Contacts of the strand formed by residues 104 - 108 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ILE* 4.2 4.5 - - + +
22B ARG* 3.8 38.6 - - + +
23B ILE* 3.7 23.6 - - + -
75B GLY 2.9 20.3 + - - +
76B GLY* 3.2 1.4 - - - -
77B VAL 2.9 27.2 + - - -
98B ILE* 4.2 1.6 - - - +
102B GLY 4.8 0.7 - - - +
103B ILE* 1.3 74.2 - - - +
105B VAL* 1.3 63.1 + - - +
144B ASP* 3.8 26.5 - - + +
145B PHE* 3.6 21.3 - - + -
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Residues in contact with VAL 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B VAL 3.8 2.5 - - - -
79B PHE* 3.6 24.9 - - + -
84B LEU* 3.9 19.7 - - + -
95B VAL* 4.0 12.1 - - + +
98B ILE* 3.9 16.4 - - + -
99B GLN* 3.7 29.8 - - + -
103B ILE 4.3 0.7 - - - +
104B VAL* 1.3 76.8 - - - +
106B GLY* 1.3 63.0 + - - +
142B GLY 3.3 18.9 + - - +
143B ALA* 4.0 4.3 - - - -
144B ASP* 2.8 29.7 + - - -
145B PHE* 3.2 10.1 - - - -
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Residues in contact with GLY 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B VAL 2.9 11.4 + - - -
78B ILE* 4.1 4.3 - - - -
79B PHE* 2.6 38.8 + - - +
105B VAL* 1.3 76.9 - - - +
107B ILE* 1.3 59.8 + - - -
143B ALA* 4.4 0.2 - - - -
145B PHE* 2.9 28.7 - - - -
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Residues in contact with ILE 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ILE* 4.3 3.6 - - - +
79B PHE* 3.4 17.7 - - + +
81B HIS* 4.1 17.7 - - - +
84B LEU* 4.1 21.3 - - + -
106B GLY* 1.3 75.7 - - - +
108B LYS* 1.3 71.1 + - - +
109B VAL* 3.5 1.3 + - + -
138B TYR* 3.8 36.3 - - + -
143B ALA* 3.6 24.0 - - + -
145B PHE 3.2 17.2 + - - +
146B ALA* 3.2 18.1 - - + +
147B LYS 3.0 20.5 + - - -
183B ILE* 4.8 4.7 - - + -
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Residues in contact with LYS 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ASP* 3.5 52.4 + - + +
35B GLU* 5.1 0.6 - - - +
36B SER* 4.2 20.6 + - - +
39B SER* 5.3 0.8 + - - -
78B ILE* 4.1 1.4 - - - +
79B PHE 3.2 8.9 + - - +
80B PHE* 4.7 13.0 - - + -
81B HIS* 5.0 5.2 + - - +
107B ILE* 1.3 80.5 - - - +
109B VAL* 1.3 60.5 + - - +
110B ASP* 3.5 37.7 - - - +
134B ARG* 4.5 4.0 + - - -
138B TYR* 4.9 2.3 + - - -
147B LYS* 3.4 18.3 - - + +
149B 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