Contacts of the helix formed by residues 85 - 102 (chain N) 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 85 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49N THR* 4.2 18.3 - - + -
84N SER* 1.3 85.7 - - - +
86N ARG* 1.3 63.3 + - + +
88N ILE* 3.4 8.6 + - + +
89N HIS* 3.0 30.0 + - - +
112N ILE* 4.5 9.7 - - + +
114N GLY* 3.5 39.9 - - - +
116N ALA* 3.6 21.8 - - + -
121N PHE* 3.5 26.1 - - + +
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Residues in contact with ARG 86 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F PHE 4.6 0.9 - - - -
100F ASP* 5.5 12.8 - - + +
84N SER* 3.2 7.7 - - - +
85N PRO* 1.3 85.0 - - - +
87N ALA* 1.3 58.4 + - - +
89N HIS* 3.5 3.2 + - + +
90N SER* 2.9 29.7 + - - -
116N ALA* 5.3 4.9 - - - +
119N GLU* 3.2 32.3 + - - +
121N PHE* 3.1 50.5 - - + +
133N GLU* 5.3 1.2 - - - +
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Residues in contact with ALA 87 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F PHE* 3.3 38.7 - - + +
101F ARG* 4.6 10.5 - - + +
84N SER* 3.2 25.2 + - - +
85N PRO 3.2 0.4 - - - -
86N ARG* 1.3 79.5 - - - +
88N ILE* 1.3 60.2 + - + +
90N SER* 3.3 1.4 + - - -
91N TRP* 2.9 30.0 + - - +
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Residues in contact with ILE 88 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F PHE* 6.5 1.1 - - + -
45N VAL* 4.7 8.1 - - + -
46N ASN* 5.1 2.5 - - - +
49N THR* 5.2 3.6 - - - +
51N LEU* 4.0 14.6 - - + -
67N LEU* 3.7 35.2 - - + -
70N MET* 5.5 7.0 - - + -
71N VAL* 3.8 28.7 - - + -
84N SER 3.2 16.2 + - - +
85N PRO* 3.4 9.6 + - + +
87N ALA* 1.3 78.5 - - + +
89N HIS* 1.3 57.3 + - - +
91N TRP* 3.5 6.3 + - + +
92N LEU* 2.9 27.1 + - + +
112N ILE* 4.1 9.4 - - + -
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Residues in contact with HIS 89 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85N PRO 3.0 17.6 + - - +
86N ARG 3.8 2.0 - - - +
88N ILE* 1.3 74.2 - - - +
90N SER* 1.3 65.2 + - - +
92N LEU* 3.2 3.2 + - - +
93N THR* 2.8 37.2 + - - -
112N ILE* 3.3 24.2 - - + +
121N PHE* 3.7 23.1 - + + -
123N GLY* 3.5 5.4 - - - -
124N TYR 3.0 33.0 - - - -
125N VAL* 3.0 20.7 - - + +
131N ALA* 3.1 23.8 - - + +
132N TYR* 3.8 11.5 + - - -
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Residues in contact with SER 90 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F VAL 3.5 2.0 + - - -
99F PHE 3.3 16.9 - - - -
100F ASP* 1.7 42.1 + - - +
86N ARG* 2.9 18.9 + - - -
87N ALA 3.4 5.2 - - - -
89N HIS* 1.3 83.7 - - - +
91N TRP* 1.3 64.7 + - - +
93N THR* 3.2 1.0 + - - -
94N ARG* 2.9 34.9 + - - +
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Residues in contact with TRP 91 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F PHE* 5.8 0.9 - + - -
98F VAL* 3.1 39.4 + - + +
99F PHE* 4.1 13.0 - + + -
66N VAL* 5.6 4.2 - - - +
70N MET* 3.2 42.3 - - + +
87N ALA 2.9 16.2 + - - +
88N ILE* 4.0 7.6 - - + +
90N SER* 1.3 77.1 - - - +
92N LEU* 1.3 54.9 + - + +
94N ARG* 2.4 80.1 + - + +
95N ALA* 2.8 24.2 + - + +
98N SER* 5.3 4.7 - - - -
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Residues in contact with LEU 92 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51N LEU* 3.3 25.8 - - + -
63N LEU* 4.0 17.9 - - + -
67N LEU* 4.0 23.6 - - + -
88N ILE 2.9 17.9 + - - +
89N HIS* 3.5 6.1 - - - +
91N TRP* 1.3 77.0 - - - +
93N THR* 1.3 57.1 + - - +
95N ALA* 3.2 7.4 + - + +
96N MET* 3.0 37.2 + - - +
110N MET* 3.8 29.8 - - + -
112N ILE* 4.0 10.3 - - + -
125N VAL* 3.9 23.1 - - + -
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Residues in contact with THR 93 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59M GLY 5.6 0.2 - - - +
62M LEU* 4.8 8.5 - - + -
63M THR* 5.2 7.0 - - - +
66M LYS* 5.9 0.2 - - - -
89N HIS* 2.8 19.9 + - - -
90N SER* 3.4 11.4 - - - -
91N TRP 3.1 0.2 - - - -
92N LEU* 1.3 74.6 - - - +
94N ARG* 1.3 69.9 + - - +
96N MET* 4.1 0.4 - - - +
97N TYR* 2.9 36.9 + - + +
125N VAL* 3.7 13.2 - - - +
129N GLY* 3.4 23.9 - - - +
131N ALA* 3.2 27.1 - - + +
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Residues in contact with ARG 94 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F PHE* 3.0 47.1 + - + -
98F VAL* 3.7 3.6 + - - +
100F ASP* 2.3 33.5 + - - -
62M LEU* 5.9 0.4 - - - +
63M THR* 5.5 3.4 + - - -
66M LYS* 3.3 34.0 - - - +
90N SER* 2.9 25.4 + - - +
91N TRP* 2.4 61.3 + - + -
93N THR* 1.3 96.0 - - - +
95N ALA* 1.3 53.3 + - - -
97N TYR* 3.8 5.4 - - - +
98N SER* 3.0 34.3 + - - +
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Residues in contact with ALA 95 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62N TYR* 6.0 1.3 - - - +
63N LEU* 4.4 26.7 - - + -
66N VAL* 6.3 1.3 - - + -
91N TRP* 2.8 23.4 + - + +
92N LEU* 3.2 13.4 + - + +
94N ARG* 1.3 74.4 - - - +
96N MET* 1.4 63.3 + - - +
98N SER* 3.3 5.0 + - - -
99N ARG* 3.2 29.5 + - - +
106N LEU* 4.0 3.1 - - + +
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Residues in contact with MET 96 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63N LEU* 3.5 29.4 - - - -
92N LEU* 3.0 22.1 + - + +
93N THR 4.1 1.1 - - - +
95N ALA* 1.4 75.4 - - - +
97N TYR* 1.3 60.9 + - - +
99N ARG* 3.8 2.8 + - - +
100N ARG* 3.3 17.0 + - - +
105N PRO* 5.3 0.5 - - - +
106N LEU* 3.7 29.7 - - + +
108N ASN* 3.1 35.2 - - + +
110N MET* 4.0 9.6 - - + -
125N VAL* 3.4 22.4 - - + +
126N ASP 3.7 7.2 - - - +
127N MET* 3.6 28.0 - - - +
129N GLY* 4.0 7.4 - - - -
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Residues in contact with TYR 97 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57M PHE* 6.2 0.2 - + - -
59M GLY 3.5 13.9 - - - -
60M ASP* 3.2 22.1 + - - -
63M THR* 3.4 41.7 - - + +
99M ARG* 4.0 0.7 - - - -
104M TYR* 2.7 39.2 - + - -
93N THR* 2.9 22.2 + - + +
94N ARG* 3.8 6.5 - - - +
96N MET* 1.3 76.4 - - - +
98N SER* 1.3 65.9 + - - +
100N ARG* 3.1 22.4 + - - +
101N SER* 3.0 40.1 + - - -
128N LEU 4.8 9.2 - - - -
129N GLY* 4.3 8.7 - - - -
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Residues in contact with SER 98 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91N TRP* 5.3 4.3 - - - -
94N ARG* 3.0 25.0 + - - +
95N ALA* 3.3 6.6 + - - -
97N TYR* 1.3 78.0 - - - +
99N ARG* 1.3 63.1 + - - +
101N SER* 3.3 19.7 + - - -
102N LYS* 3.0 21.5 + - - +
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Residues in contact with ARG 99 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88H TYR* 5.2 6.3 + - - -
91H ARG* 4.5 15.2 - - - +
59N ASP* 4.0 13.7 + - - -
62N TYR* 3.8 38.3 + - - +
95N ALA 3.2 8.1 + - - +
96N MET 4.1 0.9 - - - +
98N SER* 1.3 78.2 - - - +
100N ARG* 1.3 61.0 + - - +
101N SER 3.5 0.3 + - - -
102N LYS* 3.6 21.8 + - - +
103N MET 3.6 1.6 + - - -
104N ASN* 2.8 77.5 + - - +
105N PRO* 3.1 18.4 + - + -
106N LEU* 3.5 27.7 - - + +
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Residues in contact with ARG 100 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57M PHE* 3.9 16.2 - - - -
60M ASP* 3.1 30.9 + - - -
99M ARG* 3.1 33.7 - - - +
102M PHE* 3.4 28.3 - - + -
103M PRO 4.5 3.0 + - - -
96N MET 3.3 14.3 + - - +
97N TYR* 3.1 28.2 + - - +
99N ARG* 1.3 75.6 - - - +
101N SER* 1.3 58.3 + - - +
103N MET* 2.9 22.0 + - - +
105N PRO* 4.1 13.6 - - + +
128N LEU* 3.4 42.9 - - + +
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Residues in contact with SER 101 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99M ARG* 4.4 13.4 + - - +
102M PHE* 3.3 29.1 - - - -
97N TYR* 3.0 32.2 + - - -
98N SER* 3.3 13.2 + - - -
100N ARG* 1.3 77.1 + - - +
102N LYS* 1.4 59.8 + - - +
103N MET* 3.2 3.9 - - - +
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Residues in contact with LYS 102 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98N SER* 3.0 32.5 + - - +
99N ARG* 3.6 29.6 + - - +
100N ARG 3.2 0.2 - - - -
101N SER* 1.4 77.0 - - - +
103N MET* 1.3 77.3 + - - +
104N ASN* 4.2 22.0 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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