Contacts of the helix formed by residues 110 - 125 (chain B) in PDB entry 2JG1
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 ASP 110 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84B LYS* 2.6 34.3 + - - -
108B GLU* 3.9 3.8 + - - -
109B ILE* 1.3 76.0 - - - +
111B ASN* 1.3 58.9 + - - +
112B GLN* 3.1 10.7 + - - +
113B GLU* 2.8 39.9 + - - +
114B ALA* 3.0 25.4 + - - +
140B GLY 5.5 0.9 - - - -
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Residues in contact with ASN 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ASP* 1.3 75.9 - - - +
112B GLN* 1.3 57.3 + - + +
114B ALA* 3.6 7.6 + - - +
115B ALA* 3.1 29.5 + - - +
140B GLY 5.2 5.2 - - - +
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Residues in contact with GLN 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A VAL* 3.6 49.5 - - + +
247A LEU* 3.9 13.2 - - - +
249A PRO* 5.4 4.6 - - - +
1312A ANP 5.8 0.8 + - - -
81B TYR* 4.0 4.0 + - - -
84B LYS* 4.8 10.5 + - - +
110B ASP* 3.1 11.0 + - - +
111B ASN* 1.3 73.8 - - + +
113B GLU* 1.3 61.2 + - + +
115B ALA* 3.5 4.9 + - - +
116B GLY* 2.9 26.3 + - - -
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Residues in contact with GLU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B PHE* 3.9 1.1 - - - -
81B TYR* 3.7 21.8 - - + +
82B ASN 4.6 0.4 - - - +
83B ILE* 3.4 24.4 - - + +
84B LYS* 2.6 56.3 + - - +
85B GLY 5.1 1.1 + - - -
108B GLU 4.0 3.8 - - - +
109B ILE* 3.5 22.7 - - + +
110B ASP* 2.8 36.0 + - - +
112B GLN* 1.3 70.8 - - + +
114B ALA* 1.3 60.0 + - - +
116B GLY* 3.3 1.0 + - - -
117B PHE* 2.9 30.7 + - - +
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Residues in contact with ALA 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B PHE* 4.7 0.2 - - - -
109B ILE* 3.8 5.3 - - - +
110B ASP 3.0 16.4 + - - +
111B ASN* 3.7 9.4 - - - +
113B GLU* 1.3 77.4 - - - +
115B ALA* 1.3 58.2 + - - +
118B ILE* 3.3 14.1 + - - +
140B GLY 6.1 0.2 - - - +
141B LEU* 3.8 23.1 - - + -
142B ASN 6.2 0.4 - - - +
145B TYR* 2.7 35.2 + - + -
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Residues in contact with ALA 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A SER* 5.9 4.3 - - - +
111B ASN 3.1 17.4 + - - +
112B GLN* 3.9 5.8 - - - +
113B GLU 3.3 0.2 - - - -
114B ALA* 1.3 72.5 - - - +
116B GLY* 1.3 66.3 + - - +
118B ILE* 3.3 8.9 + - - +
119B LYS* 3.2 27.8 + - + +
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Residues in contact with GLY 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A LEU* 6.4 2.0 - - - -
81B TYR* 3.3 35.2 - - - -
112B GLN 2.9 12.9 + - - -
113B GLU 3.3 0.2 + - - -
115B ALA* 1.3 78.0 - - - +
117B PHE* 1.3 60.5 + - - +
119B LYS* 3.4 7.4 + - - +
120B HIS* 3.0 18.4 + - - +
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Residues in contact with PHE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B LEU* 4.0 18.6 - - + -
7B LEU* 4.1 7.6 - - + -
56B SER* 3.6 22.0 - - - -
57B GLY* 3.9 13.7 - - - -
58B PHE* 3.5 24.7 - + + -
81B TYR* 3.6 27.0 - - + -
113B GLU 2.9 8.2 + - - +
115B ALA 3.3 0.2 - - - -
116B GLY* 1.3 75.1 - - - +
118B ILE* 1.3 55.3 + - + +
120B HIS* 3.1 9.8 + + - +
121B PHE* 2.7 58.6 + + + +
124B MSE 4.7 1.3 - - + -
145B TYR* 3.3 27.4 - + - +
149B ILE* 3.9 24.0 - - + -
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Residues in contact with ILE 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B ALA 3.3 15.0 + - - +
115B ALA* 3.3 11.4 + - - +
116B GLY 3.3 0.6 - - - -
117B PHE* 1.3 79.8 - - + +
119B LYS* 1.3 61.9 + - - +
121B PHE* 3.4 5.1 + - + +
122B GLU* 2.9 39.2 + - + +
145B TYR* 3.5 20.6 - - + +
148B GLN* 4.1 23.1 - - + +
149B ILE* 3.8 31.9 - - + +
152B ARG* 3.6 37.0 - - + +
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Residues in contact with LYS 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B ALA* 3.2 16.4 + - + +
116B GLY* 3.7 9.2 - - - +
118B ILE* 1.3 79.7 - - - +
120B HIS* 1.3 64.9 - - - +
122B GLU* 3.6 29.5 + - - +
123B GLN* 3.2 38.2 + - - +
152B ARG* 5.4 2.4 - - - +
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Residues in contact with HIS 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B SER* 4.0 4.3 - - - -
79B ALA* 2.9 37.2 + - + -
80B PHE 4.5 3.4 + - - -
81B TYR* 4.2 17.5 - + + -
116B GLY 3.0 14.5 + - - +
117B PHE* 3.1 20.6 + + - +
119B LYS* 1.3 77.4 - - - +
121B PHE* 1.3 60.8 + - - +
123B GLN* 3.3 15.7 + - - +
124B MSE 3.3 57.5 + - + +
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Residues in contact with PHE 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B LEU* 3.4 29.6 - - + -
5B LEU* 3.8 18.2 - - + -
117B PHE* 2.7 46.5 + + + +
118B ILE* 3.6 7.6 - - + +
120B HIS* 1.3 70.4 - - - +
122B GLU* 1.3 67.9 + - - +
124B MSE 2.9 22.6 + - + +
125B MSE 3.3 29.7 + - + +
131B VAL* 4.0 6.1 - - + -
149B ILE* 3.5 25.6 - - + -
152B ARG* 4.0 17.5 - - + -
153B CYS* 3.5 33.7 - - - -
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Residues in contact with GLU 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B ILE* 2.9 30.9 + - - +
119B LYS* 3.6 34.3 + - - +
121B PHE* 1.3 75.6 - - - +
123B GLN* 1.3 63.7 + - + +
125B MSE 3.2 28.2 + - - +
126B GLU 4.7 0.5 + - - -
152B ARG* 2.8 46.4 + - + -
156B LYS* 5.8 1.7 - - - -
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Residues in contact with GLN 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B LYS* 3.2 23.0 + - - +
120B HIS* 3.6 17.7 + - - +
121B PHE 3.2 0.4 - - - -
122B GLU* 1.3 76.8 - - + +
124B MSE 1.3 60.6 + - + +
125B MSE 3.3 0.2 - - - -
126B GLU* 3.7 19.9 - - - +
127B LYS* 3.7 10.7 - - - -
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Residues in contact with MSE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B LEU* 4.0 22.0 - - + -
54B LEU* 3.9 27.8 - - + -
56B SER* 3.6 25.4 - - - +
79B ALA* 4.4 6.3 - - - -
117B PHE* 4.7 1.6 - - + -
120B HIS* 3.3 40.8 + - + +
121B PHE* 2.9 30.4 + - + +
123B GLN* 1.3 76.2 - - + +
125B MSE 1.3 66.2 + - + +
126B GLU 3.2 2.9 - - - -
127B LYS* 2.9 36.0 + - + +
128B VAL* 3.5 15.9 + - + +
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Residues in contact with MSE 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B LEU* 4.0 6.5 - - + -
121B PHE* 3.3 52.6 + - + +
122B GLU* 3.2 22.7 + - - +
124B MSE 1.3 79.4 - - - +
126B GLU* 1.3 58.9 + - - +
127B LYS 3.5 0.3 + - - -
128B VAL* 3.7 34.6 - - + +
131B VAL* 4.1 2.9 - - + -
152B ARG* 4.1 13.5 - - + +
153B CYS* 4.1 22.9 - - - -
156B LYS* 3.8 26.5 - - + +
158B VAL* 4.1 20.2 - - - +
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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