Contacts of the helix formed by residues 114 - 128 (chain J) in PDB entry 4GUN
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 SER 114 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108J ILE* 3.8 9.8 + - - +
109J VAL* 5.2 4.0 - - - -
112J TYR* 3.0 9.7 + - - +
113J GLY* 1.4 76.7 - - - +
115J VAL* 1.4 62.5 + - - +
116J SER* 3.7 12.9 + - - -
117J ASN* 3.2 23.4 + - - +
118J LEU 3.2 15.2 + - - -
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Residues in contact with VAL 115 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97J HIS* 3.7 41.7 - - + +
98J PRO* 3.6 30.1 - - + +
100J THR* 6.0 4.5 - - + -
105J GLY* 6.2 0.4 - - - -
108J ILE* 3.7 24.4 - - + +
109J VAL* 6.3 1.3 - - + -
114J SER* 1.4 69.7 - - - +
116J SER* 1.3 54.7 + - - +
118J LEU* 3.1 5.1 + - - +
119J ILE* 2.8 44.9 + - + +
197J TRP* 4.1 16.2 - - + -
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Residues in contact with SER 116 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97J HIS* 4.8 10.3 - - - -
114J SER* 3.7 11.5 + - - -
115J VAL* 1.3 79.7 - - - +
117J ASN* 1.4 57.3 + - - +
119J ILE* 3.4 10.0 + - - +
120J ASP* 3.0 37.5 + - - +
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Residues in contact with ASN 117 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112J TYR* 2.8 37.7 + - - +
114J SER* 3.2 11.9 + - - +
115J VAL 3.3 0.2 - - - -
116J SER* 1.4 77.2 + - - +
118J LEU* 1.4 66.0 + - - +
120J ASP* 3.2 12.2 + - - +
121J ILE* 3.0 38.9 + - - +
142K GLN 4.9 3.6 + - - -
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Residues in contact with LEU 118 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108J ILE* 3.8 35.9 - - + -
112J TYR* 3.7 42.9 - - + +
114J SER 3.2 10.0 + - - +
115J VAL* 3.1 9.7 + - - +
117J ASN* 1.4 78.6 - - - +
119J ILE* 1.4 55.0 + - - +
121J ILE* 3.3 3.0 + - - +
122J THR* 2.9 35.0 + - - +
137J ILE* 4.1 34.8 - - + -
147J LEU* 4.8 0.9 - - + -
149J VAL* 3.8 20.4 - - + -
197J TRP* 4.4 8.1 - - + -
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Residues in contact with ILE 119 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97J HIS* 4.0 14.6 - - + +
115J VAL* 2.8 43.5 + - + +
116J SER* 3.6 8.5 - - - +
118J LEU* 1.4 67.5 - - + +
120J ASP* 1.3 62.7 + - - +
122J THR* 3.3 7.0 + - - -
123J ASN* 2.8 46.6 + - - +
192J TRP* 3.7 54.1 - - + -
197J TRP* 4.3 6.1 - - + +
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Residues in contact with ASP 120 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116J SER* 3.0 25.0 + - - +
117J ASN* 3.2 16.5 + - - +
119J ILE* 1.3 80.2 - - - +
121J ILE* 1.3 55.6 + - + +
123J ASN* 3.4 9.5 + - - +
124J SER* 3.0 29.0 + - - -
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Residues in contact with ILE 121 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112J TYR* 3.5 31.6 - - + -
117J ASN* 3.0 34.6 + - - +
118J LEU* 3.5 7.0 - - - +
120J ASP* 1.3 72.9 - - + +
122J THR* 1.3 64.6 + - - +
124J SER* 3.4 8.4 + - - -
125J LYS* 3.1 24.3 + - + +
149J VAL* 3.8 20.4 - - + -
142K GLN* 3.5 48.7 - - + +
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Residues in contact with THR 122 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118J LEU 2.9 16.9 + - - -
119J ILE 3.3 4.2 + - - -
121J ILE* 1.3 73.6 - - - +
123J ASN* 1.4 54.4 + - - +
125J LYS* 3.1 4.2 + - - +
126J LEU* 2.8 45.2 + - + +
135J ALA* 4.4 8.7 - - + -
137J ILE* 3.7 17.5 - - + +
149J VAL* 3.6 31.4 - - + +
167J ILE* 5.9 0.7 - - + -
169J ILE* 4.8 3.8 - - + -
192J TRP* 3.5 30.1 - - + -
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Residues in contact with ASN 123 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119J ILE* 2.8 33.8 + - - +
120J ASP* 3.7 10.2 + - - +
122J THR* 1.4 70.4 - - - +
124J SER* 1.4 56.2 + - - +
126J LEU* 3.4 15.2 + - - +
127J ALA* 3.0 29.6 + - - +
188J PHE* 3.6 21.3 + - + +
189J LYS* 4.5 10.0 - - - +
192J TRP* 2.8 33.7 + - - +
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Residues in contact with SER 124 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120J ASP 3.0 17.3 + - - -
121J ILE* 3.5 9.0 - - - -
123J ASN* 1.4 75.5 - - - +
125J LYS* 1.4 62.3 + - - +
127J ALA* 3.4 9.5 + - - +
128J GLY* 3.2 17.5 + - - -
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Residues in contact with LYS 125 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121J ILE* 3.1 20.5 + - + +
122J THR 3.4 8.1 - - - +
124J SER* 1.4 71.7 - - - +
126J LEU* 1.3 66.7 + - - +
128J GLY* 3.4 10.5 + - - -
129J ILE* 3.5 14.9 + - - +
135J ALA* 5.0 1.1 - - + -
149J VAL* 3.4 44.3 + - + +
150J VAL* 4.2 3.4 - - - +
151J THR* 3.6 35.9 + - + +
142K GLN* 5.4 2.9 - - - +
162K HIS* 5.0 18.5 + - + +
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Residues in contact with LEU 126 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122J THR* 2.8 31.9 + - + +
123J ASN* 3.5 24.0 - - - +
124J SER 3.3 0.2 - - - -
125J LYS* 1.3 76.1 - - - +
127J ALA* 1.4 60.6 + - - +
129J ILE* 3.2 31.1 + - + +
135J ALA* 3.4 25.4 - - + +
169J ILE* 3.8 30.5 - - + +
171J ALA* 4.1 5.2 - - + -
184J ARG* 3.3 9.7 + - - -
188J PHE* 3.5 43.7 - - + -
192J TRP* 4.7 2.5 - - + +
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Residues in contact with ALA 127 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123J ASN 3.0 13.6 + - - +
124J SER* 3.5 12.3 - - - +
126J LEU* 1.4 74.4 - - - +
128J GLY* 1.3 57.5 + - - +
129J ILE 4.1 0.5 - - - +
184J ARG* 2.7 22.8 + - - +
185J PRO* 6.2 4.5 - - + -
188J PHE* 3.9 8.6 - - + -
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Residues in contact with GLY 128 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124J SER 3.2 10.0 + - - -
125J LYS* 3.4 6.2 + - - -
126J LEU 3.3 1.0 - - - -
127J ALA* 1.3 75.8 - - - +
129J ILE* 1.4 63.0 + - - +
130J GLN* 3.3 14.9 + - - +
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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