Contacts of the helix formed by residues 139 - 153 (chain C) in PDB entry 3GZN
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 PRO 139 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44C ASN* 5.6 1.3 - - - +
137C GLN 3.7 4.9 - - - +
138C LEU* 1.4 93.7 - - + +
140C GLU* 1.3 59.8 + - - +
141C SER* 4.6 6.5 - - - +
142C THR* 3.5 22.6 + - + +
143C SER* 3.1 25.0 + - - -
161C ARG* 5.1 1.6 - - - +
440C ASP* 5.3 0.7 - - - +
443C HIS* 4.6 20.4 - - + +
449C TYR* 4.1 17.2 - - - +
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Residues in contact with GLU 140 (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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139C PRO* 1.3 72.4 - - - +
141C SER* 1.3 61.6 + - - +
143C SER* 3.5 6.4 + - - -
144C LEU* 2.9 45.9 + - + +
409C TYR* 3.6 32.7 + - + +
437C ARG* 4.4 12.2 + - - +
440C ASP* 3.3 47.1 + - + +
441C ARG* 5.0 4.7 + - - +
443C HIS* 6.0 0.2 - - - -
444C LYS* 4.5 19.7 + - + +
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Residues in contact with SER 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C GLU* 4.2 6.1 + - - -
139C PRO* 4.6 7.0 - - - +
140C GLU* 1.3 79.4 - - - +
142C THR* 1.3 69.2 + - - +
144C LEU* 3.5 7.0 + - - +
145C ARG* 3.1 25.1 + - - +
444C LYS* 5.6 13.9 - - - +
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Residues in contact with THR 142 (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 PRO* 4.2 21.5 - - + -
117C GLU* 2.9 33.7 + - + +
120C LEU* 4.7 2.9 - - + +
138C LEU* 3.7 29.2 - - + -
139C PRO* 3.5 26.0 + - + +
140C GLU 3.3 0.2 - - - -
141C SER* 1.3 80.3 + - - +
143C SER* 1.3 65.2 + - - +
145C ARG* 3.2 4.3 + - - +
146C LEU* 3.0 26.1 + - + +
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Residues in contact with SER 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C LEU* 4.0 21.0 - - - +
139C PRO 3.1 19.3 + - - -
140C GLU* 3.6 8.3 - - - -
142C THR* 1.3 76.7 - - - +
144C LEU* 1.3 56.0 + - - -
146C LEU* 3.9 2.1 - - - +
147C ALA* 3.0 31.4 + - - +
157C LEU* 5.2 0.5 - - - +
159C ILE* 3.3 34.3 - - - +
405C LEU* 4.0 7.0 - - - +
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Residues in contact with LEU 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C GLU* 2.9 40.4 + - + +
141C SER* 3.9 6.1 - - - +
143C SER* 1.3 69.3 - - - +
145C ARG* 1.3 64.8 + - - +
147C ALA* 3.7 1.7 + - - +
148C ASP* 3.2 22.9 + - - +
405C LEU* 4.0 23.3 - - + +
406C ALA* 5.1 4.7 - - + +
409C TYR* 3.9 40.8 - - + -
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Residues in contact with ARG 145 (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 GLU* 2.9 36.2 + - - -
120C LEU* 3.2 44.8 + - + +
121C ASP* 2.6 34.7 + - - +
141C SER 3.1 13.4 + - - +
142C THR* 3.2 8.3 + - - +
144C LEU* 1.3 77.1 - - - +
146C LEU* 1.3 58.3 + - - +
148C ASP* 3.2 6.9 + - - +
149C VAL* 2.9 37.3 + - + +
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Residues in contact with LEU 146 (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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43C ILE* 3.5 28.0 - - + -
116C PRO* 5.9 2.2 - - + +
120C LEU* 3.9 17.7 - - + +
127C PHE* 3.9 35.0 - - + -
133C VAL* 4.6 0.2 - - + -
135C ALA* 3.9 9.0 - - + -
138C LEU* 4.1 7.4 - - + -
142C THR* 3.0 18.0 + - + +
143C SER* 3.9 3.1 - - - +
145C ARG* 1.3 73.0 - - - +
147C ALA* 1.3 59.5 + - - +
149C VAL* 3.8 0.6 - - - +
150C LEU* 2.9 54.7 + - + +
157C LEU* 3.8 26.5 - - + -
159C ILE* 6.0 0.7 - - + -
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Residues in contact with ALA 147 (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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143C SER 3.0 18.8 + - - +
144C LEU 3.8 3.6 - - - +
146C LEU* 1.3 76.5 - - - +
148C ASP* 1.3 57.8 + - - +
150C LEU* 3.9 0.9 - - - +
151C TRP* 2.9 31.4 + - - +
157C LEU* 3.5 22.4 - - + +
159C ILE* 5.0 0.2 - - + -
172C ILE* 4.5 5.3 - - + +
405C LEU* 3.6 37.8 + - + +
406C ALA 5.6 0.2 - - - +
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Residues in contact with ASP 148 (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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144C LEU 3.2 11.2 + - - +
145C ARG* 3.2 10.5 + - - +
146C LEU 3.2 0.2 - - - -
147C ALA* 1.3 77.9 - - - +
149C VAL* 1.3 72.2 + - + +
151C TRP* 3.1 7.2 + - - +
152C ASN* 3.0 43.7 + - - +
406C ALA* 5.0 13.5 - - + +
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Residues in contact with VAL 149 (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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120C LEU* 3.9 31.9 - - + +
124C PRO* 4.3 26.5 - - + +
145C ARG* 2.9 30.3 + - + +
146C LEU 3.9 3.1 - - - +
148C ASP* 1.3 77.3 - - + +
150C LEU* 1.3 67.4 + - + +
152C ASN* 3.4 5.1 + - - +
153C SER* 2.8 29.7 + - - +
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Residues in contact with LEU 150 (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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127C PHE* 3.5 37.9 - - + -
133C VAL* 3.8 31.0 - - + -
146C LEU* 2.9 40.1 + - + +
147C ALA 4.2 2.0 - - - +
149C VAL* 1.3 78.6 - - + +
151C TRP* 1.3 59.4 + - - +
153C SER* 3.6 4.7 - - - +
154C GLN* 2.9 9.2 + - - -
155C ILE* 2.9 54.6 + - + +
157C LEU* 4.0 19.5 - - + -
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Residues in contact with TRP 151 (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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147C ALA 2.9 21.3 + - - +
148C ASP* 3.5 9.4 - - - +
150C LEU* 1.3 77.4 - - - +
152C ASN* 1.3 73.7 + - - +
154C GLN* 3.1 24.0 + - - +
155C ILE 5.3 0.4 - - - -
172C ILE* 3.6 30.5 - - + -
174C LYS* 3.6 56.7 - - + +
402C CYS 3.4 26.5 - - - -
404C SER* 3.6 31.4 - - - -
405C LEU 6.1 0.4 - - - +
407C GLU* 5.2 3.8 - - - -
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Residues in contact with ASN 152 (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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148C ASP* 3.0 42.1 + - - +
149C VAL* 4.0 3.8 - - - +
151C TRP* 1.3 88.6 - - - +
153C SER* 1.3 58.7 + - - +
154C GLN* 3.3 12.2 + - - +
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Residues in contact with SER 153 (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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127C PHE* 5.9 0.2 - - - +
128C CYS* 4.2 22.8 - - - -
149C VAL* 2.8 22.2 + - - +
150C LEU* 3.6 11.3 - - - +
151C TRP 3.2 0.2 - - - -
152C ASN* 1.3 75.9 - - - +
154C GLN* 1.3 69.3 + - - +
155C ILE* 3.0 21.5 - - - +
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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