Contacts of the strand formed by residues 98 - 104 (chain C) in PDB entry 1AXC
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 THR 98 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91C ARG 4.9 0.2 - - - +
92C ALA* 4.2 12.1 - - - +
96C ALA* 3.2 19.8 - - - +
97C ASP* 1.3 94.0 + - + +
99C LEU* 1.3 61.3 + - - +
100C ALA 4.5 0.2 + - - -
115C GLU* 3.9 33.2 - - + +
116C MET 3.3 13.2 - - - +
117C LYS* 4.0 15.3 - - + +
118C LEU* 3.8 10.2 - - - +
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Residues in contact with LEU 99 (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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2C PHE* 4.6 2.2 - - + -
68C MET* 3.9 33.0 - - + -
70C VAL* 5.0 1.8 - - + -
75C MET* 4.1 22.2 - - + -
90C LEU* 4.5 13.7 - - + -
91C ARG 4.0 15.3 - - - +
92C ALA* 4.1 5.6 - - + -
98C THR* 1.3 74.8 - - - +
100C ALA* 1.3 70.0 + - - +
101C LEU* 3.9 14.4 - - + +
115C GLU* 3.5 2.8 - - - +
116C MET* 2.7 59.1 + - + +
118C LEU* 3.7 16.6 - - + +
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Residues in contact with ALA 100 (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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89C THR 3.5 1.4 - - - +
90C LEU* 3.4 4.9 - - - -
91C ARG* 2.9 65.2 + - + +
98C THR 4.3 0.4 + - - -
99C LEU* 1.3 74.6 - - - +
101C LEU* 1.3 62.5 + - - +
102C VAL* 5.2 1.3 - - + +
113C ASP* 4.9 7.0 - - - +
114C TYR 3.4 9.2 - - - +
115C GLU* 4.5 8.3 - - + +
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Residues in contact with LEU 101 (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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75C MET* 4.3 16.6 - - + -
78C ILE* 3.7 31.4 - - + -
79C LEU* 4.2 21.8 - - + -
88C ILE* 5.0 0.4 - - + -
89C THR 3.4 5.8 - - - +
90C LEU* 3.8 24.0 - - + -
99C LEU* 3.9 21.5 - - + +
100C ALA* 1.3 77.1 - - - +
102C VAL* 1.3 62.8 + - - +
103C PHE* 3.8 14.6 - - + -
112C SER 3.8 0.9 - - - +
113C ASP* 3.6 1.4 - - - -
114C TYR* 2.9 39.7 + - + +
116C MET* 4.1 16.6 - - + -
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Residues in contact with VAL 102 (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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87C ILE 3.2 5.9 - - - +
88C ILE* 3.6 0.9 - - - -
89C THR* 2.9 43.8 + - - +
91C ARG* 3.9 25.4 - - + +
100C ALA 5.2 2.0 - - - +
101C LEU* 1.3 74.1 - - - +
103C PHE* 1.3 63.9 + - - +
104C GLU* 4.3 17.1 - - + +
111C VAL* 4.2 19.3 - - + -
112C SER 3.2 8.3 - - - +
113C ASP* 3.4 27.1 - - + +
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Residues in contact with PHE 103 (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* 3.4 41.3 - - + -
79C LEU* 4.1 8.5 - - + -
81C CYS 3.9 5.2 - - - -
82C ALA* 3.7 31.4 - - + -
86C ASP* 3.6 18.4 - - + +
87C ILE 3.6 3.1 - - - -
88C ILE* 3.9 25.4 - - + -
101C LEU* 3.8 19.5 - - + -
102C VAL* 1.3 77.8 - - - +
104C GLU* 1.3 62.9 + - - +
105C ALA 4.0 0.2 - - - -
110C LYS 4.0 1.0 - - - +
111C VAL* 3.4 5.0 - - - +
112C SER* 2.7 45.0 + - - +
114C TYR* 3.4 32.8 - + - -
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Residues in contact with GLU 104 (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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5C ARG* 4.0 23.9 + - - -
86C ASP* 3.3 5.8 - - - -
87C ILE* 3.1 50.2 + - + +
89C THR* 4.5 7.3 + - - -
102C VAL* 4.3 18.1 - - + +
103C PHE* 1.3 77.4 - - - +
105C ALA* 1.3 68.9 + - - +
106C PRO* 3.4 1.0 - - - +
110C LYS 3.8 4.0 - - - -
111C VAL* 4.4 14.6 - - + -
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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