Contacts of the helix formed by residues 83 - 98 (chain C) in PDB entry 2UYK
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 ASP 83 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46C VAL* 3.8 33.0 - - + +
78C ILE* 5.9 0.2 - - + -
80C ASP* 2.8 35.2 + - - +
82C ASN* 1.3 77.0 - - - +
84C PHE* 1.3 58.8 + - - +
85C ALA 3.4 2.0 - - - -
86C THR* 3.3 9.5 + - - -
87C ILE* 2.9 43.8 + - + +
118C LYS* 4.0 21.4 + - - +
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Residues in contact with PHE 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ILE* 6.5 1.3 - - + -
114A PRO* 4.3 19.1 - - + -
76C VAL* 5.7 0.4 - - + -
78C ILE* 4.2 7.9 - - + -
80C ASP 4.0 0.6 + - - -
81C LEU* 3.1 37.5 + - + +
82C ASN 3.3 0.4 - - - -
83C ASP* 1.3 78.6 - - - +
85C ALA* 1.3 59.1 + - - +
87C ILE* 3.8 14.1 - - + +
88C ASN* 2.9 56.0 + - - -
105C ARG* 3.5 14.4 - - - -
107C CYS* 3.2 31.2 - - + -
1129C SER* 3.4 25.4 - - - -
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Residues in contact with ALA 85 (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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81C LEU 4.7 0.4 + - - -
82C ASN 4.7 4.8 + - - +
83C ASP 3.4 0.6 - - - -
84C PHE* 1.3 77.9 - - - +
86C THR* 1.3 58.4 + - - +
88C ASN* 3.4 8.1 + - - +
89C GLU* 3.0 28.6 + - - +
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Residues in contact with THR 86 (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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45C ASP* 5.2 0.9 - - - +
46C VAL* 3.7 26.3 - - + +
47C GLN* 3.9 25.8 - - + -
82C ASN 5.4 1.6 + - - -
83C ASP* 3.3 11.8 + - - -
85C ALA* 1.3 79.0 - - - +
87C ILE* 1.3 62.5 + - - +
89C GLU* 3.3 8.0 + - + +
90C VAL* 3.1 23.6 + - + +
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Residues in contact with ILE 87 (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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46C VAL* 4.0 21.5 - - + +
50C ALA* 4.3 18.0 - - + +
76C VAL* 4.5 12.8 - - + -
78C ILE* 3.7 28.9 - - + -
83C ASP* 2.9 37.5 + - + +
84C PHE* 3.8 12.8 - - + +
86C THR* 1.3 75.7 - - - +
88C ASN* 1.3 58.7 + - - +
90C VAL* 3.3 3.3 + - - +
91C TYR* 2.9 37.5 + - + +
105C ARG* 5.7 1.3 - - - +
118C LYS 4.9 1.6 - - - +
119C LEU* 4.1 24.0 - - + -
121C ILE* 5.9 0.9 - - + -
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Residues in contact with ASN 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLY* 4.9 4.9 - - - -
16A PRO* 3.6 14.8 - - + +
84C PHE* 2.9 56.0 + - - +
85C ALA* 3.7 7.1 - - - +
87C ILE* 1.3 72.3 - - - +
89C GLU* 1.3 53.1 + - - +
91C TYR* 3.6 4.3 - - - +
92C LYS* 2.8 37.5 + - - +
105C ARG* 2.8 35.2 + - - +
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Residues in contact with GLU 89 (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 ALA 3.0 14.0 + - - +
86C THR* 3.3 12.3 + - - +
88C ASN* 1.3 76.7 - - - +
90C VAL* 1.3 63.9 + - + +
92C LYS* 3.8 6.0 - - - +
93C GLN* 3.0 32.5 + - + +
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Residues in contact with VAL 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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47C GLN* 3.7 30.3 - - + +
50C ALA* 3.9 10.3 - - + -
51C ARG* 3.5 46.0 + - + +
54C LEU* 4.2 5.2 - - + -
86C THR* 3.1 14.6 + - + +
87C ILE 3.7 5.8 - - - +
89C GLU* 1.3 76.8 - - + +
91C TYR* 1.3 59.0 + - - +
93C GLN* 3.3 6.8 + - - +
94C PHE* 2.9 28.1 + - - +
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Residues in contact with TYR 91 (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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16A PRO* 3.3 35.1 + - + -
54C LEU* 3.7 26.9 - - + -
74C MET* 3.2 42.4 - - - +
76C VAL* 3.8 15.7 - - + -
87C ILE* 2.9 23.9 + - + +
88C ASN* 3.6 7.4 - - - +
90C VAL* 1.3 78.7 - - - +
92C LYS* 1.3 62.6 + - - +
94C PHE* 3.2 2.3 + - - +
95C PHE* 3.1 46.5 + + - -
103C PRO* 3.8 11.1 + - + +
105C ARG* 3.3 36.0 - - - +
121C ILE* 4.8 3.1 - - + -
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Residues in contact with LYS 92 (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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16A PRO* 3.7 21.0 - - + +
88C ASN 2.8 18.7 + - - +
89C GLU* 3.8 6.1 - - - +
91C TYR* 1.3 77.2 - - - +
93C GLN* 1.3 65.0 + - + +
95C PHE* 3.3 3.1 + - - +
96C ASP* 2.9 39.1 + - - +
102C TYR* 2.8 41.2 + - + +
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Residues in contact with GLN 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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51C ARG* 5.5 2.2 - - - +
89C GLU* 3.0 25.6 + - + +
90C VAL* 3.3 6.5 + - - +
92C LYS* 1.3 77.7 - - + +
94C PHE* 1.3 54.1 + - - +
96C ASP* 3.3 8.6 + - - +
97C GLU* 2.8 52.5 + - + +
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Residues in contact with PHE 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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51C ARG* 4.1 28.2 - - - +
54C LEU* 3.7 55.4 - - + -
55C GLU* 4.1 12.1 - - - -
57C VAL* 6.3 0.7 - - + -
58C LYS* 3.9 10.1 - - + -
68C VAL* 3.7 35.4 - - + -
71C ILE* 5.1 4.7 - - + -
74C MET* 6.1 0.4 - - + -
90C VAL 2.9 17.9 + - - +
91C TYR 3.4 4.0 - - - +
92C LYS 3.2 0.2 - - - -
93C GLN* 1.3 75.4 - - - +
95C PHE* 1.3 83.7 + + - +
97C GLU* 3.3 6.9 + - - +
98C HIS* 2.8 45.0 + + - -
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Residues in contact with PHE 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C LEU* 4.6 0.9 - - + -
68C VAL* 3.6 35.2 - - + -
71C ILE* 4.3 7.6 - - + -
74C MET* 3.7 14.8 - - - -
91C TYR* 3.1 54.4 + + - -
92C LYS 4.0 0.7 - - - +
94C PHE* 1.3 97.6 - + - +
96C ASP* 1.3 63.9 + - - +
98C HIS* 3.1 6.4 + - - -
100C ALA* 3.0 42.4 + - + +
101C THR 3.9 3.8 - - - -
102C TYR* 3.6 26.7 - + + -
103C PRO* 3.5 33.2 - - + -
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Residues in contact with ASP 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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92C LYS* 2.9 35.2 + - - +
93C GLN* 3.7 8.0 - - - +
95C PHE* 1.3 77.2 - - - +
97C GLU* 1.3 58.1 + - + +
99C GLN* 3.0 24.5 + - - +
100C ALA 4.9 1.9 - - - +
102C TYR* 2.7 33.0 + - - -
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Residues in contact with GLU 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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51C ARG* 2.9 40.6 + - - -
93C GLN* 2.8 31.3 + - + +
94C PHE* 3.7 5.5 - - - +
95C PHE 3.3 0.4 - - - -
96C ASP* 1.3 73.0 - - + +
98C HIS* 1.3 67.0 + - + +
99C GLN* 3.3 6.0 + - - +
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Residues in contact with HIS 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ARG* 4.9 5.2 - - - -
55C GLU* 5.1 0.2 - - - -
58C LYS* 2.8 36.3 + - + -
68C VAL* 3.6 36.3 - - + +
69C GLY* 5.3 1.9 + - - -
94C PHE* 2.8 47.9 + + - +
95C PHE 3.1 7.1 + - - +
96C ASP 3.1 0.8 - - - -
97C GLU* 1.3 88.4 - - + +
99C GLN* 1.3 71.8 + - - +
100C ALA* 3.1 4.1 + - + +
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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