Contacts of the helix formed by residues 124 - 130 (chain A) 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 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A LEU 3.4 3.6 - - - +
120A LEU* 3.5 28.9 - - + +
121A ASP 4.6 1.6 - - - +
122A ASN* 3.8 4.0 - - - +
123A ASP* 1.4 88.5 - - - +
125A SER* 1.3 58.4 + - - +
126A PHE 2.9 6.1 + - - -
127A PHE* 3.2 27.5 + - + +
128A CYS* 5.2 1.2 - - - -
149A VAL* 4.3 24.6 - - + +
153A SER* 5.6 0.7 + - - -
446C GLN 5.9 0.9 - - - +
447C GLY* 4.2 20.9 - - - +
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Residues in contact with SER 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A ASP* 3.3 14.6 + - - -
124A PRO* 1.3 76.7 - - - +
126A PHE* 1.3 64.4 + - - +
127A PHE 3.0 1.1 - - - -
128A CYS* 3.0 29.5 + - - +
129A ARG* 4.5 0.9 + - - -
443C HIS* 5.5 3.7 - - - -
447C GLY 3.5 20.0 + - - -
448C ARG* 4.0 15.7 - - - -
449C TYR 5.5 0.2 - - - -
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Residues in contact with PHE 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A THR* 4.3 6.1 - - + -
67A ILE* 3.5 31.4 - - + -
112A VAL* 3.9 24.2 - - + -
119A LEU* 4.0 20.2 - - + -
123A ASP* 2.9 35.7 + - - +
124A PRO 2.9 1.0 + - - +
125A SER* 1.3 78.8 + - - +
127A PHE* 1.3 67.1 + + + +
128A CYS 3.3 1.4 + - - -
129A ARG* 3.1 70.3 + - - +
130A PHE* 3.6 25.7 - + - -
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Residues in contact with PHE 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A CYS* 4.4 2.0 - - - -
43A ILE* 4.4 16.4 - - + -
67A ILE* 3.6 30.3 - - + -
116A PRO* 4.9 5.8 - - + -
119A LEU* 4.1 23.8 - - + -
120A LEU* 3.6 30.3 - - + -
123A ASP 4.8 2.9 - - - -
124A PRO* 3.2 21.1 + - + +
125A SER 3.0 1.2 - - - -
126A PHE* 1.3 75.6 - + - +
128A CYS* 1.3 60.2 + - - +
129A ARG 3.1 7.3 + - - -
130A PHE* 3.6 27.6 + + + -
133A VAL* 4.3 14.1 - - + -
146A LEU* 4.1 10.8 - - + -
149A VAL* 5.2 0.4 - - + -
150A LEU* 3.5 27.8 - - + -
153A SER* 6.2 0.2 - - - -
155A ILE* 3.8 17.6 - - - +
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Residues in contact with CYS 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A PRO 5.2 0.9 - - - -
125A SER* 3.0 27.2 + - - +
127A PHE* 1.3 78.8 - - - +
129A ARG* 1.3 59.2 - - - +
130A PHE 3.4 1.8 - - - +
153A SER* 4.2 13.7 - - - -
155A ILE* 4.1 7.6 - - - -
448C ARG* 4.0 20.6 - - - -
452C VAL* 4.7 17.2 - - + +
453C SER* 3.6 22.1 + - - -
456C GLN* 3.8 33.9 - - - +
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Residues in contact with ARG 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A HIS* 3.9 24.6 + - - +
123A ASP* 5.3 3.2 + - - -
125A SER 4.5 1.0 + - - -
126A PHE* 3.1 54.3 + - - +
128A CYS* 1.3 78.4 - - - +
130A PHE* 1.3 86.3 + - + +
131A THR 4.2 0.5 + - - -
73C SER* 4.6 21.2 - - - +
35D GLU* 4.6 5.0 - - - +
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Residues in contact with PHE 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A HIS* 3.2 42.6 - + - +
41A CYS* 3.4 46.0 - - + -
65A THR* 3.5 12.6 - - - -
126A PHE* 3.6 39.5 - + - -
127A PHE* 3.6 22.0 + + - +
128A CYS 3.4 2.0 - - - +
129A ARG* 1.3 92.6 - - + +
131A THR* 1.3 63.2 + - - +
132A VAL 3.9 12.6 - - - +
133A VAL* 4.2 9.2 - - + -
155A ILE* 3.6 16.8 - - - +
453C SER* 5.1 0.7 + - - -
455C TYR* 4.0 8.5 - - - -
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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