Contacts of the strand formed by residues 104 - 108 (chain I) 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 VAL 104 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19I ILE* 4.2 3.8 - - + +
22I ARG* 3.8 38.8 - - + +
23I ILE* 3.7 24.0 - - + -
75I GLY 2.9 19.5 + - - +
76I GLY* 3.2 1.9 - - - -
77I VAL* 2.9 27.2 + - - -
98I ILE* 4.2 1.1 - - - +
102I GLY 4.8 0.4 - - - +
103I ILE* 1.3 75.3 - - - +
105I VAL* 1.3 63.3 + - - +
144I ASP* 3.8 26.9 - - + +
145I PHE* 3.6 22.0 - - + -
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Residues in contact with VAL 105 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77I VAL 3.8 2.0 - - - -
79I PHE* 3.6 24.5 - - + -
84I LEU* 3.9 20.6 - - + -
95I VAL* 4.0 11.2 - - + +
98I ILE* 3.9 16.6 - - + -
99I GLN* 3.7 30.3 - - + -
103I ILE 4.3 0.9 - - - +
104I VAL* 1.3 76.0 - - - +
106I GLY* 1.3 62.0 + - - +
142I GLY 3.3 18.9 + - - +
143I ALA* 4.2 4.0 - - - -
144I ASP* 2.8 30.1 + - - -
145I PHE* 3.2 10.3 - - - -
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Residues in contact with GLY 106 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77I VAL 2.9 11.3 + - - -
78I ILE* 4.1 3.4 - - - -
79I PHE* 2.6 38.3 + - - +
105I VAL* 1.3 78.8 - - - +
107I ILE* 1.3 59.8 + - - +
143I ALA* 4.4 0.2 - - - -
145I PHE* 2.9 27.6 - - - -
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Residues in contact with ILE 107 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78I ILE* 4.3 3.8 - - - +
79I PHE* 3.4 17.5 - - + +
81I HIS* 4.1 17.9 - - - +
84I LEU* 4.1 20.9 - - + -
106I GLY* 1.3 76.0 - - - +
108I LYS* 1.3 69.1 + - - +
109I VAL* 4.3 1.1 - - + -
138I TYR* 3.8 37.5 - - + -
143I ALA* 3.6 24.0 - - + -
145I PHE 3.2 17.1 + - - +
146I ALA* 3.2 18.3 - - + +
147I LYS 3.0 20.8 + - - -
183I ILE* 4.8 4.5 - - + -
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Residues in contact with LYS 108 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I ASP* 3.5 52.4 + - + +
35I GLU* 5.1 1.0 - - - +
36I SER* 4.2 20.2 + - - +
39I SER* 5.3 0.8 + - - -
78I ILE* 4.1 1.6 - - - +
79I PHE 3.2 8.5 + - - +
80I PHE* 4.7 15.0 - - + -
81I HIS* 5.0 5.5 + - - +
107I ILE* 1.3 80.3 - - - +
109I VAL* 1.3 60.7 + - - +
110I ASP* 3.5 37.9 - - - +
134I ARG* 4.5 3.1 + - - -
138I TYR* 4.9 2.4 + - - -
147I LYS* 3.5 19.2 - - + +
149I ARG* 5.7 3.4 - - - +
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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