Contacts of the helix formed by residues 93 - 101 (chain H) in PDB entry 1XFB
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 PRO 93 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84H LEU 6.1 0.2 - - - +
85H TYR 6.4 0.4 - - - -
86H GLN 3.6 2.7 - - - +
87H LYS* 3.6 23.1 - - + -
91H GLY 3.6 7.4 - - - +
92H VAL* 1.3 90.1 - - + +
94H PHE* 1.3 67.5 + - - +
95H VAL* 4.2 7.2 - - + +
96H ARG* 2.8 49.6 + - + +
97H THR* 3.1 6.1 + - - -
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Residues in contact with PHE 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57H ARG* 3.4 28.7 - - + -
60H ARG* 4.1 6.7 - - + -
61H GLN* 3.8 24.2 - - + -
64H PHE* 3.3 35.4 - + + -
79H PHE* 3.8 10.5 - - + -
83H THR* 3.9 8.3 - - + +
86H GLN* 3.1 49.4 + - + +
87H LYS 3.8 10.5 - - - -
88H ASP* 3.7 28.5 - - + -
92H VAL 3.2 2.4 + - - -
93H PRO* 1.3 71.9 - - - +
95H VAL* 1.3 63.2 + - - +
97H THR* 3.3 7.1 + - - -
98H ILE* 3.1 30.4 + - - +
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Residues in contact with VAL 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H PHE* 4.2 12.3 - - + -
84H LEU* 3.2 52.3 - - + +
86H GLN 5.9 0.2 - - - +
93H PRO* 3.0 6.9 - - + -
94H PHE* 1.3 77.8 - - - +
96H ARG* 1.3 62.6 + - - +
98H ILE* 3.4 1.4 + - - +
99H GLN* 2.8 51.6 + - + +
105H VAL* 4.0 13.5 - - + -
141H ASP 3.8 19.3 - - - +
142H GLY* 4.6 0.7 - - - -
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Residues in contact with ARG 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92H VAL* 4.1 11.4 - - + +
93H PRO* 2.8 40.5 + - + +
95H VAL* 1.3 78.2 - - - +
97H THR* 1.3 58.2 + - - +
99H GLN* 3.1 17.0 + - - +
100H ASP* 2.8 54.0 + - - +
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Residues in contact with THR 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64H PHE* 3.6 25.4 - - - +
65H SER* 5.6 1.6 - - - -
88H ASP* 4.4 7.8 + - - +
92H VAL* 3.7 15.9 + - - +
93H PRO 3.1 8.6 + - - -
94H PHE* 3.5 12.9 - - - -
96H ARG* 1.3 77.9 - - - +
98H ILE* 1.3 66.8 + - + +
100H ASP* 3.0 19.0 + - - +
101H LYS* 3.2 27.1 + - - +
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Residues in contact with ILE 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64H PHE* 3.5 44.9 - - + +
77H VAL* 3.9 23.3 - - + -
79H PHE* 4.1 11.4 - - + -
94H PHE 3.1 20.7 + - - +
95H VAL 3.9 2.7 - - - +
97H THR* 1.3 81.6 - - + +
99H GLN* 1.3 63.3 + - - +
101H LYS* 3.2 12.8 + - + +
103H ILE* 3.2 54.8 + - + +
104H VAL 4.2 1.3 - - - +
105H VAL* 3.9 15.0 - - + -
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Residues in contact with GLN 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95H VAL* 2.8 36.3 + - - +
96H ARG* 3.1 16.7 + - - +
98H ILE* 1.3 78.7 - - - +
100H ASP* 1.3 60.5 + - - +
102H GLY* 2.8 22.5 + - - -
103H ILE 3.9 7.6 - - - +
105H VAL* 3.7 14.6 - - + -
141H ASP 5.4 0.2 - - - +
142H GLY* 3.7 30.7 + - - -
144H ASP* 5.5 1.2 + - - -
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Residues in contact with ASP 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71H LYS* 5.4 1.9 + - - -
96H ARG* 2.8 45.9 + - - +
97H THR* 3.0 10.3 + - - +
99H GLN* 1.3 70.2 - - - +
101H LYS* 1.3 58.5 + - + +
102H GLY* 3.0 9.2 + - - -
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Residues in contact with LYS 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64H PHE 4.4 3.8 - - - -
66H ALA 3.0 28.9 + - - -
67H ASP* 3.5 10.6 - - - +
68H ASP* 3.4 25.0 + - - +
70H VAL* 4.0 20.6 - - + -
71H LYS* 3.3 40.3 - - + +
97H THR* 3.2 28.4 + - - +
98H ILE* 3.7 10.3 - - - +
99H GLN 3.2 1.0 - - - -
100H ASP* 1.3 75.7 - - + +
102H GLY* 1.3 61.7 + - - +
103H ILE* 3.2 13.0 + - + +
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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
------------------------------------------------------------
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