Contacts of the helix formed by residues 116 - 127 (chain F) in PDB entry 3GTL
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 116 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495A GLU* 5.2 0.3 - - - +
498A ARG* 4.8 11.2 + - - -
114F GLU* 5.6 0.7 - - + -
115F THR* 1.3 78.8 + - - +
117F PRO* 1.3 71.5 - - - +
118F LEU* 3.3 15.5 + - - +
119F ARG* 3.3 38.0 + - + +
120F ILE* 2.9 28.2 + - - +
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Residues in contact with PRO 117 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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383A TYR* 5.9 2.9 - - + -
495A GLU* 3.6 23.6 - - - +
98F ALA* 4.0 5.6 - - - +
101F ILE* 3.4 36.1 - - + +
102F SER* 3.7 31.6 - - - +
115F THR 3.5 7.1 - - - +
116F ASP* 1.3 94.5 - - - +
118F LEU* 1.3 57.5 + - - +
120F ILE* 3.4 2.9 + - + +
121F ALA* 3.1 19.1 + - - +
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Residues in contact with LEU 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495A GLU* 3.8 19.1 - - - +
498A ARG* 4.9 13.9 - - + +
499A ALA* 4.5 21.1 - - + +
502A SER* 4.6 15.9 - - - +
503A GLN* 4.2 17.9 - - - +
94F LEU* 4.6 16.6 - - + -
98F ALA* 3.7 13.6 - - + +
116F ASP* 3.3 13.6 + - - +
117F PRO* 1.3 77.9 - - - +
119F ARG* 1.3 63.8 + - + +
120F ILE 3.2 1.8 - - - -
121F ALA* 3.4 1.8 + - - +
122F MET* 3.1 36.9 + - + +
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Residues in contact with ARG 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F GLU* 3.0 39.2 + - + +
116F ASP* 3.3 35.5 + - + +
118F LEU* 1.3 76.9 - - - +
120F ILE* 1.3 66.3 + - - +
121F ALA 3.4 0.2 - - - -
122F MET* 3.3 38.3 + - + +
123F LYS* 3.5 19.1 + - - +
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Residues in contact with ILE 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383A TYR* 6.4 2.7 - - + -
101F ILE* 3.7 34.5 - - + -
107F VAL* 4.5 17.7 - - + -
111F LEU* 4.6 17.7 - - + -
114F GLU* 3.3 44.4 - - + +
115F THR* 3.9 2.9 - - - +
116F ASP 2.9 20.9 + - - +
117F PRO* 3.5 4.5 - - + +
118F LEU 3.2 0.2 - - - -
119F ARG* 1.3 78.9 - - - +
121F ALA* 1.3 58.3 + - - +
123F LYS* 3.4 11.6 + - + +
124F GLU* 3.0 30.4 + - + +
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Residues in contact with ALA 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F LEU* 3.6 31.2 - - - +
97F ARG* 4.3 6.1 - - + -
98F ALA* 4.1 3.8 - - + +
101F ILE* 3.5 20.4 - - + -
117F PRO 3.1 10.4 + - - +
118F LEU 3.4 6.0 + - - +
120F ILE* 1.3 73.5 - - - +
122F MET* 1.3 61.7 + - - +
124F GLU* 3.7 13.4 - - - +
125F LEU* 3.0 28.2 + - - +
130F ILE* 3.9 3.7 - - + +
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Residues in contact with MET 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503A GLN* 4.8 12.6 - - - +
90F ARG* 4.7 11.7 - - - +
94F LEU* 3.8 18.4 - - + -
118F LEU* 3.1 31.8 + - + +
119F ARG* 3.3 45.8 - - + +
120F ILE 3.3 0.2 - - - -
121F ALA* 1.3 79.1 - - - +
123F LYS* 1.3 56.2 + - - +
125F LEU* 3.4 7.1 - - + +
126F ALA* 2.9 26.2 + - - +
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Residues in contact with LYS 123 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109F VAL* 3.9 20.4 - - + -
110F ASP 4.1 13.2 - - - +
111F LEU* 5.3 2.0 - - - -
112F GLU* 5.0 14.8 - - - +
114F GLU* 5.5 12.0 + - + +
119F ARG 3.5 10.1 + - - +
120F ILE* 3.4 14.0 + - + +
121F ALA 3.3 0.4 - - - -
122F MET* 1.3 75.3 - - - +
124F GLU* 1.3 64.2 + - - +
125F LEU 3.1 1.3 - - - -
126F ALA* 3.2 23.2 + - - +
127F GLU* 3.0 44.8 + - - +
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Residues in contact with GLU 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F ARG* 3.0 49.9 + - - -
101F ILE* 3.2 17.7 - - - +
107F VAL* 4.3 3.3 - - + -
108F PHE* 3.4 21.8 + - + +
109F VAL* 3.5 26.0 - - + +
120F ILE* 3.0 21.4 + - + +
121F ALA* 3.7 8.2 - - - +
122F MET 3.5 0.2 - - - -
123F LYS* 1.3 76.5 - - - +
125F LEU* 1.3 57.9 + - - +
127F GLU* 3.6 1.9 + - - +
128F LYS 3.5 2.3 + - - -
129F LYS* 3.1 36.6 + - - +
130F ILE* 3.9 13.0 - - + -
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Residues in contact with LEU 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85F MET* 4.5 17.5 - - + -
90F ARG* 3.7 28.0 - - + +
93F ILE* 4.6 4.0 - - + -
94F LEU* 4.4 12.1 - - + -
121F ALA 3.0 18.0 + - - +
122F MET* 3.4 7.6 - - + +
124F GLU* 1.3 73.3 - - - +
126F ALA* 1.3 58.3 + - - +
127F GLU 2.9 4.7 - - - -
128F LYS* 2.8 34.1 + - - +
130F ILE* 3.6 20.3 - - + +
148F VAL* 4.3 18.8 - - + -
153F VAL* 4.3 21.5 - - + -
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Residues in contact with ALA 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122F MET 2.9 15.7 + - - +
123F LYS* 3.4 20.6 - - - +
125F LEU* 1.3 77.2 - - - +
127F GLU* 1.3 64.7 + - + +
128F LYS* 3.6 1.8 + - - +
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Residues in contact with GLU 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F VAL* 3.3 26.4 - - + +
123F LYS* 3.0 53.7 + - - +
124F GLU 3.7 2.2 - - - +
125F LEU 2.9 1.4 - - - -
126F ALA* 1.3 83.4 - - + +
128F LYS* 1.3 62.1 + - - +
129F LYS* 2.9 26.0 + - + +
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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