Contacts of the helix formed by residues 105 - 120 (chain C) 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 105 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C HIS* 4.7 0.2 - - - +
96C TYR* 3.4 23.6 - - + +
102C GLU* 4.7 0.2 - - - +
103C PRO 3.4 6.0 - - - +
104C ILE* 1.3 92.1 - - + +
106C THR* 1.3 65.4 + - - +
107C ALA* 4.3 4.0 - - + +
108C GLN* 3.1 22.1 + - + +
109C LEU* 3.1 10.9 + - - +
139C ASN* 4.7 12.6 - - + -
78c GLU* 3.6 21.3 - - - +
80c ARG* 3.8 19.7 - - - +
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Residues in contact with THR 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C HIS* 4.8 0.5 - - - -
71C ILE* 3.7 19.1 - - + +
104C ILE 3.6 1.2 + - - -
105C PRO* 1.3 71.6 - - - +
107C ALA* 1.3 64.7 + - - +
108C GLN 3.3 0.2 + - - -
109C LEU* 3.3 2.6 + - - +
110C VAL* 2.9 27.0 + - + +
135C ILE* 4.4 8.1 - - + +
136C CYS 4.1 5.4 - - - +
137C GLY* 3.2 43.9 + - - +
138C TRP 4.0 1.2 + - - -
139C ASN* 4.3 13.0 - - - +
144C TYR* 4.1 15.8 - - + +
146C PHE* 4.2 16.8 - - + -
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Residues in contact with ALA 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C PRO* 3.2 3.5 - - + -
106C THR* 1.3 80.8 - - - +
108C GLN* 1.3 66.5 + - + +
110C VAL* 3.4 3.4 + - - +
111C GLN* 2.9 32.3 + - - +
144C TYR* 5.3 9.0 - - + -
146C PHE* 3.9 28.6 - - + -
59D VAL* 5.9 0.2 - - + -
60D PHE* 4.3 15.7 - - + -
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Residues in contact with GLN 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C TYR* 4.7 0.9 - - + -
104C ILE* 4.1 11.7 - - + -
105C PRO* 3.1 20.2 + - + +
107C ALA* 1.3 80.6 - - - +
109C LEU* 1.3 66.2 + - - +
111C GLN* 3.1 20.7 + - - +
112C ARG* 3.0 54.2 + - - +
77c LYS* 2.9 39.4 + - - +
78c GLU* 3.3 37.5 - - - +
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Residues in contact with LEU 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C ILE* 3.6 17.5 - - + -
71C ILE* 3.6 37.0 - - + -
89C ALA* 3.5 26.9 - - + +
92C LEU* 4.4 5.2 - - + -
93C ALA* 4.1 9.0 - - + +
104C ILE* 3.7 27.2 - - + +
105C PRO 3.1 9.4 + - - +
106C THR 3.6 7.4 - - - +
108C GLN* 1.3 75.8 - - - +
110C VAL* 1.3 64.8 + - - +
112C ARG* 3.3 2.4 + - - +
113C VAL* 2.9 42.7 + - + +
135C ILE* 4.3 12.3 - - + -
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Residues in contact with VAL 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C THR* 2.9 19.7 + - + +
107C ALA* 3.5 9.0 - - - +
109C LEU* 1.3 76.3 - - - +
111C GLN* 1.3 57.0 + - - +
113C VAL* 3.8 2.4 - - - +
114C ALA* 3.0 28.1 + - + +
135C ILE* 3.6 33.2 - - + -
146C PHE* 3.6 38.6 - - + -
148C SER* 5.3 4.2 - - - -
154C TYR* 3.7 37.9 - - + -
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Residues in contact with GLN 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C ALA 2.9 15.2 + - - +
108C GLN* 3.1 36.1 + - - +
110C VAL* 1.3 76.0 - - - +
112C ARG* 1.3 61.2 + - + +
114C ALA* 3.3 7.3 + - - +
115C SER* 2.9 31.8 + - - -
154C TYR* 3.3 35.4 + - + +
60D PHE* 3.9 20.6 - - - -
91D ARG* 5.5 3.5 + - - -
77c LYS* 4.1 23.1 + - - +
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Residues in contact with ARG 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C LEU* 4.0 34.7 - - + +
96C TYR* 4.0 28.0 - - - +
100C TYR* 5.0 8.9 + - - -
104C ILE* 4.6 10.3 - - - -
108C GLN* 3.0 51.3 + - - +
109C LEU* 4.0 2.9 - - - +
111C GLN* 1.3 75.4 - - + +
113C VAL* 1.3 66.0 + - - +
115C SER* 3.1 9.8 + - - -
116C VAL* 3.0 24.3 + - - +
74c TYR* 6.4 0.4 - - - -
77c LYS* 4.1 33.7 - - - +
78c GLU* 5.7 0.2 + - - -
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Residues in contact with VAL 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C LEU* 6.4 0.2 - - + -
85C LEU* 5.3 6.7 - - + +
89C ALA* 3.7 35.2 - - + +
92C LEU* 4.1 9.4 - - + -
109C LEU* 2.9 28.1 + - + +
110C VAL* 3.8 6.3 - - - +
112C ARG* 1.3 75.1 - - - +
114C ALA* 1.3 63.7 + - - +
116C VAL* 3.1 8.6 + - - +
117C MET* 3.0 29.6 + - + +
133C LEU* 3.8 29.2 - - + -
135C ILE* 4.6 9.9 - - + -
148C SER* 4.5 4.0 - - - +
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Residues in contact with ALA 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C VAL 3.0 20.2 + - - +
111C GLN 3.5 5.4 - - - +
113C VAL* 1.3 79.5 - - - +
115C SER* 1.3 58.4 + - - +
117C MET* 3.2 9.0 + - - +
118C GLN* 2.9 25.1 + - - +
148C SER* 5.0 4.7 - - - -
152C GLY* 3.2 32.8 - - - +
154C TYR* 3.8 21.3 - - + -
84D ASN* 5.5 1.6 - - - +
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Residues in contact with SER 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C GLN 2.9 16.5 + - - -
112C ARG* 3.1 12.1 + - - +
114C ALA* 1.3 74.5 - - - +
116C VAL* 1.3 65.4 + - - +
118C GLN* 3.2 9.6 + - - +
119C GLU* 3.0 27.2 + - - +
84D ASN* 5.6 6.8 - - - +
85D VAL* 6.2 3.6 - - - -
88D ASN* 5.8 1.7 + - - -
77c LYS* 5.9 1.2 + - - -
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Residues in contact with VAL 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C LEU* 4.1 22.0 - - + -
88C ARG* 3.8 54.5 - - + +
92C LEU* 4.2 13.9 - - + -
112C ARG 3.0 14.7 + - - +
113C VAL* 3.1 10.1 + - - +
115C SER* 1.3 76.9 - - - +
117C MET* 1.3 63.8 + - - +
119C GLU* 3.3 23.3 + - - +
120C TYR* 3.3 16.5 - - + -
129C PHE* 4.6 4.9 - - + -
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Residues in contact with MET 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C LEU* 3.9 32.3 - - + -
113C VAL* 3.0 20.7 + - + +
114C ALA* 3.6 8.3 - - - +
116C VAL* 1.3 76.1 - - - +
118C GLN* 1.3 62.9 + - - +
120C TYR* 3.4 13.9 + - - +
121C THR* 3.6 12.3 - - - +
129C PHE* 4.1 19.0 + - + -
131C VAL 3.5 25.4 - - - +
133C LEU* 4.1 13.2 - - + -
148C SER* 3.5 29.2 - - - +
149C ASP 3.7 18.6 - - - +
150C PRO* 4.0 11.1 - - + +
152C GLY* 4.0 11.2 - - - +
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Residues in contact with GLN 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C ALA 2.9 13.4 + - - +
115C SER* 3.2 11.5 + - - +
117C MET* 1.3 75.3 - - - +
119C GLU* 1.3 73.2 + - - +
121C THR* 2.7 32.1 + - - +
122C GLN* 3.3 29.5 + - - +
151C SER 3.9 11.9 - - - +
152C GLY* 4.1 1.4 - - - +
81D SER* 3.8 28.9 - - - +
82D ASP* 3.4 18.6 + - - +
85D VAL* 3.3 30.6 - - + +
128D ARG* 4.3 1.0 - - - +
130D PHE* 4.9 0.2 - - - -
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Residues in contact with GLU 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C ARG* 4.1 18.8 + - - -
115C SER* 3.0 15.0 + - - +
116C VAL* 3.3 27.3 + - - +
118C GLN* 1.3 84.8 + - - +
120C TYR* 1.3 67.4 + - + +
121C THR 3.0 1.8 + - - -
122C GLN* 3.2 3.0 + - - -
123C SER* 2.9 45.0 + - - +
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Residues in contact with TYR 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B GLN* 3.3 29.2 - - + -
128B ASN* 5.7 1.8 - - - -
10C THR* 4.6 0.3 + - - -
88C ARG* 4.1 22.7 + - - -
116C VAL* 3.3 17.5 - - + -
117C MET 3.4 3.8 + - - +
118C GLN 3.1 1.8 - - - -
119C GLU* 1.3 94.3 - - + +
121C THR* 1.3 59.0 + - - +
122C GLN 3.5 0.7 - - - -
123C SER* 5.9 0.9 - - - -
126C VAL* 3.9 42.9 - - + +
127C ARG 3.6 8.7 - - - +
128C PRO* 3.5 25.7 - - + +
129C PHE* 3.4 31.4 - + + -
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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
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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