Contacts of the helix formed by residues 105 - 119 (chain C) in PDB entry 1GN2
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99C ILE* 4.7 0.2 - - - -
100C ALA* 3.6 16.2 + - - +
103C PHE* 2.9 5.3 + - - +
104C GLY* 1.3 80.4 - - - +
106C PHE* 1.3 63.1 + - - +
107C ASP* 3.2 8.8 + - - +
108C LYS* 2.8 38.6 + - - +
109C PHE* 3.0 12.7 + - - +
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Residues in contact with PHE 106 (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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89C ASP 4.4 7.6 - - - -
90C LYS* 3.9 37.0 - - + +
91C PRO* 3.1 40.2 - - + -
96C ALA* 6.1 0.7 - - + +
99C ILE* 4.1 17.0 - - + +
100C ALA* 4.5 5.2 - - + +
105C SER* 1.3 72.9 - - - +
107C ASP* 1.3 68.0 + - - +
109C PHE* 3.6 14.9 - + - +
110C ARG* 3.1 57.6 + - - +
182C TRP* 4.6 2.7 - + - -
187C TRP* 3.5 24.2 - + - -
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Residues in contact with ASP 107 (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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90C LYS* 4.4 13.4 + - - -
105C SER* 3.0 7.6 + - - +
106C PHE* 1.3 86.5 - - - +
108C LYS* 1.3 58.3 + - + +
110C ARG* 3.5 27.6 + - - +
111C ALA* 3.1 24.6 + - - +
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Residues in contact with LYS 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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51A ARG* 3.8 39.7 + - + +
52A ALA* 4.2 16.0 + - - +
54A GLU* 5.2 9.0 - - + -
56A HIS* 4.8 0.2 + - - -
103C PHE* 3.3 22.7 - - - +
104C GLY* 4.8 4.9 - - - -
105C SER* 2.8 23.4 + - - +
107C ASP* 1.3 76.9 - - + +
109C PHE* 1.3 64.1 + - - +
111C ALA* 3.2 8.1 + - + +
112C GLN* 3.2 21.5 + - - +
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Residues in contact with PHE 109 (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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99C ILE* 4.0 13.7 - - + -
103C PHE* 3.6 47.7 - + + +
105C SER 3.0 8.2 + - - +
106C PHE* 3.6 28.9 - + - +
108C LYS* 1.3 75.6 - - - +
110C ARG* 1.3 73.1 + - + +
112C GLN* 3.1 5.2 + - - +
113C PHE* 2.9 47.3 + + - +
128C LEU* 3.8 29.6 - - + -
139C ILE* 3.8 12.9 - - + +
157C LEU* 4.4 12.8 - - + -
182C TRP* 3.6 28.9 - + - -
187C TRP* 4.3 4.9 - + - -
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Residues in contact with ARG 110 (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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90C LYS* 5.4 7.7 - - - +
106C PHE* 3.1 39.7 + - - +
107C ASP* 3.7 21.6 + - - +
109C PHE* 1.3 95.0 - - + +
111C ALA* 1.3 60.8 + - - +
112C GLN 3.3 0.2 - - - -
113C PHE* 4.0 1.4 - - - +
114C HIS* 3.3 21.5 + - + +
179C LYS 5.3 0.2 + - - -
182C TRP* 3.3 64.6 - - + +
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Residues in contact with ALA 111 (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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56A HIS* 4.2 13.3 - - + +
107C ASP 3.1 14.3 + - - +
108C LYS* 3.2 11.0 + - - +
109C PHE 3.1 0.6 - - - -
110C ARG* 1.3 74.7 - - - +
112C GLN* 1.3 66.7 + - - +
114C HIS* 3.5 6.9 + - - +
115C ALA* 3.1 22.5 + - - +
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Residues in contact with GLN 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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47A LEU* 4.1 18.6 - - - +
51A ARG* 3.0 37.0 + - - +
56A HIS* 3.7 21.0 + - + +
59A ILE* 3.9 16.8 - - + +
63A GLU* 3.1 21.9 + - - +
66A LEU* 6.1 0.2 - - - +
103C PHE* 3.8 6.5 - - - -
108C LYS 3.2 7.0 + - - +
109C PHE 3.1 7.7 + - - +
111C ALA* 1.3 78.7 - - - +
113C PHE* 1.3 67.5 + - - +
115C ALA* 2.9 5.7 + - - +
116C ALA* 2.9 20.4 + - - +
139C ILE* 3.5 27.0 + - + +
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Residues in contact with PHE 113 (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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109C PHE* 2.9 33.0 + + + +
110C ARG* 4.1 4.7 - - - +
112C GLN* 1.3 77.4 - - - +
114C HIS* 1.3 62.6 + - - +
116C ALA* 3.4 7.4 + - - +
117C ALA* 3.0 20.6 + - - +
126C ALA* 3.6 25.5 - - + +
127C ALA 4.0 3.8 - - - -
128C LEU* 3.9 28.0 - - + -
139C ILE* 3.9 19.2 - - + +
157C LEU* 4.2 22.0 - - + -
159C LEU* 3.8 34.1 - - + -
181C PHE* 4.2 8.3 - + - -
182C TRP* 3.7 23.1 - + + -
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Residues in contact with HIS 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 ARG* 3.3 17.9 + - + +
111C ALA* 3.7 6.6 + - - +
112C GLN 3.1 0.4 - - - -
113C PHE* 1.3 82.9 - - - +
115C ALA* 1.3 57.5 + - - +
117C ALA* 3.4 2.8 + - - +
118C THR* 2.7 52.6 + - + +
159C LEU* 6.1 1.6 - - - -
175C VAL* 3.8 27.4 + - + -
178C ALA* 3.7 30.5 - - + -
179C LYS* 4.0 29.3 + - + +
182C TRP* 5.0 8.3 - - - +
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Residues in contact with ALA 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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56A HIS* 4.1 25.4 - - + -
59A ILE* 4.1 15.0 - - + -
111C ALA 3.1 13.8 + - - +
112C GLN* 2.9 11.1 + - - +
114C HIS* 1.3 79.5 + - - +
116C ALA* 1.3 61.4 + - - +
118C THR* 3.5 4.7 + - - -
119C THR* 3.1 33.5 + - + +
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Residues in contact with ALA 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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59A ILE* 4.3 8.0 - - + +
63A GLU* 4.4 9.4 - - + +
112C GLN 2.9 10.7 + - - +
113C PHE 3.6 8.1 - - - +
114C HIS 3.3 0.2 - - - -
115C ALA* 1.3 76.0 - - - +
117C ALA* 1.3 61.1 + - - +
119C THR* 4.2 0.4 - - - -
120C VAL* 3.6 3.5 - - - +
126C ALA* 4.3 8.4 - - + +
139C ILE* 4.1 22.2 - - + -
140C PHE 4.8 0.4 - - - +
141C GLN* 3.0 46.1 + - + +
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Residues in contact with ALA 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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113C PHE 3.0 12.4 + - - +
114C HIS* 4.1 4.0 - - - +
116C ALA* 1.3 78.6 - - - +
118C THR* 1.3 63.2 + - + +
119C THR 3.6 0.5 + - - -
120C VAL* 3.7 11.3 + - - +
126C ALA* 3.4 24.7 - - + +
159C LEU* 4.1 13.9 - - + -
161C MET* 3.2 44.8 - - + +
174C LYS* 4.9 1.6 - - - -
178C ALA* 5.1 1.3 - - + -
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Residues in contact with THR 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 HIS* 2.7 37.8 + - - +
115C ALA* 3.5 7.4 + - - -
117C ALA* 1.3 77.9 - - - +
119C THR* 1.3 61.5 + - - +
120C VAL 3.6 0.9 - - - -
161C MET* 4.8 0.9 - - + -
174C LYS* 3.0 32.4 + - + +
175C VAL* 4.1 26.5 - - + +
178C ALA* 3.8 27.6 - - + -
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Residues in contact with THR 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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59A ILE* 3.9 22.9 - - + +
60A LEU* 3.8 13.3 - - - +
115C ALA* 3.1 19.5 + - - +
117C ALA 3.4 0.6 - - - -
118C THR* 1.3 81.3 - - - +
120C VAL* 1.3 67.7 + - - +
121C GLN* 3.3 12.6 + - - +
141C GLN* 2.7 25.7 + - - -
174C LYS* 5.1 0.9 - - - +
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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