Contacts of the strand formed by residues 104 - 108 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ILE* 4.2 4.5 - - + +
22C ARG* 3.8 39.5 - - + +
23C ILE* 3.7 23.6 - - + -
75C GLY 2.9 19.8 + - - +
76C GLY* 3.2 1.4 - - - -
77C VAL 2.9 27.2 + - - -
98C ILE* 4.2 1.8 - - - +
102C GLY 4.8 0.4 - - - +
103C ILE* 1.3 74.3 - - - +
105C VAL* 1.3 63.0 + - - +
144C ASP* 3.8 26.7 - - + +
145C PHE* 3.6 21.7 - - + -
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Residues in contact with VAL 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C VAL 3.8 2.2 - - - -
79C PHE* 3.6 25.1 - - + -
84C LEU* 3.9 19.7 - - + -
95C VAL* 4.0 11.9 - - + +
98C ILE* 3.9 16.2 - - + -
99C GLN* 3.7 30.3 - - + -
103C ILE 4.3 1.1 - - - +
104C VAL* 1.3 75.3 - - - +
106C GLY* 1.3 63.3 + - - +
142C GLY 3.3 18.9 + - - +
143C ALA* 4.0 4.5 - - - -
144C ASP* 2.8 29.9 + - - -
145C PHE* 3.2 9.9 - - - -
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Residues in contact with GLY 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C VAL 2.9 11.5 + - - -
78C ILE* 4.1 3.4 - - - -
79C PHE* 2.6 38.5 + - - +
105C VAL* 1.3 78.0 - - - +
107C ILE* 1.3 59.1 + - - -
145C PHE* 2.9 28.4 - - - -
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Residues in contact with ILE 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C ILE* 4.3 3.6 - - - +
79C PHE* 3.4 17.3 - - + +
81C HIS* 4.1 17.3 - - - +
84C LEU* 4.1 21.5 - - + -
106C GLY* 1.3 75.1 - - - +
108C LYS* 1.3 71.2 + - - +
109C VAL* 3.5 1.5 + - + +
135C CYS* 6.5 0.2 - - - -
138C TYR* 3.8 36.3 - - + -
143C ALA* 3.6 24.7 - - + -
145C PHE 3.2 17.3 + - - +
146C ALA* 3.2 17.7 - - + +
147C LYS 3.0 20.5 + - - -
183C ILE* 4.8 4.5 - - + -
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Residues in contact with LYS 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C ASP* 3.5 52.6 + - + +
35C GLU* 5.1 0.4 - - - +
36C SER* 4.2 20.2 + - - +
39C SER* 5.3 0.8 + - - -
78C ILE* 4.1 1.4 - - - +
79C PHE 3.2 8.7 + - - +
80C PHE* 4.7 13.5 - - + -
81C HIS* 5.0 5.4 + - - +
107C ILE* 1.3 80.7 - - - +
109C VAL* 1.3 61.2 + - - +
110C ASP* 3.5 39.2 - - - +
134C ARG* 4.5 4.0 + - - -
138C TYR* 4.9 2.1 + - - -
147C LYS* 3.4 18.3 - - + +
149C ARG* 5.7 3.1 - - - +
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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