Contacts of the helix formed by residues 107 - 121 (chain X) 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 107 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98X PHE* 3.6 17.0 - - + -
104X TYR* 4.0 12.3 - - + -
105X ASN 3.4 4.0 - - - +
106X ILE* 1.4 96.2 - - + +
108X LEU* 1.3 66.6 + - - +
109X LYS* 3.4 2.5 - - + +
110X HIS* 3.2 10.7 + - + +
111X LEU* 3.1 19.3 + - - +
144X ASP* 5.5 8.5 - - - +
147X GLN* 6.1 0.7 - - - +
70a LEU* 4.0 28.9 - - + -
72a GLU* 5.2 9.0 - - - +
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Residues in contact with LEU 108 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73X VAL* 3.8 29.4 - - + -
106X ILE 3.6 2.9 + - - -
107X PRO* 1.3 72.1 - - - +
109X LYS* 1.3 57.6 + - - +
111X LEU* 3.2 8.6 + - + +
112X ALA* 2.9 29.6 + - + +
137X LEU* 3.5 29.4 - - + +
138X GLY 4.3 0.9 - - - +
139X SER* 3.7 29.6 + - - +
147X GLN* 3.2 52.6 - - + +
148X LEU 4.0 0.9 - - - +
149X TYR* 4.0 10.3 - - + -
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Residues in contact with LYS 109 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107X PRO* 3.4 2.7 - - + +
108X LEU* 1.3 77.3 - - - +
110X HIS* 1.3 57.3 + - - +
112X ALA* 3.5 3.1 + - - +
113X ASP* 2.9 37.3 + - - +
147X GLN* 4.0 11.7 - - - +
149X TYR* 3.4 34.5 - - + +
70a LEU* 6.1 1.8 - - + -
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Residues in contact with HIS 110 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94X GLU* 5.8 0.7 - - - -
98X PHE* 3.4 39.3 - + - -
102X PHE* 5.9 0.7 - + - -
106X ILE* 3.8 5.3 - - - +
107X PRO* 3.2 15.9 + - + +
108X LEU 3.1 0.6 - - - -
109X LYS* 1.3 76.9 - - - +
111X LEU* 1.3 64.9 + - - +
113X ASP* 3.1 6.4 + - + +
114X ARG* 2.9 43.9 + - + +
66a HIS* 4.8 5.1 - + - -
69a GLU* 2.8 56.2 + - + +
70a LEU* 3.3 28.7 - - + +
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Residues in contact with LEU 111 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69X VAL* 3.8 13.9 - - + -
73X VAL* 3.8 34.3 - - + -
91X ALA* 3.7 22.4 - - + +
94X GLU* 3.9 14.1 - - + -
95X ALA* 4.2 5.8 - - + +
106X ILE* 3.7 26.1 - - + +
107X PRO 3.1 11.7 + - - +
108X LEU* 3.7 9.4 - - + +
110X HIS* 1.3 74.6 - - - +
112X ALA* 1.3 64.0 + - - +
114X ARG* 3.3 2.7 + - - +
115X VAL* 2.9 46.0 + - + +
137X LEU* 4.1 13.5 - - + -
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Residues in contact with ALA 112 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108X LEU 2.9 17.2 + - - +
109X LYS 3.6 4.9 - - - +
111X LEU* 1.3 78.0 - - - +
113X ASP* 1.3 64.5 + - - +
115X VAL* 3.4 1.1 + - - +
116X ALA* 2.9 28.1 + - - +
137X LEU* 4.0 21.0 - - + +
149X TYR* 4.2 22.4 - - + -
151X ILE* 4.4 5.3 - - + +
157X SER* 3.8 17.7 - - - +
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Residues in contact with ASP 113 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B ARG* 4.0 24.5 + - - -
92B GLN* 5.3 10.8 + - - +
109X LYS* 2.9 25.1 + - - +
110X HIS* 3.1 7.6 + - + +
112X ALA* 1.3 76.1 - - - +
114X ARG* 1.3 56.2 + - - +
116X ALA* 3.7 3.4 - - - +
117X MET* 2.9 37.3 + - + +
149X TYR* 6.3 1.3 - - - -
157X SER* 4.3 12.2 + - - +
69a GLU* 4.9 17.8 - - + +
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Residues in contact with ARG 114 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B GLN* 5.7 1.6 + - - -
94X GLU* 2.8 54.0 + - + +
106X ILE* 5.1 0.4 - - + -
110X HIS* 2.9 40.4 + - + +
111X LEU* 3.7 2.9 - - - +
113X ASP* 1.3 74.3 - - - +
115X VAL* 1.3 63.7 + - - +
117X MET* 3.1 8.6 + - - +
118X TYR* 3.0 21.6 + - - +
65a PHE* 5.7 4.4 - - - -
69a GLU* 3.8 22.7 + - - +
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Residues in contact with VAL 115 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87X LEU* 4.7 16.4 - - + +
90X ILE* 4.8 10.8 - - + -
91X ALA* 3.9 20.4 - - + +
94X GLU* 4.8 5.2 - - + -
111X LEU* 2.9 44.2 + - + +
112X ALA* 4.1 3.6 - - - +
114X ARG* 1.3 72.5 - - - +
116X ALA* 1.3 58.6 + - - +
118X TYR* 3.2 8.3 + - - +
119X VAL* 2.9 30.4 + - + +
135X PHE* 3.4 34.3 - - + -
137X LEU* 5.1 2.7 - - + -
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Residues in contact with ALA 116 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112X ALA 2.9 19.2 + - - +
113X ASP* 3.7 4.7 - - - +
115X VAL* 1.3 77.4 - - - +
117X MET* 1.3 61.1 + - + +
119X VAL* 3.3 1.6 + - - +
120X HIS* 2.9 28.6 + - - +
151X ILE* 4.0 19.5 - - + -
155X GLY* 3.4 25.7 - - - +
157X SER* 3.9 18.2 - - - -
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Residues in contact with MET 117 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ALA 4.4 4.7 - - - +
88B ARG* 4.1 9.4 - - + -
89B SER* 3.4 50.3 - - - +
92B GLN* 4.3 22.9 - - + -
113X ASP* 2.9 23.0 + - + +
114X ARG* 3.1 6.7 + - - +
116X ALA* 1.3 77.0 - - + +
118X TYR* 1.3 58.8 + - - +
120X HIS* 3.3 17.7 + - - +
121X ALA* 3.0 27.9 + - - +
155X GLY 5.8 1.6 - - - +
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Residues in contact with TYR 118 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87X LEU* 4.3 9.0 - - + -
90X ILE* 3.4 51.8 - - + +
94X GLU* 6.1 1.1 - - - -
114X ARG 3.0 12.6 + - - +
115X VAL* 3.3 13.5 - - - +
117X MET* 1.3 77.4 - - - +
119X VAL* 1.3 61.7 + - - +
121X ALA* 3.3 12.5 + - + +
122X TYR* 3.3 50.0 + + - -
131X PHE* 4.1 8.1 - + - -
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Residues in contact with VAL 119 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87X LEU* 3.7 37.5 - - + -
115X VAL 2.9 18.9 + - - +
116X ALA* 3.6 7.9 - - - +
118X TYR* 1.3 76.4 - - - +
120X HIS* 1.3 64.2 + - - +
122X TYR* 3.0 20.1 + - - +
123X THR* 4.0 5.0 - - - +
131X PHE* 4.1 17.8 + - + +
133X CYS 6.0 0.2 - - - +
135X PHE* 4.3 11.7 - - + -
151X ILE* 4.7 1.1 - - + -
152X ASP 3.8 16.2 - - - +
153X PRO* 3.6 26.5 - - + +
155X GLY* 3.9 5.2 - - - -
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Residues in contact with HIS 120 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ALA* 3.6 23.3 - - + -
86B ASP* 2.7 33.7 + - - -
89B SER* 3.4 33.8 - - - -
134B LEU* 4.8 1.1 - - + -
116X ALA 2.9 17.2 + - - +
117X MET* 3.6 17.6 + - - +
119X VAL* 1.3 76.6 - - - +
121X ALA* 1.3 65.2 + - - +
122X TYR 3.0 0.6 + - - -
123X THR* 2.9 31.4 + - - -
124X LEU* 3.9 27.6 - - + +
154X SER 3.8 13.7 - - - +
155X GLY* 4.2 3.4 - - - +
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Residues in contact with ALA 121 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C ALA 4.5 9.0 + - - +
117X MET 3.0 12.4 + - - +
118X TYR* 3.4 17.3 - - + +
119X VAL 3.1 0.6 - - - -
120X HIS* 1.3 81.7 - - - +
122X TYR* 1.3 61.9 + - + +
123X THR 3.4 1.3 - - - -
124X LEU* 4.3 8.9 + - + -
125X TYR* 3.5 30.2 - - + -
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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