Contacts of the helix formed by residues 105 - 120 (chain i) 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 i).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96i TYR* 3.5 28.5 - - + +
102i GLU* 4.5 2.0 - - - +
103i PRO 3.3 8.7 - - - +
104i ILE* 1.3 91.9 - - + +
106i THR* 1.3 66.0 + - - +
107i ALA* 4.4 4.9 - - + +
108i GLN* 3.1 14.5 + - + +
109i LEU* 3.1 17.3 + - - +
139i ASN* 4.6 15.7 - - + -
78q GLU* 3.9 11.9 - - - +
80q ARG* 4.0 22.2 - - - +
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Residues in contact with THR 106 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70i HIS* 4.8 0.9 + - - -
71i ILE* 3.7 21.1 - - + +
104i ILE 3.5 2.0 + - - -
105i PRO* 1.3 71.2 - - - +
107i ALA* 1.3 57.9 + - - +
109i LEU* 3.2 2.1 + - + +
110i VAL* 2.9 28.1 + - - +
135i ILE* 4.2 12.8 - - + -
136i CYS 4.1 6.1 - - - +
137i GLY* 3.2 44.1 + - - +
138i TRP 3.8 5.4 + - - -
139i ASN* 4.8 4.9 - - - +
144i TYR* 4.2 15.7 - - + +
146i PHE* 3.9 17.7 - - + -
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Residues in contact with ALA 107 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105i PRO* 5.0 4.7 - - + -
106i THR* 1.3 79.7 - - - +
108i GLN* 1.3 63.5 + - - +
110i VAL* 3.3 3.9 + - - +
111i GLN* 2.9 39.5 + - - +
144i TYR* 5.6 7.9 - - + -
146i PHE* 3.9 25.6 - - + -
154i TYR* 5.4 0.9 - - - -
60j PHE* 4.1 20.2 - - + -
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Residues in contact with GLN 108 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96i TYR* 4.6 1.8 - - + -
104i ILE* 3.9 12.8 - - + -
105i PRO* 3.1 21.0 + - + +
107i ALA* 1.3 79.4 - - - +
109i LEU* 1.3 66.3 + - - +
111i GLN* 3.2 19.8 + - - +
112i ARG* 3.0 53.3 + - - +
77q LYS* 3.2 39.4 + - - +
78q GLU* 3.4 39.7 - - - +
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Residues in contact with LEU 109 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67i ILE* 3.6 30.1 - - + -
71i ILE* 3.6 31.0 - - + -
89i ALA* 3.6 25.8 - - + +
92i LEU* 4.2 12.3 - - + -
93i ALA* 4.3 4.0 - - + +
104i ILE* 3.7 22.8 - - + +
105i PRO 3.1 10.3 + - - +
106i THR 3.6 7.0 - - - +
108i GLN* 1.3 76.8 - - - +
110i VAL* 1.3 62.1 + - - +
112i ARG* 3.3 1.8 + - - -
113i VAL* 2.9 35.2 + - + +
135i ILE* 4.4 12.1 - - + -
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Residues in contact with VAL 110 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106i THR 2.9 18.4 + - - +
107i ALA 3.5 8.1 - - - +
109i LEU* 1.3 75.9 - - - +
111i GLN* 1.3 58.2 + - - +
113i VAL* 4.0 1.3 - - - +
114i ALA* 2.9 28.2 + - - +
135i ILE* 3.8 28.9 - - + -
146i PHE* 3.6 38.8 - - + -
148i SER* 4.8 9.3 - - - -
154i TYR* 3.6 40.2 - - + -
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Residues in contact with GLN 111 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107i ALA* 2.9 27.6 + - - +
108i GLN* 3.2 31.6 + - - +
110i VAL* 1.3 74.9 - - - +
112i ARG* 1.3 62.0 + - + +
114i ALA* 3.3 8.0 + - - +
115i SER* 2.9 30.7 + - - -
154i TYR* 3.4 36.9 + - + +
60j PHE* 4.6 11.3 - - - -
91j ARG* 5.6 1.9 + - - -
77q LYS* 4.2 18.4 + - - +
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Residues in contact with ARG 112 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92i LEU* 3.9 39.8 + - + +
96i TYR* 4.1 25.3 - - - +
100i TYR* 5.4 4.0 + - - -
104i ILE* 4.5 9.6 - - - -
108i GLN* 3.0 50.7 + - - +
109i LEU 3.9 3.1 - - - +
111i GLN* 1.3 75.6 - - + +
113i VAL* 1.3 66.6 + - - +
115i SER* 3.1 10.4 + - - +
116i VAL* 3.1 24.3 + - - +
77q LYS* 4.9 14.6 - - - +
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Residues in contact with VAL 113 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73i LEU* 6.4 0.2 - - + -
85i LEU* 4.2 22.7 - - + +
88i ARG* 6.5 0.4 - - + -
89i ALA* 3.8 26.9 - - + -
92i LEU* 4.0 12.3 - - + -
109i LEU* 2.9 29.1 + - + +
110i VAL 4.1 2.7 - - - +
112i ARG* 1.3 75.3 - - - +
114i ALA* 1.3 58.9 + - - +
116i VAL* 3.2 7.4 + - + +
117i MET* 2.9 27.9 + - + +
133i LEU* 3.9 26.9 - - + -
135i ILE* 4.6 12.1 - - + -
148i SER* 5.5 1.3 - - - +
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Residues in contact with ALA 114 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110i VAL 2.9 19.7 + - - +
111i GLN* 3.4 6.3 - - - +
113i VAL* 1.3 77.7 - - - +
115i SER* 1.3 56.7 + - - +
117i MET* 3.2 11.4 + - - -
118i GLN* 2.9 29.2 + - - +
148i SER* 5.1 4.2 - - - -
152i GLY* 3.2 29.0 - - - +
154i TYR* 4.1 19.5 - - + -
84j ASN* 5.3 2.0 - - - +
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Residues in contact with SER 115 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111i GLN 2.9 16.0 + - - -
112i ARG* 3.1 12.2 + - - +
114i ALA* 1.3 72.8 - - - +
116i VAL* 1.3 67.3 + - - +
118i GLN* 3.1 10.3 + - - +
119i GLU* 3.0 24.8 + - - +
84j ASN* 5.9 2.8 - - - +
85j VAL* 6.1 3.4 - - - -
88j ASN* 5.9 1.2 + - - -
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Residues in contact with VAL 116 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85i LEU* 4.2 20.0 - - + -
88i ARG* 3.8 54.7 - - + +
92i LEU* 4.6 12.8 - - + -
112i ARG 3.1 10.6 + - - +
113i VAL* 3.4 11.4 - - + +
115i SER* 1.3 80.9 - - - +
117i MET* 1.3 62.8 + - - +
119i GLU* 3.3 24.4 - - - +
120i TYR* 3.4 9.8 - - + -
129i PHE* 4.4 4.7 - - + -
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Residues in contact with MET 117 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85i LEU* 4.0 33.2 - - + -
113i VAL* 2.9 21.4 + - + +
114i ALA* 3.6 9.9 - - - +
116i VAL* 1.3 76.8 - - - +
118i GLN* 1.3 62.9 + - - +
120i TYR* 3.2 13.5 + - - +
121i THR* 3.7 12.0 - - - +
128i PRO* 5.8 0.2 - - - +
129i PHE* 4.0 17.4 - - + -
131i VAL 3.5 25.4 - - - +
133i LEU* 4.3 6.3 - - + -
148i SER* 3.5 28.9 - - - +
149i ASP 3.7 22.9 - - - +
150i PRO* 3.8 11.7 - - + +
152i GLY* 4.1 6.5 - - - -
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Residues in contact with GLN 118 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114i ALA 2.9 16.6 + - - +
115i SER* 3.1 9.9 + - - +
117i MET* 1.3 75.2 - - - +
119i GLU* 1.3 71.8 + - - +
121i THR* 2.7 25.5 + - - +
122i GLN* 3.3 26.9 + - - +
151i SER 3.9 13.7 - - - +
152i GLY* 4.2 2.2 - - - +
81j SER* 3.8 24.5 - - - +
82j ASP* 3.6 15.0 + - - -
85j VAL* 3.3 33.6 - - + +
128j ARG* 3.9 5.7 - - - +
130j PHE* 4.3 2.6 - - - -
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Residues in contact with GLU 119 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88i ARG* 4.2 11.4 + - - -
115i SER 3.0 14.0 + - - +
116i VAL* 3.3 16.4 - - - +
118i GLN* 1.3 85.0 + - - +
120i TYR* 1.3 72.6 + - + +
121i THR 3.1 1.4 + - - -
122i GLN* 3.2 2.3 + - - -
123i SER* 2.9 47.4 + - - +
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Residues in contact with TYR 120 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127h GLN* 2.9 42.7 + - + -
10i THR* 4.5 0.2 + - - -
88i ARG* 4.2 22.1 + - - -
116i VAL 3.4 16.2 - - - -
117i MET 3.2 8.6 + - - +
118i GLN 3.1 1.6 - - - -
119i GLU* 1.3 94.3 - - + +
121i THR* 1.3 59.4 + - - +
122i GLN 3.5 0.4 - - - -
123i SER* 5.0 2.0 - - - -
126i VAL* 3.9 33.2 - - + +
127i ARG 3.6 12.7 - - - +
128i PRO* 3.4 24.7 - - + +
129i PHE* 3.5 26.4 - + + -
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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