Contacts of the helix formed by residues 105 - 119 (chain B) in PDB entry 1GN3
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 105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99B ILE* 4.0 2.1 - - - +
100B ALA* 3.9 13.4 - - - +
103B PHE* 2.7 8.4 + - - +
104B GLY* 1.3 77.4 - - - +
106B PHE* 1.3 64.3 + - - +
107B ASP* 2.9 11.3 + - - +
108B LYS* 2.8 37.7 + - - +
109B PHE* 3.1 13.5 + - - +
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Residues in contact with PHE 106 (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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89B ASP 4.1 4.9 - - - -
90B LYS* 3.5 40.4 - - + +
91B PRO* 3.2 34.5 - - + -
99B ILE* 3.9 14.3 - - + +
100B ALA* 4.9 2.8 - - - +
105B SER* 1.3 75.8 + - - +
107B ASP* 1.3 62.1 + - - +
109B PHE* 3.4 12.9 + + - -
110B ARG* 2.9 68.5 + - - +
182B TRP* 4.8 4.7 - + + -
187B TRP* 3.4 26.9 - + - -
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Residues in contact with ASP 107 (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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54A GLU* 5.2 2.2 - - - +
90B LYS* 4.0 17.9 + - - -
105B SER* 2.9 7.2 + - - +
106B PHE* 1.3 78.2 - - - +
108B LYS* 1.3 69.9 + - + +
110B ARG* 3.6 32.6 + - - +
111B ALA* 3.2 24.1 + - - +
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Residues in contact with LYS 108 (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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51A ARG* 3.3 39.1 + - + +
52A ALA* 4.1 15.7 + - - +
54A GLU* 4.3 23.1 - - - +
56A HIS* 4.7 1.2 + - - -
103B PHE* 2.9 27.6 - - - +
104B GLY* 4.7 6.8 - - - -
105B SER* 2.8 23.0 + - - +
107B ASP* 1.3 79.7 - - + +
109B PHE* 1.3 62.8 + - - +
111B ALA* 3.2 7.1 - - - +
112B GLN* 3.2 23.2 + - - +
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Residues in contact with PHE 109 (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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99B ILE* 3.9 11.9 - - + -
103B PHE* 3.5 40.9 - + + +
105B SER 3.1 12.0 + - - +
106B PHE* 3.7 16.6 - + - +
107B ASP 3.1 0.2 - - - -
108B LYS* 1.3 77.3 - - - +
110B ARG* 1.3 71.1 + - - +
112B GLN* 3.3 3.4 + - - +
113B PHE* 2.9 38.3 + + - +
128B LEU* 4.0 30.7 - - + -
139B ILE* 3.5 29.4 - - + -
157B LEU* 4.4 8.1 - - + -
182B TRP* 3.7 29.2 - + - -
187B TRP* 4.4 12.6 - + - -
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Residues in contact with ARG 110 (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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89B ASP 5.0 3.2 + - - -
90B LYS* 4.5 11.5 - - - +
106B PHE* 2.9 52.4 + - - +
107B ASP* 3.6 27.9 + - - +
109B PHE* 1.3 83.9 - - - +
111B ALA* 1.3 52.1 + - - +
113B PHE* 2.8 5.9 + - - +
114B HIS* 2.6 37.3 + - + +
182B TRP* 3.6 47.5 - - + +
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Residues in contact with ALA 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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54A GLU* 4.9 9.9 - - - +
56A HIS* 4.3 14.3 - - + +
107B ASP 3.2 16.4 - - - +
108B LYS* 3.2 9.0 - - - +
110B ARG* 1.3 78.2 - - - +
112B GLN* 1.3 58.8 + - - +
114B HIS* 3.1 9.9 + - - +
115B ALA* 2.9 27.5 + - - +
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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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47A LEU* 3.7 24.6 - - - +
51A ARG* 2.5 51.7 + - - +
56A HIS* 3.8 22.2 + - + +
59A ILE* 4.2 10.2 - - + +
63A GLU* 3.6 17.9 + - - +
103B PHE* 3.6 6.9 - - - -
108B LYS 3.2 11.0 + - - +
109B PHE* 3.8 3.8 - - - +
111B ALA* 1.3 82.0 - - - +
113B PHE* 1.3 58.7 + - - +
115B ALA* 3.2 2.3 + - - +
116B ALA* 2.8 28.8 + - - +
139B ILE* 3.8 22.1 - - + +
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Residues in contact with PHE 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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109B PHE* 2.9 33.5 + + + +
110B ARG 2.8 12.2 + - - +
112B GLN* 1.3 79.1 - - - +
114B HIS* 1.3 63.0 + - - +
116B ALA* 3.2 6.0 - - - +
117B ALA* 3.2 19.6 + - - +
126B ALA* 3.4 43.7 - - + -
128B LEU* 4.1 10.5 - - + -
139B ILE* 4.2 17.3 - - + -
157B LEU* 4.0 19.7 - - + -
158B LEU 4.6 1.3 - - - -
159B LEU* 3.7 30.1 - - + -
181B PHE* 4.0 11.9 - + - -
182B TRP* 3.5 22.2 - + + -
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Residues in contact with HIS 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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110B ARG* 2.6 14.8 + - + +
111B ALA* 3.2 13.7 - - - +
113B PHE* 1.3 77.4 - - - +
115B ALA* 1.3 56.8 + - - +
117B ALA* 3.4 3.3 + - - +
118B THR* 2.6 66.3 + - + +
159B LEU* 6.3 0.4 - - - -
175B VAL* 3.9 28.6 - - + +
178B ALA* 3.8 19.9 + - + +
179B LYS* 4.2 14.4 - - + +
182B TRP* 5.1 7.4 + - - +
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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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56A HIS* 3.7 31.4 - - + +
59A ILE* 4.0 13.2 - - + -
111B ALA 2.9 12.1 + - - +
112B GLN 3.2 7.2 + - - +
114B HIS* 1.3 78.7 - - + +
116B ALA* 1.3 69.3 + - - +
118B THR* 3.6 5.8 - - - -
119B THR* 2.9 33.5 + - + +
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Residues in contact with ALA 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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59A ILE* 3.9 13.2 - - - +
63A GLU* 4.3 5.6 - - - +
112B GLN 2.8 14.4 + - - +
113B PHE* 3.2 13.7 - - - +
115B ALA* 1.3 79.1 - - - +
117B ALA* 1.3 63.5 + - - +
119B THR* 3.2 0.7 + - - -
120B VAL* 3.9 0.7 - - - +
126B ALA* 4.2 9.6 - - + -
139B ILE* 3.9 23.1 - - + -
140B PHE 4.9 3.4 - - - +
141B GLN* 2.9 36.8 + - + +
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Residues in contact with ALA 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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113B PHE 3.2 8.9 + - - +
114B HIS* 3.8 4.0 - - - +
116B ALA* 1.3 83.7 - - - +
118B THR* 1.3 61.0 + - - +
119B THR 3.2 1.2 + - - -
120B VAL* 3.4 20.0 + - - +
126B ALA* 3.3 26.9 - - + +
159B LEU* 4.0 14.4 - - + -
161B MET* 3.5 32.6 - - + +
174B LYS* 4.8 1.7 + - - -
178B ALA* 5.1 2.7 - - + -
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Residues in contact with THR 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 HIS* 2.6 57.3 + - + +
115B ALA* 3.4 8.5 + - - -
117B ALA* 1.3 73.2 - - - +
119B THR* 1.3 62.4 + - - +
120B VAL 3.5 0.7 - - - -
161B MET* 4.5 6.1 - - + -
174B LYS* 2.7 29.8 + - + +
175B VAL* 4.0 24.9 - - + +
178B ALA* 4.1 13.9 - - + -
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Residues in contact with THR 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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59A ILE* 3.5 21.6 - - + +
60A LEU* 3.6 18.4 + - - +
115B ALA* 2.9 21.7 + - + +
117B ALA 3.2 0.8 - - - -
118B THR* 1.3 85.7 - - - +
120B VAL* 1.3 67.6 + - - +
121B GLN* 3.3 5.0 + - - +
141B GLN* 2.7 29.0 + - - -
174B LYS* 4.5 0.4 - - - +
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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