Contacts of the helix formed by residues 129 - 135 (chain D) in PDB entry 1XVP
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 129 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126D GLY* 4.1 21.1 - - - +
127D THR 3.4 1.2 - - - -
128D MET* 1.3 107.7 - - + +
130D GLU* 1.3 72.6 + - - +
131D GLN 3.0 5.7 + - - -
132D PHE* 3.4 29.5 + + - +
168D MET* 4.1 9.4 - - - -
205D VAL* 3.1 33.4 - - + -
206D LEU* 3.2 36.6 - - + -
208D THR* 4.7 1.6 - - - -
209D THR* 3.5 23.8 - - + -
219D CYS* 3.2 32.1 - - + +
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Residues in contact with GLU 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D GLY 4.4 4.0 - - - +
127D THR* 3.4 25.6 - - - +
128D MET 3.6 0.2 - - - -
129D PHE* 1.3 86.7 - - - +
131D GLN* 1.3 58.5 + - + +
132D PHE 3.2 0.9 - - - -
133D VAL* 3.1 31.6 - - - +
134D GLN* 4.5 1.0 + - - -
219D CYS* 4.1 7.4 - - - -
220D GLY* 4.3 20.9 + - - -
221D PRO* 4.8 1.9 - - + +
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Residues in contact with GLN 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D THR* 3.9 12.4 + - - +
128D MET* 3.5 25.4 - - - +
129D PHE 3.0 0.8 - - - -
130D GLU* 1.3 77.4 - - + +
132D PHE* 1.3 59.1 + - - +
133D VAL 3.1 6.4 + - - -
134D GLN* 3.5 38.5 + - - +
135D PHE* 3.0 21.5 - - + -
167D PHE* 3.9 16.7 - - + -
171D GLN* 5.6 1.2 - - - +
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Residues in contact with PHE 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D MET* 3.6 5.4 - - + -
129D PHE* 3.5 43.7 - + - +
130D GLU 3.2 1.8 - - - -
131D GLN* 1.3 75.4 - - - +
133D VAL* 1.3 64.0 + - - +
134D GLN 3.1 3.4 + - - -
135D PHE* 3.5 7.0 + - - -
137D PRO* 3.8 1.9 - - - +
160D HIS* 3.2 24.8 + - - -
164D ILE* 3.3 27.1 - - + -
167D PHE* 3.2 36.8 - + - -
168D MET* 3.8 29.6 - - + -
219D CYS* 3.7 17.9 - - + -
222D LEU* 3.9 7.9 - - + -
224D TYR* 3.4 22.4 - + - +
1003D CID 4.8 7.6 - - - -
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Residues in contact with VAL 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D GLU 3.1 23.1 - - - +
132D PHE* 1.3 78.4 - - - +
134D GLN* 1.3 78.9 + - + +
135D PHE 3.3 0.9 - - - -
136D ARG 4.3 0.3 + - - -
137D PRO* 2.9 29.3 - - + +
142D PHE* 4.8 11.0 - - + -
221D PRO* 3.6 23.3 - - + -
222D LEU* 3.5 19.5 - - + -
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Residues in contact with GLN 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D GLU 4.5 1.0 + - - -
131D GLN* 3.5 51.1 + - - +
132D PHE 3.1 1.4 - - - -
133D VAL* 1.3 98.4 - - + +
135D PHE* 1.3 72.8 + - + +
136D ARG* 3.6 10.3 + - - -
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Residues in contact with PHE 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D GLN* 3.0 27.6 - - + -
132D PHE 3.5 2.6 + - - -
133D VAL 3.3 3.0 - - - -
134D GLN* 1.3 90.7 - - + +
136D ARG* 1.3 88.9 + - - +
137D PRO* 3.3 1.6 - - - -
159D THR* 6.2 0.2 - - - +
160D HIS* 2.8 28.4 + - + +
163D ASP* 4.0 28.5 - - + +
164D ILE* 3.4 20.6 - - + -
167D PHE* 3.8 45.3 - + + -
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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