Contacts of the helix formed by residues 86 - 95 (chain A) in PDB entry 1XR2
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 GLY 86 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A TYR* 3.5 29.4 - - - -
85A ARG* 1.3 80.4 - - - +
87A LEU* 1.3 54.2 + - - -
88A SER 3.1 2.2 - - - -
89A THR* 2.9 4.3 + - - -
90A TYR* 2.8 31.9 + - - +
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Residues in contact with LEU 87 (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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24A PHE* 4.8 5.8 - - + -
31A GLU* 3.2 43.2 + - + +
34A PHE* 4.0 23.1 - - + -
35A GLU* 5.0 4.0 - - + +
63A TYR* 3.8 24.9 - - + -
86A GLY* 1.3 70.1 - - - -
88A SER* 1.3 64.9 + - - +
90A TYR* 3.4 16.3 - - + +
91A PHE* 2.9 65.3 + - + -
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Residues in contact with SER 88 (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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24A PHE* 6.2 1.5 - - - -
31A GLU* 5.6 0.6 + - - -
85A ARG* 3.5 26.5 + - - +
87A LEU* 1.3 79.5 - - - +
89A THR* 1.3 63.3 + - - +
91A PHE* 4.1 3.4 - - - +
92A ASP* 2.4 36.7 + - - +
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Residues in contact with THR 89 (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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77A VAL* 4.6 1.6 - - + -
81A PHE* 4.0 31.9 + - + +
83A GLU 3.6 4.0 + - - -
84A TYR* 3.4 31.6 - - + -
85A ARG* 2.7 29.8 + - - +
86A GLY 2.9 7.0 + - - -
88A SER* 1.3 76.5 + - - +
90A TYR* 1.3 67.0 + - - +
92A ASP* 3.0 19.1 + - - +
93A MET* 3.0 18.6 + - - +
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Residues in contact with TYR 90 (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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62A SER* 3.0 17.2 + - - -
63A TYR* 3.7 13.9 + + + -
64A TYR* 3.2 32.5 + - + -
65A ASP 3.2 8.0 + - - -
68A LEU* 3.5 24.9 - - + +
69A ASP* 2.7 32.4 + - - -
72A VAL* 4.4 6.3 - - + -
84A TYR* 3.7 22.4 - - - +
86A GLY 2.8 16.8 + - - +
87A LEU* 3.4 22.0 - - + +
89A THR* 1.3 72.1 - - - +
91A PHE* 1.3 74.3 + + - +
93A MET* 2.9 25.8 + - - +
94A ALA* 3.1 10.7 + - - +
128A LYS* 5.6 5.4 - - - -
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Residues in contact with PHE 91 (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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21A LEU* 3.8 22.2 - - + -
24A PHE* 3.7 33.9 - + - -
25A TRP* 3.5 34.8 - + + +
34A PHE* 4.3 7.4 - + - -
63A TYR* 3.6 21.8 - - + -
64A TYR* 4.3 7.4 - + - -
87A LEU* 2.9 49.5 + - + +
88A SER* 4.2 3.4 - - - +
90A TYR* 1.3 88.8 - + - +
92A ASP* 1.3 57.3 + - - +
94A ALA* 3.7 2.7 - - - -
95A ARG* 2.8 39.6 + - + +
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Residues in contact with ASP 92 (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 PHE* 3.6 18.1 - - + -
88A SER* 2.4 30.9 + - - +
89A THR* 3.0 12.6 + - + +
91A PHE* 1.3 74.7 - - - +
93A MET* 1.3 62.4 - - - +
95A ARG 2.8 19.6 - - - +
98A LYS* 4.0 3.6 + - + +
99A ALA* 3.5 12.5 + - - -
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Residues in contact with MET 93 (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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68A LEU* 3.8 29.8 - - + -
71A ALA* 5.4 1.3 - - + -
72A VAL* 4.4 6.3 - - + -
76A ALA 3.8 12.8 - - - +
77A VAL* 3.9 19.7 - - + -
78A PRO* 3.8 28.3 - - + -
81A PHE* 3.6 30.1 - - + -
84A TYR* 4.3 17.3 - - - -
89A THR* 3.0 17.0 + - + +
90A TYR* 2.9 9.3 + - - +
92A ASP* 1.3 78.0 - - - +
94A ALA* 1.3 58.4 + - - +
99A ALA* 3.2 2.4 - - - +
100A LEU* 2.7 43.0 + - + +
113A LEU* 4.3 2.1 - - - +
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Residues in contact with ALA 94 (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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64A TYR* 3.5 52.8 + - + -
68A LEU* 4.1 2.2 - - + -
90A TYR 3.1 13.0 + - - +
91A PHE* 3.8 7.4 - - + +
92A ASP 3.2 0.2 - - - -
93A MET* 1.3 79.4 - - - +
95A ARG* 1.3 60.3 + - + +
99A ALA* 3.7 6.2 - - - +
102A MET* 4.9 2.6 - - - +
113A LEU* 3.4 26.9 - - + +
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Residues in contact with ARG 95 (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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25A TRP* 3.3 78.2 - - - +
64A TYR* 4.2 11.8 + - - +
91A PHE* 2.8 28.8 + - + +
92A ASP* 2.8 23.0 - - - +
93A MET 3.6 0.4 - - - -
94A ALA* 1.3 77.4 - - - +
96A GLY* 1.3 63.4 + - - +
99A ALA* 3.6 7.0 - - - -
493A ARG* 5.8 4.0 - - - +
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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