6.7 - - - +
155A THR* 4.4 15.7 - - + -
165A ILE* 2.9 33.8 + - + +
166A GLU 3.8 2.5 - - - +
168A HIS* 1.3 78.1 - - + +
170A ALA* 1.3 63.4 + - - +
171A LYS 3.4 0.2 + - - -
172A TYR* 3.2 23.0 + - - +
183A ILE* 5.7 1.3 - - + -
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Residues in contact with ALA 170 (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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11A ALA* 4.2 19.3 - - + +
14A TYR* 4.1 32.7 - - + -
15A THR* 5.7 2.2 - - - +
127A LEU* 5.2 1.1 - - - -
166A GLU* 2.6 27.0 + - + +
167A ARG* 3.7 6.3 - - - +
169A VAL* 1.3 71.4 - - - +
171A LYS* 1.3 67.1 + - + +
172A TYR 4.8 0.2 - - - -
173A VAL* 3.2 21.3 - - - +
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Residues in contact with LYS 171 (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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11A ALA* 6.0 0.4 - - - -
167A ARG* 2.8 46.7 + - - +
168A HIS* 3.7 30.2 - - + +
169A VAL 3.2 0.2 - - - -
170A ALA* 1.3 78.0 - - - +
172A TYR* 1.3 70.2 + - + +
173A VAL* 3.4 6.8 + - - +
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Residues in contact with TYR 172 (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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126A GLY* 4.1 12.8 - - - -
127A LEU* 3.4 17.8 + - - +
168A HIS* 3.1 31.0 - + + -
169A VAL* 3.2 17.2 + - - +
170A ALA 3.2 0.4 - - - -
171A LYS* 1.3 84.6 - - + +
173A VAL* 1.3 60.0 + - - +
174A ALA 3.6 1.8 - - - +
175A THR* 3.2 37.9 - - - +
177A PHE* 3.3 59.9 - + + -
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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