Contacts of the helix formed by residues 93 - 103 (chain C) in PDB entry 4U9W
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 LYS 93 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85C TYR* 5.5 0.4 - - - -
90C TRP 5.6 2.5 - - - +
91C GLY 3.7 5.5 + - - +
92C TRP* 1.3 75.6 - - - +
94C ASP* 1.3 66.1 + - - +
95C ARG 3.3 1.5 + - - +
96C GLU* 3.3 17.9 + - + +
97C LYS* 3.0 25.0 + - - +
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Residues in contact with ASP 94 (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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74C PHE* 3.6 18.8 - - + -
78C LYS* 3.0 25.8 + - - +
92C TRP* 2.5 39.7 + - - +
93C LYS* 1.3 70.5 - - - +
95C ARG* 1.3 57.7 + - + +
97C LYS 3.5 0.2 + - - -
98C ARG* 3.0 39.9 + - - +
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Residues in contact with ARG 95 (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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93C LYS* 3.3 1.2 - - + +
94C ASP* 1.3 79.7 - - + +
96C GLU* 1.3 76.6 + - - +
98C ARG* 3.3 6.6 + - - +
99C GLU* 2.8 65.3 + - + +
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Residues in contact with GLU 96 (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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93C LYS* 3.3 20.5 + - + +
95C ARG* 1.3 92.2 - - - +
97C LYS* 1.3 56.5 + - - +
99C GLU* 3.6 15.4 - - - +
100C GLU* 3.2 24.3 + - - +
303C GOL 6.0 2.2 - - - -
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Residues in contact with LYS 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C PHE* 3.7 13.2 - - + -
77C THR* 5.0 1.6 - - + -
85C TYR* 2.8 35.3 + - - -
92C TRP* 3.6 29.8 - - + -
93C LYS 3.0 18.3 + - - +
94C ASP 3.8 2.7 - - - +
96C GLU* 1.3 77.1 - - - +
98C ARG* 1.3 59.4 + - - +
99C GLU 3.2 0.2 - - - -
100C GLU* 2.8 25.7 + - - +
101C MET* 2.9 44.7 + - + +
139C GLU* 3.2 16.1 + - - +
303C GOL 2.8 25.0 + - - +
2G GLY* 3.8 2.2 - - - -
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Residues in contact with ARG 98 (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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70C VAL* 6.3 0.7 - - + -
71C ASP* 3.6 22.6 + - - +
74C PHE* 3.4 56.5 - - + +
75C ASP* 4.9 3.4 + - - -
94C ASP* 3.0 26.9 + - - +
95C ARG* 3.3 6.8 + - - +
97C LYS* 1.3 76.2 - - - +
99C GLU* 1.3 55.8 + - - +
101C MET* 3.3 2.7 + - - -
102C THR* 2.7 47.0 + - + +
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Residues in contact with GLU 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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95C ARG* 2.8 58.3 + - + +
96C GLU* 3.6 12.8 - - - +
98C ARG* 1.3 76.8 - - - +
100C GLU* 1.3 54.3 + - - +
102C THR* 3.0 7.0 + - - -
103C ASP* 2.7 36.5 + - - +
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Residues in contact with GLU 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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96C GLU 3.2 11.9 + - - +
97C LYS* 2.8 39.4 + - - +
99C GLU* 1.3 80.9 - - - +
101C MET* 1.3 60.7 + - - +
102C THR 3.4 0.5 + - - -
103C ASP* 3.6 3.0 + - - -
123C HIS* 3.3 8.4 + - + -
125C ARG* 2.8 32.9 + - - +
138C TYR* 3.8 32.8 - - + +
139C GLU* 4.3 2.3 - - - +
303C GOL 3.1 33.6 + - - -
2G GLY* 4.0 2.5 - - - -
3G ARG* 5.0 0.2 - - - +
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Residues in contact with MET 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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62C VAL* 3.5 3.5 - - - +
70C VAL* 5.2 2.9 - - + +
73C ALA* 3.7 4.3 - - + -
74C PHE* 3.7 43.3 - - + +
77C THR* 3.7 10.3 - - - +
97C LYS* 2.9 38.5 + - + +
98C ARG* 4.0 4.7 - - + +
99C GLU 3.3 0.4 - - - -
100C GLU* 1.3 77.3 - - + +
102C THR* 1.3 64.1 + - + +
103C ASP 3.6 0.4 - - - -
106C ALA* 4.2 2.8 - - - +
108C TYR* 2.4 55.4 + - - +
121C PHE* 3.6 33.2 - - + -
123C HIS* 4.2 13.9 - - + +
139C GLU* 5.0 5.2 - - + +
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Residues in contact with THR 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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62C VAL* 4.0 14.6 - - + +
70C VAL* 3.6 29.4 - - + -
98C ARG* 2.7 32.2 + - + +
99C GLU* 3.4 6.6 + - - -
101C MET* 1.3 80.8 - - + +
103C ASP* 1.3 68.1 + - - +
104C ASP* 3.6 3.8 + - - +
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Residues in contact with ASP 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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62C VAL* 3.1 13.2 - - - +
99C GLU 2.7 14.0 + - - +
100C GLU* 3.7 1.1 - - - +
101C MET 3.6 1.0 - - - -
102C THR* 1.3 80.2 - - - +
104C ASP* 1.3 77.3 + - - +
105C ARG* 2.9 50.7 + - - +
106C ALA* 3.2 9.5 + - - +
125C ARG* 3.1 29.3 + - - +
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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