Contacts of the helix formed by residues 88 - 97 (chain D) in PDB entry 1YXU
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 MET 88 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76D ASP* 3.2 39.0 + - + +
77D TRP* 3.1 29.9 - - - +
78D GLY* 4.0 9.4 - - - -
86D VAL 3.4 2.7 + - - -
87D PRO* 1.3 71.6 - - - +
89D GLU* 1.3 62.7 + - - +
91D VAL* 3.1 14.6 + - + +
92D LEU* 2.9 60.7 + - + +
190D GLY 3.8 13.2 - - - +
191D ALA* 4.6 1.3 - - - -
192D LEU* 4.5 24.0 - - + +
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Residues in contact with GLU 89 (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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49D PHE 5.2 0.2 - - - +
67D LYS* 2.5 40.2 + - - +
69D VAL* 4.3 12.1 - - - +
87D PRO* 3.0 9.0 - - + +
88D MET* 1.3 77.9 - - - +
90D VAL* 1.3 62.9 + - - +
92D LEU* 3.3 2.4 + - - +
93D LEU* 3.1 37.6 + - + +
118D LEU* 3.9 17.6 - - + +
120D LEU* 5.6 0.2 - - - +
187D PHE* 3.8 17.0 + - + +
188D GLY* 3.7 32.9 + - - +
850D AMP 3.4 6.9 + - - -
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Residues in contact with VAL 90 (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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80D LEU* 4.6 3.6 - - + -
86D VAL* 4.1 17.9 - - + -
87D PRO* 2.9 26.9 + - + +
89D GLU* 1.3 77.1 - - - +
91D VAL* 1.3 62.6 + - - +
92D LEU 3.3 0.2 + - - -
93D LEU* 3.3 3.7 + - - +
94D LYS* 3.1 28.0 + - + +
106D LEU* 4.3 10.1 - - + -
109D TRP* 3.9 40.2 - - + +
116D PHE* 5.2 0.4 - - + -
118D LEU* 3.9 33.9 - - + -
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Residues in contact with VAL 91 (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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78D GLY* 4.1 6.1 - - - -
79D GLU 3.9 34.3 - - - +
80D LEU* 4.3 4.0 - - + +
81D PRO* 6.0 2.9 - - + -
86D VAL* 3.7 24.9 - - + -
87D PRO 3.4 5.1 + - - +
88D MET* 3.1 22.9 + - + +
90D VAL* 1.3 78.0 - - - +
92D LEU* 1.3 61.5 + - - +
94D LYS* 3.6 8.5 + - - +
95D LYS* 3.3 36.5 + - + +
192D LEU* 5.0 8.5 - - + -
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Residues in contact with LEU 92 (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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88D MET* 2.9 39.3 + - + +
89D GLU 3.8 4.0 - - - +
91D VAL* 1.3 77.8 - - + +
93D LEU* 1.3 61.6 + - - +
95D LYS* 3.2 5.2 + - - +
96D VAL* 3.1 26.6 + - - +
163D VAL* 3.7 27.9 - - + +
187D PHE* 3.5 29.8 - - + +
190D GLY* 3.4 34.1 - - - +
191D ALA 3.5 22.4 - - - +
192D LEU* 4.0 10.8 - - + +
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Residues in contact with LEU 93 (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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89D GLU* 3.1 31.4 + - + +
90D VAL 3.7 3.6 - - - +
92D LEU* 1.3 75.3 - - - +
94D LYS* 1.3 63.4 + - - +
96D VAL* 3.3 8.5 + - + +
97D SER* 3.2 24.6 + - - -
104D ILE* 3.7 39.3 - - + +
106D LEU* 3.8 32.9 + - + +
118D LEU* 3.8 27.8 - - + -
120D LEU* 4.0 11.9 - - + -
187D PHE* 4.0 19.3 - - + -
850D AMP 5.9 0.4 - - - +
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Residues in contact with LYS 94 (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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80D LEU* 3.6 34.2 - - + +
81D PRO* 4.4 20.3 - - + +
82D ASN* 4.9 5.1 - - - +
90D VAL* 3.1 18.1 + - + +
91D VAL* 3.9 6.5 - - - +
93D LEU* 1.3 76.7 - - - +
95D LYS* 1.3 61.7 - - + +
96D VAL 3.5 0.2 + - - -
97D SER* 3.5 18.9 + - - +
106D LEU* 4.5 11.4 - - + -
109D TRP* 3.9 22.7 - - - +
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Residues in contact with LYS 95 (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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81D PRO* 6.2 4.0 - - + -
91D VAL* 3.3 22.8 + - + +
92D LEU* 3.2 10.0 + - - +
93D LEU 3.2 0.6 - - - -
94D LYS* 1.3 80.6 - - + +
96D VAL* 1.3 59.2 + - - +
97D SER 3.8 1.7 + - - +
161D CYS* 2.8 47.5 + - - +
162D GLY* 4.1 7.0 - - - -
163D VAL* 3.8 11.4 - - + -
192D LEU* 3.6 32.8 - - + -
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Residues in contact with VAL 96 (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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92D LEU 3.1 13.4 + - - +
93D LEU* 3.5 17.5 - - - +
95D LYS* 1.3 79.1 - - - +
97D SER* 1.3 59.2 + - - +
98D SER* 3.6 1.9 + - - -
100D PHE* 5.6 1.7 - - - +
103D VAL* 3.6 33.1 - - + +
104D ILE 4.5 6.5 - - - +
157D HIS* 2.9 30.5 + - + -
158D CYS* 4.0 35.0 - - - -
161D CYS* 4.0 3.4 - - + -
163D VAL* 4.0 16.2 - - + -
187D PHE* 4.2 8.5 - - + -
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Residues in contact with SER 97 (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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93D LEU 3.2 14.6 + - - -
94D LYS* 3.5 13.6 + - - +
95D LYS 3.6 3.5 - - - +
96D VAL* 1.3 74.3 - - - +
98D SER* 1.3 64.5 + - - +
104D ILE 5.4 0.9 - - - -
105D ARG* 3.9 40.2 + - - +
106D LEU* 5.0 5.2 - - - -
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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