Contacts of the helix formed by residues 93 - 101 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84L LEU 6.1 0.2 - - - +
85L TYR 6.4 0.2 - - - -
86L GLN 3.6 2.9 - - - +
87L LYS* 3.6 22.6 - - + -
91L GLY 3.6 7.2 - - - +
92L VAL* 1.3 90.2 - - + +
94L PHE* 1.3 67.3 + - - +
95L VAL* 4.2 6.5 - - + +
96L ARG* 2.8 50.1 + - + +
97L THR* 3.1 6.6 + - - -
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Residues in contact with PHE 94 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57L ARG* 3.4 29.6 - - + -
60L ARG* 4.1 7.9 - - + -
61L GLN* 3.8 24.0 - - + -
64L PHE* 3.3 34.5 - + + -
79L PHE* 3.8 10.8 - - + -
83L THR* 3.9 8.7 - - + +
86L GLN* 3.1 49.8 + - + +
87L LYS 3.8 11.0 - - - -
88L ASP* 3.7 28.0 - - + -
92L VAL 3.2 3.1 + - - -
93L PRO* 1.3 70.2 - - - +
95L VAL* 1.3 61.3 + - - +
97L THR* 3.3 7.7 + - - -
98L ILE* 3.1 29.8 + - - +
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Residues in contact with VAL 95 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79L PHE* 4.2 12.3 - - + -
84L LEU* 3.2 51.4 - - + +
93L PRO* 3.0 6.3 - - + -
94L PHE* 1.3 79.2 - - - +
96L ARG* 1.3 63.5 + - - +
98L ILE* 3.4 1.6 + - - +
99L GLN* 2.8 51.4 + - + +
105L VAL* 4.0 14.1 - - + -
141L ASP 3.8 19.5 - - - +
142L GLY* 4.6 0.4 - - - -
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Residues in contact with ARG 96 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92L VAL* 4.1 11.0 - - + +
93L PRO* 2.8 40.9 + - + +
95L VAL* 1.3 79.6 - - - +
97L THR* 1.3 57.6 + - - +
99L GLN* 3.1 16.4 + - - +
100L ASP* 2.8 53.7 + - - +
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Residues in contact with THR 97 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64L PHE* 3.6 24.5 - - + +
65L SER* 5.6 1.1 - - - -
88L ASP* 4.4 7.8 + - - -
92L VAL* 3.7 15.3 + - - +
93L PRO 3.1 8.6 + - - -
94L PHE* 3.5 12.6 - - - -
96L ARG* 1.3 77.7 - - - +
98L ILE* 1.3 67.1 + - + +
100L ASP* 3.0 19.4 + - - +
101L LYS* 3.2 27.1 + - + +
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Residues in contact with ILE 98 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64L PHE* 3.5 44.9 - - + +
77L VAL* 3.9 23.3 - - + -
79L PHE* 4.1 12.1 - - + -
94L PHE 3.1 20.4 + - - +
95L VAL 3.9 2.2 - - - +
97L THR* 1.3 80.7 - - + +
99L GLN* 1.3 63.5 + - - +
101L LYS* 3.2 13.3 + - + +
103L ILE* 3.2 55.8 + - + +
104L VAL 4.2 1.3 - - - +
105L VAL* 3.9 14.1 - - + -
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Residues in contact with GLN 99 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95L VAL* 2.8 36.8 + - - +
96L ARG* 3.3 17.0 - - - +
98L ILE* 1.3 78.1 - - - +
100L ASP* 1.3 61.3 + - - +
102L GLY* 2.8 22.2 + - - -
103L ILE 3.9 7.1 - - - +
105L VAL* 3.7 15.2 - - + +
141L ASP 5.4 0.2 - - - +
142L GLY* 3.7 30.7 + - - -
144L ASP* 5.5 1.2 + - - -
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Residues in contact with ASP 100 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71L LYS* 5.4 1.9 + - - -
96L ARG* 2.8 44.6 + - - +
97L THR* 3.0 10.0 + - - +
99L GLN* 1.3 70.0 - - - +
101L LYS* 1.3 59.2 + - + +
102L GLY* 3.0 9.4 + - - -
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Residues in contact with LYS 101 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64L PHE 4.4 3.8 - - - -
66L ALA 3.0 29.5 + - - -
67L ASP* 3.5 9.8 - - - +
68L ASP* 3.4 24.9 + - - +
70L VAL* 4.0 21.1 - - + -
71L LYS* 3.3 38.8 - - + +
97L THR* 3.2 27.8 + - + +
98L ILE* 3.7 10.8 - - + +
99L GLN 3.2 1.2 - - - -
100L ASP* 1.3 76.0 - - + +
102L GLY* 1.3 61.0 + - - +
103L ILE* 3.4 12.4 + - + +
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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