Contacts of the helix formed by residues 108 - 124 (chain U) 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 LEU 108 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72U HIS* 5.0 3.0 - - - -
73U VAL* 3.7 20.4 - - + -
106U ILE 3.9 1.4 + - - -
107U PRO* 1.4 69.9 - - - +
109U LYS* 1.3 60.2 + - - +
111U LEU* 4.0 13.9 - - + -
112U ALA* 2.9 33.0 + - + +
137U LEU* 3.8 20.6 - - + +
138U GLY* 3.7 12.8 - - - +
139U SER* 3.7 27.6 - - - +
144U ASP* 5.1 3.8 + - - -
147U GLN* 3.4 46.0 - - + +
149U TYR* 3.8 16.6 - - + +
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Residues in contact with LYS 109 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107U PRO* 4.2 15.9 - - + -
108U LEU* 1.3 79.3 - - - +
110U HIS* 1.4 58.5 + - + +
112U ALA* 4.3 0.5 - - - +
113U ASP* 3.0 32.2 + - - +
144U ASP* 3.8 21.5 + - - +
147U GLN* 5.5 5.0 - - + +
149U TYR* 4.4 26.8 - - + +
69V GLU 5.1 3.6 - - - -
70V LEU* 3.4 31.1 + - + +
71V ASN* 4.8 11.3 + - - +
72V GLU* 4.2 13.3 + - - +
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Residues in contact with HIS 110 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98U PHE* 3.4 35.7 - + - -
102U PHE* 5.7 1.0 - - - -
106U ILE* 4.6 5.4 - - + -
107U PRO* 3.4 22.1 + - + +
108U LEU 3.2 0.4 - - - -
109U LYS* 1.4 77.4 - - + +
111U LEU* 1.3 58.9 + - - +
112U ALA 3.3 2.2 - - - -
113U ASP* 3.3 8.7 + - - +
114U ARG* 3.0 64.4 + - + +
69V GLU* 4.2 28.0 + - + +
70V LEU* 4.2 16.6 - - + +
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Residues in contact with LEU 111 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69U VAL* 4.0 12.3 - - + -
73U VAL* 3.8 41.5 - - + -
91U ALA* 4.2 7.6 - - + +
94U GLU* 3.4 29.2 - - + +
95U ALA* 4.7 0.7 - - + +
106U ILE* 3.9 28.7 - - + -
107U PRO 3.0 16.7 + - - +
108U LEU* 3.1 12.5 + - + +
110U HIS* 1.3 72.5 - - - +
112U ALA* 1.3 64.8 + - - +
114U ARG* 3.9 2.9 - - + +
115U VAL* 3.1 29.0 + - + +
137U LEU* 4.3 7.9 - - + -
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Residues in contact with ALA 112 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108U LEU* 2.9 18.7 + - + +
109U LYS 4.3 0.4 - - - +
111U LEU* 1.3 77.6 - - - +
113U ASP* 1.3 62.3 + - - +
116U ALA* 2.9 34.7 + - - +
137U LEU* 6.0 2.5 - - + -
149U TYR* 3.6 38.8 - - + -
151U ILE* 3.4 13.3 - - + +
157U SER* 4.3 7.6 - - - -
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Residues in contact with ASP 113 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88O ARG* 6.2 1.8 - - - -
92O GLN* 6.2 1.3 - - - +
109U LYS 3.0 20.8 - - - +
110U HIS* 3.3 13.9 + - - +
111U LEU 3.3 0.2 - - - -
112U ALA* 1.3 77.9 - - - +
114U ARG* 1.3 64.2 + - - +
116U ALA* 3.9 5.3 - - - +
117U MET* 3.1 26.9 + - - +
149U TYR* 4.9 6.1 - - - -
157U SER* 3.8 13.3 + - - +
69V GLU 5.5 3.1 - - - +
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Residues in contact with ARG 114 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92O GLN* 3.6 36.7 + - - +
94U GLU* 3.9 27.5 - - + +
106U ILE* 6.0 1.8 - - + -
110U HIS* 3.0 51.4 + - + +
111U LEU* 3.9 7.0 - - + +
113U ASP* 1.3 79.6 + - - +
115U VAL* 1.3 64.3 + - - +
117U MET* 3.2 33.8 + - - +
118U TYR* 3.2 17.8 + - - +
69V GLU* 5.0 2.2 + - - +
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Residues in contact with VAL 115 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87U LEU* 4.6 15.3 - - + +
90U ILE* 5.4 2.7 - - + -
91U ALA* 4.0 14.4 - - + -
94U GLU* 2.1 42.8 - - - +
111U LEU* 3.1 27.4 + - + +
114U ARG* 1.3 74.9 - - - +
116U ALA* 1.3 56.4 + - - +
118U TYR* 3.2 5.3 + - + +
119U VAL* 2.9 27.9 + - + +
135U PHE* 3.8 33.4 - - + -
137U LEU* 5.0 2.0 - - + -
151U ILE* 4.0 7.0 - - + -
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Residues in contact with ALA 116 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112U ALA 2.9 20.1 + - - +
113U ASP* 3.9 4.7 - - - +
115U VAL* 1.3 73.1 - - - +
117U MET* 1.3 59.2 + - - +
119U VAL* 3.4 1.1 + - - -
120U HIS* 3.0 22.3 + - - +
151U ILE* 3.8 26.0 - - + +
155U GLY* 3.2 23.4 - - - +
157U SER* 3.7 19.3 - - - +
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Residues in contact with MET 117 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88O ARG* 5.0 9.4 - - + +
89O SER* 3.8 39.9 - - - +
92O GLN* 5.4 9.4 - - + -
113U ASP 3.1 16.1 + - - +
114U ARG* 3.2 32.3 + - - +
116U ALA* 1.3 73.9 - - - +
118U TYR* 1.3 65.5 + - - +
120U HIS* 3.1 27.2 + - + +
121U ALA* 3.2 18.1 + - + +
124U LEU* 6.0 1.1 - - + -
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Residues in contact with TYR 118 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86U SER* 6.0 1.1 - - - -
87U LEU* 4.1 17.0 - - + -
90U ILE* 3.9 44.6 - - + +
94U GLU* 4.2 8.5 - - - +
114U ARG 3.2 8.1 + - - +
115U VAL* 3.4 8.1 - - + +
117U MET* 1.3 82.6 - - - +
119U VAL* 1.4 60.5 + - - +
120U HIS 3.6 0.2 + - - -
121U ALA* 3.6 11.4 + - + +
122U TYR* 2.9 46.5 + + - -
131U PHE* 4.0 15.9 - + - -
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Residues in contact with VAL 119 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87U LEU* 3.5 29.4 - - + -
115U VAL 2.9 20.6 + - - +
116U ALA* 3.5 10.1 - - - +
118U TYR* 1.4 74.9 - - - +
120U HIS* 1.4 60.6 + - - +
121U ALA 3.5 0.3 + - - -
122U TYR* 3.8 5.9 + - - +
123U THR* 4.2 1.9 - - - +
131U PHE* 3.3 26.5 - - + -
135U PHE* 4.3 8.5 - - + -
151U ILE* 4.3 10.8 - - + -
152U ASP 3.4 19.7 - - - +
153U PRO* 3.3 32.0 - - + +
155U GLY* 3.7 4.5 - - - +
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Residues in contact with HIS 120 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85O ALA* 3.3 36.2 + - + +
86O ASP* 3.6 19.0 - - - -
88O ARG* 5.7 0.4 - - + -
89O SER* 3.8 21.3 - - - -
134O LEU* 4.5 0.8 - - - +
116U ALA 3.0 14.5 + - - +
117U MET* 3.1 20.8 + - - +
119U VAL* 1.4 75.3 - - - +
121U ALA* 1.3 60.9 + - - +
122U TYR 3.2 1.1 - - - -
123U THR* 2.8 30.8 + - - -
124U LEU* 3.3 41.2 - - + +
154U SER 3.3 22.9 + - - +
155U GLY* 4.2 3.4 - - - +
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Residues in contact with ALA 121 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117U MET* 3.2 16.2 + - + +
118U TYR* 3.8 16.8 - - + +
119U VAL 3.4 1.0 - - - -
120U HIS* 1.3 76.1 - - - +
122U TYR* 1.3 66.1 + - + +
124U LEU* 3.3 16.8 + - - +
125U TYR* 3.0 39.6 - - + +
128U VAL* 5.1 0.2 - - - -
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Residues in contact with TYR 122 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121T GLN* 2.7 43.3 - - + +
11U ALA* 4.7 0.3 - - - +
118U TYR* 2.9 46.6 + + - -
119U VAL 4.0 2.0 - - - +
120U HIS 3.2 0.6 - - - -
121U ALA* 1.3 76.7 - - + +
123U THR* 1.3 66.0 + - - +
124U LEU 3.0 4.0 + - - -
125U TYR 3.2 19.2 + - - +
128U VAL* 3.4 39.2 - - + +
129U ARG 3.0 16.4 - - - +
130U PRO* 4.0 9.9 - - + +
131U PHE* 2.9 41.0 - + + -
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Residues in contact with THR 123 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85O ALA* 5.5 0.3 - - - +
86O ASP* 5.1 0.2 + - - -
132O ARG* 3.2 22.1 + - - -
11U ALA* 4.1 13.8 - - - +
23U VAL* 4.1 27.3 - - + +
119U VAL 4.2 4.3 - - - +
120U HIS* 2.8 30.6 + - - +
122U TYR* 1.3 75.8 - - - +
124U LEU* 1.4 65.5 + - - +
125U TYR 3.5 0.8 + - - -
130U PRO* 4.3 16.2 - - + -
153U PRO 3.9 21.1 - - - +
154U SER* 4.0 15.9 - - - +
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Residues in contact with LEU 124 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89O SER* 4.4 12.1 - - - +
131O MET* 3.9 0.6 - - + +
132O ARG* 3.4 41.8 + - - +
134O LEU* 3.3 35.7 - - + -
12U SER* 4.9 2.0 - - - -
117U MET* 6.0 1.1 - - + -
120U HIS* 3.3 50.9 - - + +
121U ALA* 3.6 11.7 - - + +
122U TYR 3.0 1.2 + - - -
123U THR* 1.4 82.2 - - - +
125U TYR* 1.3 89.3 + - + +
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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