Contacts of the helix formed by residues 77 - 93 (chain Y) in PDB entry 5A0Q
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 PRO 77 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41Y LYS 4.4 4.0 - - - +
42Y ILE* 4.8 4.7 - - + -
75Y LEU 4.4 1.6 - - - +
76Y SER* 1.3 87.3 - - - +
78Y THR* 1.3 57.0 + - - +
80Y ALA* 3.6 1.7 + - + -
81Y ALA* 3.1 17.4 + - - +
104Y LEU* 3.1 30.1 - - + +
106Y GLY* 3.4 18.8 - - - +
107Y TYR 3.3 28.9 - - - +
108Y ASP* 3.5 26.7 - - + +
111Y GLU* 5.0 1.8 - - - +
114Y ALA* 4.2 13.5 - - + +
116Y TYR* 4.3 7.6 - - + -
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Residues in contact with THR 78 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102Q GLN 5.7 2.0 + - - -
103Q GLU* 5.3 0.9 + - - -
76Y SER* 3.5 13.5 - - - -
77Y PRO* 1.3 75.9 - - + +
79Y ALA* 1.3 60.5 + - - +
81Y ALA* 3.2 6.4 + - - +
82Y ASN* 2.8 44.2 + - - +
111Y GLU* 3.4 30.3 + - - +
116Y TYR* 2.3 37.9 - - + +
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Residues in contact with ALA 79 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101Q TYR* 3.5 26.3 - - + +
102Q GLN 5.5 0.9 - - - -
103Q GLU* 3.6 27.8 - - - +
75Y LEU* 3.8 16.4 - - + -
76Y SER* 3.0 21.0 + - - +
78Y THR* 1.3 79.9 + - - +
80Y ALA* 1.3 61.3 + - - +
82Y ASN 3.6 0.2 + - - -
83Y PHE* 3.2 21.7 + - - +
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Residues in contact with ALA 80 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101Q TYR* 5.2 1.6 - - - -
42Y ILE* 3.7 36.6 - - + -
60Y ILE* 5.2 1.4 - - + +
64Y VAL* 4.7 13.7 - - + -
75Y LEU* 4.6 5.8 - - + +
76Y SER 3.0 13.6 + - - +
77Y PRO 3.9 1.8 - - - +
79Y ALA* 1.3 76.2 - - - +
81Y ALA* 1.4 56.4 + - - +
83Y PHE* 3.3 12.5 + - - +
84Y THR* 3.1 29.5 + - - +
104Y LEU* 3.8 8.7 - - + +
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Residues in contact with ALA 81 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77Y PRO 3.1 19.0 + - - +
78Y THR* 3.4 9.6 - - - +
79Y ALA 3.2 0.4 - - - -
80Y ALA* 1.4 72.9 - - - +
82Y ASN* 1.3 59.0 + - - +
83Y PHE 3.1 1.1 - - - -
84Y THR* 3.1 5.7 - - - +
85Y ARG* 3.0 27.9 + - - +
104Y LEU* 3.9 3.4 - - + -
116Y TYR* 4.3 9.4 - - + -
118Y MET* 3.5 28.8 - - + +
124Y LEU* 3.9 17.0 - - + +
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Residues in contact with ASN 82 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100Q GLN 3.0 21.6 - - - +
101Q TYR 3.8 4.9 + - - +
102Q GLN* 3.4 33.5 + - + +
64X GLN* 4.0 0.5 + - - -
78Y THR* 2.8 36.7 + - - +
81Y ALA* 1.3 71.7 - - - +
83Y PHE* 1.3 63.5 + - - +
85Y ARG* 3.1 33.4 + - - +
86Y ARG* 3.2 21.5 + - - +
116Y TYR* 6.3 0.4 - - - -
124Y LEU* 3.5 12.7 - - - +
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Residues in contact with PHE 83 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100Q GLN* 3.7 20.9 - - + -
101Q TYR* 3.8 35.4 - + + -
60Y ILE* 4.1 17.5 - - + -
63Y ASN* 3.6 43.3 - - + -
64Y VAL* 4.0 23.1 - - + -
79Y ALA 3.2 15.1 + - - +
80Y ALA 3.3 9.2 - - - +
81Y ALA 3.1 0.6 - - - -
82Y ASN* 1.3 77.5 - - - +
84Y THR* 1.4 56.2 + - - +
86Y ARG* 3.2 15.7 + - + +
87Y ASN* 2.8 38.6 - - - +
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Residues in contact with THR 84 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44Y LEU* 4.8 3.4 - - + +
56Y PHE* 2.7 32.9 - - - -
60Y ILE* 4.2 13.5 - - - -
80Y ALA 3.1 15.5 + - - +
81Y ALA* 3.1 19.1 - - - +
83Y PHE* 1.4 73.4 - - - +
85Y ARG* 1.3 63.3 + - - +
87Y ASN* 3.2 12.5 + - - +
88Y LEU* 3.1 28.2 + - - +
102Y LEU* 5.8 0.2 - - - +
104Y LEU* 4.0 8.3 - - + -
118Y MET* 3.6 29.9 - - + -
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Residues in contact with ARG 85 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102Q GLN* 3.9 1.0 - - - +
60X GLN* 3.3 40.2 + - - +
61X THR 4.8 0.4 - - - +
64X GLN* 1.9 40.8 - - - +
81Y ALA 3.0 18.6 + - - +
82Y ASN* 3.1 25.0 + - - +
83Y PHE 3.2 0.2 - - - -
84Y THR* 1.3 77.1 - - - +
86Y ARG* 1.3 98.2 + - - +
88Y LEU* 3.4 6.2 + - - -
89Y ALA* 3.2 21.2 + - + +
118Y MET* 5.7 4.5 - - + -
122Y ALA* 3.7 16.2 - - + +
124Y LEU* 3.0 39.4 - - + +
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Residues in contact with ARG 86 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99Q LEU* 3.7 16.4 + - - +
100Q GLN* 3.8 30.8 - - + +
102Q GLN* 4.6 0.2 - - - +
61X THR* 4.8 8.7 + - - +
64X GLN* 2.9 27.1 + - - +
65X ARG* 5.0 17.9 - - - +
82Y ASN 3.2 11.5 + - - +
83Y PHE* 3.2 12.0 + - + +
85Y ARG* 1.3 135.3 + - - +
87Y ASN* 1.3 63.0 + - - +
89Y ALA* 3.4 14.2 + - - +
90Y ASP* 2.8 35.8 + - - +
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Residues in contact with ASN 87 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56Y PHE* 4.1 13.9 - - + -
59Y TYR* 3.3 33.9 + - + -
60Y ILE* 3.0 25.6 - - - +
83Y PHE* 2.8 36.7 - - - +
84Y THR* 3.2 6.9 + - - +
86Y ARG* 1.3 79.3 - - - +
88Y LEU* 1.3 64.4 + - - +
90Y ASP* 3.2 13.2 + - - +
91Y CYS* 3.1 28.5 + - - -
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Residues in contact with LEU 88 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56Y PHE* 3.2 35.0 - - + -
84Y THR* 3.1 18.7 + - - +
85Y ARG* 4.0 1.8 - - - +
87Y ASN* 1.3 78.3 - - - +
89Y ALA* 1.3 61.0 + - - +
91Y CYS* 3.4 5.2 + - + +
92Y LEU* 3.2 17.3 + - - +
98Y TYR* 4.4 17.5 - - + +
100Y VAL* 3.9 27.1 - - + +
102Y LEU* 6.2 1.6 - - + -
118Y MET* 5.1 11.2 - - + -
119Y ASP 3.8 19.7 - - - +
120Y TYR 4.0 11.4 - - - +
121Y LEU 3.5 6.9 - - - +
122Y ALA* 3.5 18.6 - - + -
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Residues in contact with ALA 89 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57X THR* 5.2 5.4 - - - +
61X THR* 4.1 18.4 - - + +
65X ARG* 5.5 6.1 - - - +
102X TYR* 5.7 1.6 + - - -
85Y ARG* 3.2 17.7 + - + +
86Y ARG* 3.8 15.7 - - - +
87Y ASN 3.2 0.2 - - - -
88Y LEU* 1.3 73.4 - - - +
90Y ASP* 1.3 65.3 + - - +
92Y LEU* 3.5 15.8 + - - +
93Y ARG* 4.0 6.9 + - - +
121Y LEU 4.1 3.1 - - - -
122Y ALA* 3.5 12.5 - - + +
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Residues in contact with ASP 90 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65X ARG* 3.6 22.2 + - - -
86Y ARG* 2.8 28.4 + - - +
87Y ASN* 3.2 12.3 + - - +
89Y ALA* 1.3 76.2 - - - +
91Y CYS* 1.3 63.9 + - - +
92Y LEU 3.4 0.5 + - - -
93Y ARG* 3.6 7.5 + - - +
94Y SER* 2.8 24.0 + - - +
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Residues in contact with CYS 91 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59Y TYR* 6.0 3.8 - - - -
87Y ASN* 3.1 20.9 + - - +
88Y LEU* 3.4 7.6 + - + +
89Y ALA 3.3 0.2 - - - -
90Y ASP* 1.3 79.2 - - - +
92Y LEU* 1.3 62.9 + - - +
94Y SER* 3.2 16.0 + - - -
96Y THR* 3.1 22.9 - - - +
97Y PRO* 3.1 18.5 - - - +
98Y TYR* 3.7 43.7 - - + +
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Residues in contact with LEU 92 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55X LEU* 5.6 5.6 - - + -
57X THR* 4.3 19.3 - - + +
58X ASP* 5.7 1.1 - - - +
88Y LEU 3.2 11.9 + - - +
89Y ALA* 3.6 11.4 - - - +
90Y ASP 3.2 0.6 - - - -
91Y CYS* 1.3 78.1 - - - +
93Y ARG* 1.3 58.5 + - - +
94Y SER 4.1 3.6 - - - +
97Y PRO* 4.1 19.8 - - + +
98Y TYR 6.0 1.1 - - - +
120Y TYR* 5.1 2.7 - - + +
121Y LEU* 3.5 51.1 - - + +
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Residues in contact with ARG 93 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97X LYS* 3.9 23.6 - - - +
99X PHE* 4.7 4.6 - - - +
100X GLY* 3.5 43.2 + - - +
102X TYR* 4.1 30.9 + - + +
89Y ALA 4.0 6.4 + - - +
90Y ASP* 3.6 8.9 + - - +
91Y CYS 3.3 0.4 - - - -
92Y LEU* 1.3 75.3 - - + +
94Y SER* 1.4 62.2 + - - +
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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