Contacts of the helix formed by residues 104 - 118 (chain m) in PDB entry 5GJQ
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 104 (chain m).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69m HIS* 5.3 0.2 - - + -
101m ARG* 4.1 15.9 - - - +
102m PRO 3.1 11.4 - - - +
103m LEU* 1.3 97.0 - - + +
105m VAL* 1.3 66.8 + - - +
106m SER* 4.7 2.7 - - - +
107m ARG* 3.2 35.7 + - + +
108m LEU* 3.3 8.7 + - - +
138m ASP* 4.0 12.6 - - + +
139m ASP* 5.9 2.9 - - - +
81u HIS* 3.4 37.9 - - + +
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Residues in contact with VAL 105 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69m HIS* 4.8 2.0 - - + -
70m ILE* 3.9 31.0 - - + -
104m PRO* 1.3 73.6 - - - +
106m SER* 1.3 64.4 + - - +
108m LEU* 3.1 4.0 + - + +
109m VAL* 2.9 21.8 + - + +
134m ILE* 4.0 22.9 - - + +
136m GLY* 4.1 7.0 - - - -
137m TYR 4.1 19.3 - - - +
138m ASP* 3.3 22.2 + - + +
143m HIS* 4.3 11.2 - - + -
145m PHE* 4.0 23.8 - - + -
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Residues in contact with SER 106 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104m PRO* 4.7 5.0 - - - +
105m VAL* 1.3 79.2 - - - +
107m ARG* 1.3 59.4 + - - +
109m VAL* 3.5 3.8 + - - +
110m SER* 2.9 31.3 + - - -
138m ASP* 4.6 1.8 + - - -
143m HIS* 5.8 4.0 - - - -
145m PHE* 4.3 23.5 - - - -
153m TYR* 5.6 0.9 - - - -
79u ASP* 3.4 30.7 + - - +
81u HIS* 4.9 2.3 - - - -
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Residues in contact with ARG 107 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101m ARG* 4.1 10.0 - - - +
103m LEU* 4.1 13.9 - - + -
104m PRO* 3.2 32.9 + - - +
105m VAL 3.1 0.8 - - - -
106m SER* 1.3 77.9 - - - +
108m LEU* 1.3 65.5 + - - +
110m SER* 3.2 8.7 + - - -
111m LEU* 2.9 31.8 + - + +
74u GLU* 3.1 47.0 + - - +
77u LEU* 4.1 20.6 - - + +
79u ASP* 3.2 29.2 + - - +
81u HIS* 3.5 20.2 - - - +
83u TYR* 3.8 15.6 + - - -
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Residues in contact with LEU 108 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66m VAL* 4.3 0.4 - - + -
70m ILE* 3.6 31.0 - - + -
87m PHE* 5.3 0.7 - - + -
88m MET* 3.6 62.4 - - + +
91m GLU* 4.3 7.6 - - + -
92m CYS* 4.2 9.2 - - - -
103m LEU* 4.0 23.4 - - + +
104m PRO 3.3 7.5 + - - +
105m VAL* 3.1 12.3 + - - +
107m ARG* 1.3 79.0 - - - +
109m VAL* 1.3 64.0 + - + +
111m LEU* 3.1 11.0 + - + +
112m ILE* 3.0 26.6 + - + +
134m ILE* 5.3 2.2 - - + -
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Residues in contact with VAL 109 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105m VAL* 2.9 22.7 + - + +
106m SER* 3.6 8.3 - - - +
108m LEU* 1.3 76.1 - - - +
110m SER* 1.3 57.1 + - - +
112m ILE* 3.0 13.1 + - - +
113m GLY* 2.9 24.6 + - - -
134m ILE* 3.8 19.5 - - + -
145m PHE* 3.7 39.0 - - + -
147m THR* 4.8 6.6 - - + +
153m TYR* 3.5 43.1 - - + -
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Residues in contact with SER 110 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106m SER 2.9 16.9 + - - -
107m ARG* 3.5 12.0 - - - -
109m VAL* 1.3 76.6 - - - +
111m LEU* 1.3 61.1 + - - +
113m GLY* 3.2 2.3 + - - -
114m SER* 2.9 30.9 + - - -
153m TYR* 3.4 26.9 + - - -
77u LEU* 6.0 3.0 - - - +
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Residues in contact with LEU 111 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87m PHE* 4.1 18.0 - - + -
91m GLU* 3.5 41.1 - - + +
103m LEU* 4.6 7.2 - - + -
107m ARG* 2.9 22.8 + - + +
108m LEU* 3.4 14.6 - - + +
110m SER* 1.3 77.2 - - - +
112m ILE* 1.3 60.6 + - - +
114m SER* 3.2 10.8 + - - +
115m LYS* 2.9 29.1 + - - +
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Residues in contact with ILE 112 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84m LEU* 4.2 27.1 - - + -
87m PHE* 4.6 9.9 - - + -
88m MET* 3.4 49.6 - - + -
108m LEU* 3.0 13.7 + - + +
109m VAL* 3.0 7.8 + - - +
111m LEU* 1.3 76.7 - - - +
113m GLY* 1.3 55.4 + - - +
115m LYS* 3.8 5.5 - - - +
116m THR* 2.6 40.8 + - + +
132m LEU* 4.3 4.7 - - + -
134m ILE* 3.8 18.6 - - + -
147m THR* 4.5 17.7 - - + +
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Residues in contact with GLY 113 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109m VAL 2.9 13.4 + - - -
110m SER 3.6 3.4 - - - -
111m LEU 3.2 0.4 - - - -
112m ILE* 1.3 77.4 - - - +
114m SER* 1.3 61.4 + - - +
116m THR* 3.2 7.7 + - - -
117m GLN* 2.9 27.1 + - - +
147m THR* 6.0 1.1 - - - +
151m ALA* 3.7 18.9 - - - +
153m TYR* 4.4 11.4 - - - -
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Residues in contact with SER 114 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110m SER* 2.9 15.9 + - - -
111m LEU* 3.5 16.4 - - - +
113m GLY* 1.3 76.3 - - - +
115m LYS* 1.3 63.3 + - - +
117m GLN* 3.4 12.5 + - - +
118m ILE* 3.5 20.9 + - - +
86n SER* 6.5 1.1 - - - +
89n ASP* 3.7 18.5 + - - -
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Residues in contact with LYS 115 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83m LEU* 5.2 8.1 - - - -
84m LEU* 4.2 11.9 - - + -
87m PHE* 3.5 54.1 - - + -
111m LEU 2.9 16.7 + - - +
112m ILE* 3.8 5.2 - - - +
113m GLY 3.2 0.2 - - - -
114m SER* 1.3 77.8 - - - +
116m THR* 1.3 60.7 - - - +
118m ILE* 3.6 12.1 + - + +
119m PRO* 3.4 15.1 - - - +
128m TYR* 3.6 28.5 + - + +
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Residues in contact with THR 116 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84m LEU* 4.0 24.0 - - + -
112m ILE* 2.6 28.4 + - + +
113m GLY* 3.2 2.9 + - - -
115m LYS* 1.3 74.6 - - - +
117m GLN* 1.3 63.0 + - - +
118m ILE 3.3 0.2 - - - -
119m PRO* 3.3 11.8 - - - +
120m THR* 3.4 13.9 - - - +
128m TYR* 3.5 33.9 + - + -
147m THR* 6.1 1.0 - - - +
148m CYS 5.4 3.1 - - - +
149m PRO* 4.7 6.1 - - + +
151m ALA* 3.1 28.3 - - - +
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Residues in contact with GLN 117 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113m GLY 2.9 18.9 + - - +
114m SER* 3.7 6.6 - - - +
115m LYS 3.3 0.4 - - - -
116m THR* 1.3 77.8 + - - +
118m ILE* 1.3 77.6 + - - +
120m THR* 2.8 31.0 + - - +
121m GLN* 3.1 27.8 + - - +
151m ALA* 3.6 8.7 - - + -
82n ALA* 3.9 31.6 - - + +
83n ASP* 3.3 20.4 + - - -
86n SER* 3.7 25.0 + - - -
131n PHE* 4.5 0.2 - - - -
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Residues in contact with ILE 118 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127l ASP* 6.0 1.1 - - - -
114m SER* 3.5 17.2 + - - +
115m LYS* 3.9 9.9 - - + +
116m THR 3.3 0.2 - - - -
117m GLN* 1.3 86.4 + - - +
119m PRO* 1.3 70.3 - - + +
120m THR 3.2 1.2 + - - -
121m GLN* 3.3 18.2 + - - +
122m ARG* 3.8 45.7 + - + +
125m ARG* 4.4 11.4 - - - +
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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
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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