Contacts of the helix formed by residues 105 - 119 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99H ILE* 4.7 0.2 - - - -
100H ALA* 3.6 16.0 + - - +
103H PHE* 2.9 4.7 + - - +
104H GLY* 1.3 80.5 - - - +
106H PHE* 1.3 63.8 + - - +
107H ASP* 3.2 8.2 + - - +
108H LYS* 2.8 38.0 + - - +
109H PHE* 3.0 12.9 + - - +
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Residues in contact with PHE 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89H ASP 4.4 6.7 - - - -
90H LYS* 3.9 37.7 - - + -
91H PRO* 3.1 40.6 - - + -
96H ALA* 6.1 0.4 - - + +
99H ILE* 4.1 16.8 - - + +
100H ALA* 4.5 5.4 - - + +
105H SER* 1.3 72.7 - - - +
107H ASP* 1.3 66.5 + - - +
109H PHE* 3.5 14.9 + + - +
110H ARG* 3.1 58.4 + - - +
182H TRP* 4.6 2.9 - + - -
187H TRP* 3.5 24.7 - + - -
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Residues in contact with ASP 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90H LYS* 4.4 13.1 + - - -
105H SER* 3.0 7.6 + - - +
106H PHE* 1.3 87.0 - - - +
108H LYS* 1.3 58.6 + - + +
110H ARG* 3.5 28.0 + - - +
111H ALA* 3.1 24.9 + - - +
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Residues in contact with LYS 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F ARG* 3.7 39.6 + - + +
52F ALA* 4.0 18.0 + - - +
54F GLU* 5.2 8.7 - - + -
103H PHE 3.3 22.4 - - - +
104H GLY* 4.8 4.5 - - - -
105H SER* 2.8 22.4 + - - +
107H ASP* 1.3 76.7 - - + +
109H PHE* 1.3 64.4 + - - +
111H ALA* 3.2 8.1 + - + +
112H GLN* 3.2 20.8 + - - +
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Residues in contact with PHE 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99H ILE* 4.0 13.5 - - + -
103H PHE* 3.6 46.4 - + + +
105H SER 3.0 8.0 + - - +
106H PHE* 3.6 28.0 - + - +
108H LYS* 1.3 75.5 - - - +
110H ARG* 1.3 73.4 + - + +
112H GLN* 3.1 4.7 + - - +
113H PHE* 2.9 47.0 + + - +
128H LEU* 3.8 30.1 - - + -
139H ILE* 3.8 13.8 - - + +
157H LEU* 4.4 12.3 - - + -
182H TRP* 3.6 28.7 - + - -
187H TRP* 4.3 5.6 - + - -
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Residues in contact with ARG 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90H LYS* 5.4 7.7 - - - +
106H PHE* 3.1 40.2 + - - +
107H ASP* 3.7 21.3 + - - +
109H PHE* 1.3 95.7 - - + +
111H ALA* 1.3 58.9 + - - +
113H PHE* 4.0 1.3 - - - +
114H HIS* 3.3 22.5 + - + +
179H LYS 5.3 0.2 + - - -
182H TRP* 3.3 65.7 - - + +
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Residues in contact with ALA 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F GLU* 6.6 0.4 - - - -
56F HIS* 3.8 13.6 - - + +
107H ASP 3.1 13.8 + - - +
108H LYS* 3.6 11.9 - - + +
109H PHE 3.1 0.8 - - - -
110H ARG* 1.3 73.7 - - - +
112H GLN* 1.3 67.7 + - - +
114H HIS* 3.5 6.4 + - - +
115H ALA* 3.1 22.5 + - - +
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Residues in contact with GLN 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F LEU* 3.8 21.4 - - - +
51F ARG* 2.8 38.4 + - + +
56F HIS* 3.3 21.5 + - + +
59F ILE* 3.8 16.4 - - + -
63F GLU* 3.3 21.5 + - - +
66F LEU* 6.1 0.2 - - - +
103H PHE* 3.8 4.4 - - - -
108H LYS 3.2 6.7 + - - +
109H PHE 3.1 7.5 + - - +
111H ALA* 1.3 78.9 - - - +
113H PHE* 1.3 67.2 + - - +
115H ALA* 2.9 5.7 + - - +
116H ALA* 2.9 20.4 + - - +
139H ILE* 3.5 24.9 + - + +
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Residues in contact with PHE 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109H PHE* 2.9 33.0 + + + +
110H ARG* 4.1 4.0 - - - +
112H GLN* 1.3 77.4 - - - +
114H HIS* 1.3 64.0 + - - +
116H ALA* 3.4 7.6 + - - +
117H ALA* 3.0 20.3 + - - +
126H ALA* 3.6 25.2 - - + +
127H ALA 4.0 3.8 - - - -
128H LEU* 3.9 27.8 - - + -
139H ILE* 3.9 19.7 - - + +
157H LEU* 4.2 21.1 - - + -
159H LEU* 3.8 34.1 - - + -
181H PHE* 4.2 8.3 - + - -
182H TRP* 3.7 23.6 - + + -
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Residues in contact with HIS 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110H ARG* 3.3 17.0 + - + +
111H ALA* 3.7 7.5 + - - +
112H GLN 3.1 0.2 - - - -
113H PHE* 1.3 81.9 - - - +
115H ALA* 1.3 59.0 + - - +
117H ALA* 3.4 3.5 + - - -
118H THR* 2.7 51.6 + - + +
159H LEU* 6.1 1.3 - - + -
175H VAL* 3.8 26.8 + - + -
178H ALA* 3.7 30.5 - - + -
179H LYS* 4.0 29.3 + - + +
182H TRP* 5.0 8.3 - - - +
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Residues in contact with ALA 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56F HIS* 3.7 31.2 - - + +
59F ILE* 4.0 12.3 - - + -
111H ALA 3.1 13.8 + - - +
112H GLN 2.9 9.8 + - - +
114H HIS* 1.3 81.2 + - - +
116H ALA* 1.3 60.3 + - - +
118H THR* 3.5 4.6 + - - -
119H THR* 3.1 33.8 + - + +
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Residues in contact with ALA 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F ILE* 3.9 12.1 - - + +
63F GLU* 4.2 9.6 - - - +
112H GLN 2.9 10.9 + - - +
113H PHE 3.6 7.9 - - - +
115H ALA* 1.3 77.0 - - - +
117H ALA* 1.3 60.7 + - - +
119H THR* 3.8 0.3 + - - -
120H VAL* 3.6 2.9 - - - +
126H ALA* 4.3 8.8 - - + +
139H ILE* 4.1 22.7 - - + -
140H PHE 4.8 0.2 - - - +
141H GLN* 3.0 43.3 + - + +
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Residues in contact with ALA 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113H PHE 3.0 12.9 + - - +
114H HIS* 3.4 3.6 + - - +
116H ALA* 1.3 76.7 - - - +
118H THR* 1.3 65.4 + - + +
119H THR 3.6 0.7 + - - -
120H VAL* 3.7 11.0 + - - +
126H ALA* 3.4 23.3 - - + +
159H LEU* 4.1 13.7 - - + -
161H MET* 3.2 46.0 - - + +
174H LYS* 4.9 1.4 - - - -
178H ALA* 5.1 1.6 - - + -
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Residues in contact with THR 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114H HIS* 2.7 38.1 + - - +
115H ALA* 3.4 7.8 + - - -
117H ALA* 1.3 76.7 - - - +
119H THR* 1.3 62.3 + - - +
120H VAL 3.6 0.4 - - - -
161H MET* 4.8 0.9 - - + -
174H LYS* 3.0 31.5 + - + +
175H VAL* 4.1 26.6 - - + +
178H ALA* 3.8 26.5 - - + -
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Residues in contact with THR 119 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F HIS 5.6 0.4 - - - +
59F ILE* 3.5 22.1 - - + +
60F LEU* 3.6 18.9 + - - +
115H ALA* 3.1 19.6 + - + +
117H ALA 3.4 0.4 - - - -
118H THR* 1.3 83.1 - - - +
120H VAL* 1.3 67.8 + - - +
121H GLN* 3.3 7.4 + - - +
141H GLN* 2.7 26.0 + - - -
174H 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