Contacts of the helix formed by residues 89 - 105 (chain C) in PDB entry 5U0A
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 ASN 89 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C ASN 3.2 1.2 + - - -
88C LYS* 1.4 78.9 - - - +
90C PRO* 1.3 61.7 - - - +
91C LYS* 3.2 6.7 + - - +
92C ARG* 2.5 61.0 + - + +
93C LYS 3.1 1.4 + - - -
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Residues in contact with PRO 90 (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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85C PRO* 3.0 33.7 - - + +
87C ASN* 3.1 24.9 - - - +
88C LYS 4.2 0.9 - - - +
89C ASN* 1.3 84.3 - - - +
91C LYS* 1.3 62.4 + - + +
93C LYS* 3.2 3.8 + - + +
94C TRP* 2.9 22.9 + - - +
238C TYR* 2.9 20.3 + - + +
241C THR* 5.1 12.3 - - + -
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Residues in contact with LYS 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C ASN* 2.8 7.7 + - - +
90C PRO* 1.3 77.7 - - + +
92C ARG* 1.3 62.9 + - - +
94C TRP* 4.1 0.9 - - - +
95C GLN* 3.0 41.4 + - - +
238C TYR* 3.4 43.8 - - + +
240C GLY* 5.9 1.0 - - - -
357C ASN* 5.6 6.3 + - - +
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Residues in contact with ARG 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C LYS* 4.5 4.9 - - - +
89C ASN* 2.5 46.1 + - + +
91C LYS* 1.3 75.3 - - - +
93C LYS* 1.3 58.2 + - - +
95C GLN* 3.3 42.4 + - - +
96C ALA* 2.9 33.1 + - - +
362C ALA 5.7 0.4 + - - -
363C GLN 3.8 11.5 + - - -
364C VAL* 3.9 7.7 - - - +
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Residues in contact with LYS 93 (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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85C PRO* 6.1 2.9 - - + -
87C ASN 5.4 0.2 - - - +
88C LYS* 3.5 32.7 + - + +
89C ASN 3.1 6.1 + - - -
90C PRO* 3.2 5.8 + - + +
92C ARG* 1.3 76.4 - - - +
94C TRP* 1.3 65.9 + - - +
96C ALA* 2.9 7.9 + - - +
97C ARG* 2.9 52.7 + - - +
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Residues in contact with TRP 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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80C THR 3.9 5.2 + - - -
81C GLY* 2.5 50.1 + - - -
82C LEU* 5.1 3.1 - - + -
84C GLN 6.1 1.6 - - - -
85C PRO* 4.6 9.3 - - + +
90C PRO 2.9 8.9 + - - +
93C LYS* 1.3 75.9 - - - +
95C GLN* 1.3 61.2 + - + +
97C ARG* 3.4 9.5 + - + +
98C ARG* 2.8 71.1 + - + +
233C ILE 5.0 4.3 - - - -
236C ILE* 3.6 29.8 - - + -
237C PRO 4.3 2.2 - - - -
238C TYR* 3.1 63.0 - + + -
239C PRO* 4.6 9.2 - - + -
358C CYS* 5.8 0.4 - - - -
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Residues in contact with GLN 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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91C LYS* 3.0 29.7 + - - +
92C ARG* 3.3 33.3 + - - +
94C TRP* 1.3 80.5 - - + +
96C ALA* 1.3 55.7 + - - +
98C ARG* 3.3 26.4 - - - +
99C SER* 2.9 26.2 + - - -
238C TYR* 6.1 0.9 - - + -
357C ASN* 4.8 8.9 + - - +
362C ALA* 4.0 5.5 + - - +
363C GLN* 3.5 29.5 - - + +
364C VAL* 3.7 10.8 - - + +
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Residues in contact with ALA 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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88C LYS* 4.9 5.8 - - - +
92C ARG* 2.9 26.2 + - - +
93C LYS* 2.9 15.3 + - - +
95C GLN* 1.3 74.3 - - - +
97C ARG* 1.3 67.9 + - - +
99C SER* 3.1 7.7 + - - -
100C GLN* 2.9 27.3 + - - +
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Residues in contact with ARG 97 (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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80C THR 5.1 3.1 - - - +
82C LEU* 5.2 13.5 - - + -
88C LYS* 3.8 20.2 - - - +
93C LYS* 2.9 51.8 + - - +
94C TRP* 3.9 14.1 - - + +
96C ALA* 1.3 77.8 - - - +
98C ARG* 1.3 62.9 + - - +
100C GLN* 3.0 21.8 + - - +
101C ILE* 2.9 39.0 + - + +
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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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80C THR 5.7 0.9 + - - -
94C TRP* 2.8 60.6 + - + +
95C GLN* 3.3 24.2 - - - +
97C ARG* 1.3 77.2 - - - +
99C SER* 1.3 57.2 + - - +
101C ILE* 4.1 5.0 - - - +
102C LEU* 2.9 46.5 + - + +
233C ILE* 4.5 11.6 + - + +
234C LEU* 5.3 2.4 - - - +
236C ILE 4.5 1.0 + - - -
357C ASN* 4.0 4.0 + - - +
358C CYS* 2.7 53.5 - - - +
363C GLN* 2.7 38.9 + - - +
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Residues in contact with SER 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 GLN 2.9 19.4 + - - -
96C ALA* 3.1 6.9 + - - -
98C ARG* 1.3 76.8 - - - +
100C GLN* 1.3 53.8 + - - +
102C LEU* 3.8 7.6 - - - +
103C SER* 2.8 34.7 + - - -
364C VAL* 3.9 26.2 + - - +
365C PRO* 5.0 4.0 - - - +
366C GLN* 5.6 1.6 + - - -
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Residues in contact with GLN 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C ALA 2.9 11.4 + - - +
97C ARG* 3.0 30.3 + - - +
99C SER* 1.3 77.2 - - - +
101C ILE* 1.3 61.1 + - + +
103C SER* 2.5 22.5 + - - +
104C LYS* 3.2 10.2 + - - +
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Residues in contact with ILE 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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80C THR* 3.7 51.1 - - + +
82C LEU* 5.1 4.5 - - + -
97C ARG* 2.9 30.9 + - + +
98C ARG* 4.4 3.6 - - - +
100C GLN* 1.3 78.2 - - + +
102C LEU* 1.3 65.7 + - - +
103C SER 3.1 1.3 - - - -
104C LYS* 3.1 15.8 + - + +
105C GLY 3.2 9.2 + - - -
106C ARG 4.6 6.7 - - - +
107C LEU* 5.7 0.9 - - - -
229C PHE* 3.5 26.8 - - + -
233C ILE* 6.1 2.7 - - + -
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Residues in contact with LEU 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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98C ARG* 2.9 41.3 + - + +
99C SER* 3.9 5.8 - - - +
101C ILE* 1.3 77.8 - - - +
103C SER* 1.3 61.9 + - - +
105C GLY* 3.5 10.0 + - - -
229C PHE* 4.6 6.4 - - + -
230C GLU* 4.7 19.3 - - + +
233C ILE* 3.4 31.4 - - + -
234C LEU* 5.1 5.8 - - + +
363C GLN* 4.5 4.0 - - - +
365C PRO* 4.3 32.5 - - + -
368C VAL* 5.5 14.1 - - + +
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Residues in contact with SER 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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99C SER* 2.8 18.6 + - - -
100C GLN* 2.5 27.5 + - - +
102C LEU* 1.3 77.1 - - - +
104C LYS* 1.3 64.5 + - - +
105C GLY* 3.3 1.2 + - - -
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Residues in contact with LYS 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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100C GLN 3.2 8.5 + - - +
101C ILE* 3.1 13.1 + - + +
103C SER* 1.3 81.9 + - - +
105C GLY* 1.3 58.3 + - - +
106C ARG* 2.8 53.2 + - - +
108C ASP* 3.8 29.3 + - - +
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Residues in contact with GLY 105 (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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52C HIS* 3.9 14.7 - - - +
101C ILE 3.2 6.7 + - - -
102C LEU 3.5 8.3 + - - -
103C SER 3.2 4.1 - - - -
104C LYS* 1.3 76.5 - - - +
106C ARG* 1.3 64.2 + - - +
229C PHE* 3.3 25.2 - - - -
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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