Contacts of the helix formed by residues 115 - 120 (chain A) in PDB entry 3ZG6
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 GLY 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A ASN 4.9 2.2 + - - -
113A VAL 3.1 6.3 + - - -
114A ASP* 1.3 77.7 + - - +
116A LEU* 1.3 56.7 + - - +
117A HIS 3.5 2.0 - - - -
118A VAL* 3.5 6.3 + - - +
119A ARG* 2.9 36.1 + - - +
129A GLU* 4.8 4.1 + - - -
133A ASN* 3.5 31.6 - - - -
135A PHE* 3.9 6.1 - - - -
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Residues in contact with LEU 116 (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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54A SER* 3.8 13.2 - - - +
57A SER* 3.9 19.7 - - - +
59A ILE* 3.9 8.7 - - + -
84A PHE 5.4 1.1 - - - +
87A ALA* 3.6 28.9 - - + +
88A ARG 4.0 3.8 - - - +
89A PRO* 3.8 23.2 - - + +
93A HIS* 3.6 22.9 - - + +
114A ASP* 3.0 34.0 + - - +
115A GLY* 1.3 74.4 - - - +
117A HIS* 1.3 59.2 + - - +
119A ARG* 4.1 12.1 - - + +
120A SER* 2.6 37.9 + - - -
274A TRP* 6.1 0.2 - - + -
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Residues in contact with HIS 117 (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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49A THR* 2.9 28.5 + - - -
53A ILE* 3.5 22.0 - - + +
93A HIS* 3.5 21.6 - + + -
96A LEU* 3.8 12.0 - - + +
108A LEU* 3.4 29.7 - - + +
110A SER* 3.5 21.1 + - - -
112A ASN* 4.8 3.1 + - - +
114A ASP* 4.6 1.8 + - - -
115A GLY 3.5 0.2 - - - -
116A LEU* 1.3 76.5 - - - +
118A VAL* 1.3 65.6 + - - +
120A SER* 2.7 22.7 + - - -
122A PHE* 3.2 21.2 + + + +
127A LEU* 3.9 18.5 - - + +
129A GLU* 5.1 4.6 + - - +
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Residues in contact with VAL 118 (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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115A GLY 3.5 7.4 + - - +
116A LEU 3.3 0.2 - - - -
117A HIS* 1.3 76.3 - - - +
119A ARG* 1.3 63.9 + - + +
121A GLY* 2.9 19.1 + - - -
122A PHE 4.0 9.1 + - - +
124A ARG* 4.3 22.4 - - + +
127A LEU* 4.0 13.0 - - + +
129A GLU* 3.6 26.2 + - - +
133A ASN* 3.6 11.2 - - - +
136A VAL* 5.8 0.9 - - + -
147A VAL* 4.5 12.8 - - + -
278A ARG 3.4 9.4 - - - +
279A VAL* 4.2 32.9 - - + -
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Residues in contact with ARG 119 (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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84A PHE 4.6 3.8 + - - -
85A GLU* 3.2 28.7 + - - +
87A ALA 5.3 3.0 + - - -
114A ASP 4.9 0.7 - - - -
115A GLY 2.9 25.1 + - - +
116A LEU* 4.1 13.6 - - + +
118A VAL* 1.3 84.9 - - + +
120A SER* 1.3 60.2 + - - +
121A GLY 3.1 1.2 + - - -
135A PHE* 3.3 39.4 - - + -
148A ARG 4.8 0.6 + - - -
149A ASP* 3.1 33.3 + - - +
274A TRP* 2.9 27.4 + - + -
277A PRO* 3.7 37.4 - - + +
278A ARG 3.2 19.7 + - - +
279A VAL* 5.9 2.7 - - + -
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Residues in contact with SER 120 (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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89A PRO* 3.7 11.1 - - - +
93A HIS* 4.4 8.1 + - - +
94A MET* 3.7 28.4 - - - +
97A VAL* 3.6 16.9 - - - +
116A LEU 2.6 20.2 + - - -
117A HIS* 2.7 23.6 + - - -
119A ARG* 1.3 72.2 - - - +
121A GLY* 1.3 57.1 + - - +
122A PHE* 4.0 1.0 - - - +
274A TRP* 3.5 12.9 - - - +
278A ARG* 3.5 19.6 + - - -
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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