Contacts of the helix formed by residues 107 - 122 (chain C) in PDB entry 6GYS
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 GLN 107 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104C ASN 4.7 3.9 + - - +
105C TYR* 3.9 9.6 + - - +
106C LEU* 1.3 87.1 - - - +
108C LYS* 1.3 57.1 + - - +
109C ASP* 3.6 8.6 - - - +
110C GLN* 2.8 44.8 + - + +
111C SER 2.7 28.2 + - - -
144C TRP* 3.4 10.1 - - - -
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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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107C GLN* 1.3 72.7 - - - +
109C ASP* 1.3 63.0 + - - +
111C SER* 2.2 25.3 + - - -
112C PHE* 2.9 38.9 + - + -
141C GLU* 3.6 29.5 + - - +
144C TRP* 3.4 57.6 - - + +
145C ASP* 5.7 2.0 + - - -
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Residues in contact with ASP 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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107C GLN* 3.8 8.8 - - - +
108C LYS* 1.3 82.6 + - - +
110C GLN* 1.3 73.1 + - - +
112C PHE* 3.7 13.1 - - + +
113C GLN* 3.0 49.8 + - + +
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Residues in contact with GLN 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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105C TYR* 3.1 16.4 + - - +
106C LEU* 3.6 2.6 - - + -
107C GLN* 2.8 54.0 + - - +
109C ASP* 1.3 91.6 + - - +
111C SER* 1.3 60.3 + - - +
113C GLN* 4.7 0.9 - - - +
114C LEU* 3.3 29.7 + - - +
182C ILE* 3.7 33.3 + - + +
183C PHE* 3.1 34.3 - - + -
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Residues in contact with SER 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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106C LEU* 3.9 15.9 - - - +
107C GLN 2.7 16.3 + - - -
108C LYS* 2.2 28.7 + - - -
110C GLN* 1.3 75.5 - - - +
112C PHE* 1.3 59.4 + - - +
114C LEU* 3.2 10.4 + - - +
115C MET* 2.9 31.0 + - - +
140C VAL* 3.5 22.3 - - - +
144C TRP* 3.8 3.2 + - - -
167C PHE* 4.2 21.4 - - - -
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Residues in contact with PHE 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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108C LYS* 2.9 51.6 + - + -
109C ASP* 3.1 12.5 + - + +
111C SER* 1.3 82.4 + - - +
113C GLN* 1.3 59.9 + - + +
115C MET* 3.2 8.2 + - + +
116C ASN* 2.9 45.0 + - - +
137C TYR* 5.3 11.9 - + + -
140C VAL* 4.1 19.1 - - + -
141C GLU* 3.0 30.1 - - + -
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Residues in contact with GLN 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 ASP* 3.0 30.2 + - + +
110C GLN 4.7 0.9 - - - +
112C PHE* 1.3 75.2 - - + +
114C LEU* 1.3 60.7 + - - +
116C ASN* 3.8 4.9 - - - +
117C PHE* 2.9 28.6 + - - +
174C MET* 4.3 3.7 - - - +
182C ILE* 3.2 39.1 - - + +
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Residues in contact with LEU 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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106C LEU* 5.1 12.1 - - + -
110C GLN 3.3 18.8 + - - +
111C SER* 3.2 10.0 + - - +
113C GLN* 1.3 76.0 - - - +
115C MET* 1.3 59.1 + - + +
117C PHE* 3.3 7.1 + - - +
118C ALA 3.0 23.9 + - - -
167C PHE* 4.8 10.1 - - + +
170C CYS* 3.3 39.5 - - + +
171C ILE* 4.0 26.7 - - + -
174C MET* 3.7 29.2 - - + -
179C LEU* 4.3 4.0 - - + -
182C ILE* 4.8 5.2 - - + -
183C PHE* 4.7 11.7 - - + -
212C PHE* 5.7 1.1 - - + -
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Residues in contact with MET 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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111C SER 2.9 22.5 + - - +
112C PHE* 3.2 12.3 + - + +
114C LEU* 1.3 76.3 - - - +
116C ASN* 1.3 51.2 + - - +
118C ALA* 3.2 4.9 + - - +
119C MET* 2.7 35.3 + - - +
133C ILE* 4.1 13.7 - - + +
136C LEU* 3.7 28.3 - - + -
137C TYR* 3.5 39.7 + - + -
140C VAL* 4.1 19.5 - - + -
166C VAL* 4.0 17.0 - - + -
167C PHE* 3.7 25.8 - - + -
170C CYS* 4.5 2.7 - - - -
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Residues in contact with ASN 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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112C PHE* 2.9 35.2 + - - +
113C GLN* 4.2 4.6 - - - +
115C MET* 1.3 73.3 - - - +
117C PHE* 1.3 65.0 + - - +
119C MET* 3.3 16.2 - - + +
120C GLU* 3.3 33.4 + - - +
137C TYR* 2.5 37.2 + - - -
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Residues in contact with PHE 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 GLN 2.9 16.3 + - - +
114C LEU 3.3 9.8 + - - +
116C ASN* 1.3 76.1 - - - +
118C ALA* 1.3 64.2 + - + +
120C GLU* 3.3 2.4 + - - -
121C ASN* 2.5 64.4 + - + +
122C LEU* 4.7 4.7 - - + -
170C CYS* 4.4 7.0 - - - -
173C TYR* 3.2 44.2 - - + -
174C MET* 3.5 31.4 - - + -
175C PRO* 3.7 18.6 - - + -
178C LYS* 4.2 20.9 - - + -
452C PHE* 4.3 12.3 - + - -
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Residues in contact with ALA 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 LEU 3.0 15.4 + - - +
115C MET* 3.7 3.4 - - - +
117C PHE* 1.3 76.3 - - + +
119C MET* 1.3 61.2 + - - +
122C LEU* 3.0 53.7 + - + +
126C TYR* 3.5 8.8 - - + -
133C ILE* 4.5 6.1 - - + -
166C VAL* 5.4 0.9 - - + -
169C MET* 4.4 12.1 - - + -
170C CYS* 3.7 19.3 - - - -
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Residues in contact with MET 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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115C MET 2.7 15.6 + - - +
116C ASN* 3.3 28.3 - - + +
117C PHE 3.2 0.4 - - - -
118C ALA* 1.3 74.2 - - - +
120C GLU* 1.3 82.5 + - + +
126C TYR* 3.0 20.1 + - - +
133C ILE* 3.7 27.7 - - + +
134C SER* 5.7 0.7 - - - +
137C TYR* 3.2 23.3 - - + +
395C ASN* 2.8 21.8 + - - +
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Residues in contact with GLU 120 (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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116C ASN* 3.3 23.0 + - - +
117C PHE* 4.0 2.0 - - - +
119C MET* 1.3 93.1 - - + +
121C ASN* 1.3 69.7 + - - +
393C SER* 4.9 1.2 + - - -
394C ASN* 3.8 5.7 + - - +
395C ASN* 3.0 31.1 + - - +
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Residues in contact with ASN 121 (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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117C PHE* 2.5 60.4 + - + +
120C GLU* 1.3 90.6 + - - +
122C LEU* 1.3 70.7 + - + +
123C GLY 3.7 0.2 - - - -
178C LYS* 5.1 3.8 - - - +
394C ASN* 3.2 42.5 - - - +
395C ASN* 3.1 6.7 - - - -
398C PHE* 3.6 6.9 - - - +
452C PHE* 3.7 19.8 - - + -
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Residues in contact with LEU 122 (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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117C PHE* 4.7 4.9 - - + -
118C ALA* 3.0 37.8 + - + +
121C ASN* 1.3 86.3 - - + +
123C GLY* 1.3 61.6 + - - +
124C ALA 3.4 2.5 - - - -
125C LEU* 3.4 25.5 + - + +
126C TYR* 3.2 15.4 - - - -
169C MET* 4.5 13.5 - - + +
170C CYS* 5.2 0.7 - - - -
173C TYR* 3.6 38.8 - - + -
395C ASN* 2.8 4.8 + - - -
398C PHE* 3.6 28.3 - - + -
452C PHE* 3.8 14.8 - - + -
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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