Contacts of the strand formed by residues 104 - 108 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ILE* 4.2 4.3 - - + +
22A ARG* 3.8 40.2 - - + +
23A ILE* 3.7 24.7 - - + -
75A GLY 2.9 19.9 + - - +
76A GLY* 3.2 1.9 - - - -
77A VAL* 2.9 26.9 + - - -
98A ILE* 4.2 1.3 - - - +
102A GLY 4.8 0.2 - - - +
103A ILE* 1.3 74.8 - - - +
105A VAL* 1.3 63.3 + - - +
144A ASP* 3.8 26.7 - - + +
145A PHE* 3.6 22.2 - - + -
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Residues in contact with VAL 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A VAL 3.8 2.0 - - - -
79A PHE* 3.6 24.9 - - + -
84A LEU* 3.9 20.4 - - + -
95A VAL* 4.0 11.4 - - + +
98A ILE* 3.9 17.0 - - + -
99A GLN* 3.7 30.3 - - + -
103A ILE 4.3 0.9 - - - +
104A VAL* 1.3 76.5 - - - +
106A GLY* 1.3 62.0 + - - +
142A GLY 3.3 19.1 + - - +
143A ALA* 4.0 3.6 - - - -
144A ASP* 2.8 29.7 + - - -
145A PHE* 3.2 10.4 - - - -
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Residues in contact with GLY 106 (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 2.9 11.7 + - - -
78A ILE* 4.1 3.6 - - - -
79A PHE* 2.6 38.3 + - - +
105A VAL* 1.3 77.7 - - - +
107A ILE* 1.3 59.4 + - - -
143A ALA* 4.4 0.2 - - - -
145A PHE* 2.9 28.7 - - - -
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Residues in contact with ILE 107 (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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78A ILE* 4.3 4.0 - - - +
79A PHE* 3.4 17.3 - - + +
81A HIS* 4.1 17.0 - - - +
84A LEU* 4.1 21.3 - - + -
106A GLY* 1.3 75.3 - - - +
108A LYS* 1.3 71.1 + - - +
109A VAL* 3.6 1.5 - - + +
135A CYS* 6.5 0.2 - - - -
138A TYR* 3.8 35.9 - - + -
143A ALA* 3.6 24.5 - - + -
145A PHE 3.2 17.4 + - - +
146A ALA* 3.2 17.7 - - + +
147A LYS 3.0 20.3 + - - -
183A ILE* 4.8 4.7 - - + -
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Residues in contact with LYS 108 (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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34A ASP* 3.5 53.9 + - + +
35A GLU* 5.1 0.6 - - - +
36A SER* 4.2 20.4 + - - +
39A SER* 5.3 0.6 + - - -
78A ILE* 4.1 1.8 - - - +
79A PHE 3.2 8.5 + - - +
80A PHE* 4.7 13.2 - - + -
81A HIS* 5.0 5.9 + - - +
107A ILE* 1.3 80.8 - - - +
109A VAL* 1.3 59.0 + - - +
110A ASP* 3.5 39.2 - - - +
134A ARG* 4.5 3.5 + - - -
138A TYR* 4.9 2.1 + - - -
147A LYS* 3.4 19.0 - - + +
149A ARG* 5.7 3.6 - - - +
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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