Contacts of the helix formed by residues 113 - 122 (chain B) in PDB entry 3ZHP
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 SER 113 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105B LEU 3.8 8.7 + - - -
106B ARG 5.1 0.9 - - - -
107B ARG 3.3 14.1 + - - -
108B GLN* 4.1 15.5 + - - -
111B THR 3.9 1.7 + - - -
112B ARG* 1.4 71.5 - - - +
114B PRO* 1.4 67.2 - - - +
115B THR 3.3 1.1 + - - -
116B VAL* 3.4 28.7 + - - +
117B GLU* 3.2 27.3 + - - +
152B HIS* 4.9 3.8 + - - -
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Residues in contact with PRO 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B TYR* 3.4 27.2 + - + +
107B ARG* 3.4 22.9 - - + +
109B ILE* 3.8 36.6 - - + +
112B ARG* 3.6 19.9 - - + +
113B SER* 1.4 81.4 - - - +
115B THR* 1.3 55.1 + - - +
117B GLU* 3.6 13.6 + - + +
118B TYR* 3.1 25.6 + - - +
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Residues in contact with THR 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B TYR* 2.7 24.3 + - + +
79B LEU* 4.3 9.4 - - + -
101B PHE* 5.3 2.2 - - + +
104B ILE* 2.5 45.1 + - + -
105B LEU* 3.7 20.8 - - + +
107B ARG* 4.7 1.9 + - - +
113B SER* 3.4 1.4 + - - -
114B PRO* 1.3 73.2 - - - +
116B VAL* 1.3 61.2 + - - +
118B TYR* 3.1 1.4 + - - +
119B ILE* 2.9 53.9 + - + +
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Residues in contact with VAL 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B LEU* 4.3 6.7 - - + +
113B SER* 3.4 29.7 + - - +
115B THR* 1.3 73.2 - - - +
117B GLU* 1.4 52.9 + - + +
119B ILE 3.6 0.3 + - - -
120B SER* 2.7 36.9 + - - +
152B HIS* 3.5 46.4 - - + +
154B PRO* 4.2 20.2 - - + -
155B LEU* 3.6 28.8 - - + +
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Residues in contact with GLU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ARG* 2.8 50.5 + - - +
113B SER 3.2 33.9 + - - +
114B PRO* 3.6 9.0 - - - +
115B THR 3.2 0.2 - - - -
116B VAL* 1.4 77.4 - - + +
118B TYR* 1.4 59.5 + - - +
120B SER* 3.3 9.0 + - - -
121B ALA* 3.2 21.8 + - - +
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Residues in contact with TYR 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B LEU 4.1 1.2 + - - -
74B TYR* 3.2 63.0 + + + -
77B GLY* 3.3 21.0 - - - -
79B LEU* 4.0 24.9 - - + +
80B VAL* 3.6 9.4 - - - +
114B PRO 3.1 15.0 + - - +
115B THR* 3.1 7.8 + - + +
117B GLU* 1.4 72.4 - - - +
119B ILE* 1.3 57.0 + - + +
121B ALA* 3.1 4.0 + - - +
122B HIS* 2.8 71.4 + + - +
125B ILE* 3.8 24.0 - - + -
1333B SO4 5.0 0.7 - - - -
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Residues in contact with ILE 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LEU* 5.5 0.7 - - + -
101B PHE* 4.1 21.5 - - + -
105B LEU* 3.7 27.1 - - + -
115B THR* 2.9 32.5 + - + +
118B TYR* 1.3 72.2 - - + +
120B SER* 1.4 60.5 + - - +
121B ALA 3.3 0.2 - - - -
122B HIS 3.0 33.2 - - - +
123B PRO* 3.3 6.9 - - - +
125B ILE* 3.8 24.9 - - + -
126B LEU* 3.7 33.2 - - + -
149B CYS* 4.4 1.6 - - - -
155B LEU* 3.8 18.8 - - + +
158B ILE* 4.4 2.1 - - - +
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Residues in contact with SER 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B VAL* 2.7 24.5 + - - +
117B GLU* 3.4 11.3 - - - -
118B TYR 3.1 0.2 - - - -
119B ILE* 1.4 78.2 - - - +
121B ALA* 1.3 59.4 + - - +
123B PRO* 4.0 9.2 - - - +
154B PRO* 4.1 17.2 - - - +
155B LEU* 4.0 7.8 - - - +
158B ILE* 4.0 17.7 - - - +
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Residues in contact with ALA 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B GLU 3.2 11.4 + - - +
118B TYR* 3.1 10.2 + - - +
120B SER* 1.3 75.1 - - - +
122B HIS* 1.4 73.3 + - + +
123B PRO* 3.4 8.1 - - - +
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Residues in contact with HIS 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B GLY* 5.8 1.3 - - - -
80B VAL* 4.2 11.7 - - + -
118B TYR* 2.8 63.5 + + - +
119B ILE* 3.0 14.8 - - - +
121B ALA* 1.4 91.2 - - + +
123B PRO* 1.4 64.1 - - - +
124B HIS* 3.3 5.2 + - + -
125B ILE* 3.6 29.1 + - + +
1333B SO4 2.9 42.0 + - - -
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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