Contacts of the helix formed by residues 129 - 138 (chain B) in PDB entry 3ZWG
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 129 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51B TYR* 3.7 18.8 - - + -
89B VAL* 5.4 0.5 - - - +
127B ARG 4.1 7.6 - - - +
128B ALA* 1.3 75.5 - - - +
130B GLN* 1.3 65.5 + - - +
131B ARG* 3.4 18.9 - - - +
132B MET* 2.9 32.9 + - - +
133B TYR 3.1 9.5 + - - -
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Residues in contact with GLN 130 (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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51B TYR* 2.8 46.9 + - + +
53B ARG* 3.5 26.2 + - - +
129B ASP* 1.3 73.1 - - - +
131B ARG* 1.3 64.3 + - - +
133B TYR* 3.2 12.0 + - - +
134B GLU* 2.7 59.4 + - - +
138B TYR* 6.1 0.2 - - - -
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Residues in contact with ARG 131 (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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129B ASP* 3.4 19.7 - - - +
130B GLN* 1.3 81.2 - - - +
132B MET* 1.3 64.4 + - + +
134B GLU* 3.3 24.9 + - - +
135B GLU* 3.3 44.7 + - - +
139B HIS* 6.3 1.4 - - - -
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Residues in contact with MET 132 (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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89B VAL* 3.7 15.3 - - + -
91B ALA* 5.1 1.6 - - - -
99B THR* 4.9 1.3 - - + -
101B ALA* 3.7 24.7 - - + -
122B TYR* 4.0 27.8 - - + +
126B LYS* 3.8 30.5 - - + +
127B ARG 3.6 19.5 - - - +
128B ALA* 4.0 7.9 - - - -
129B ASP* 2.9 25.9 + - - +
131B ARG* 1.3 70.9 - - + +
133B TYR* 1.3 66.8 + - - +
135B GLU* 3.2 11.6 + - - +
136B LEU* 2.9 34.7 + - + +
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Residues in contact with TYR 133 (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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51B TYR* 4.1 10.5 - - + -
53B ARG* 3.8 33.1 + - + +
87B VAL* 3.4 33.8 - - + +
88B GLY 5.4 1.3 - - - -
89B VAL* 3.8 20.7 - - + +
103B LEU* 4.2 11.0 - - + -
105B SER* 5.3 0.3 + - - -
129B ASP 3.1 9.7 + - - +
130B GLN* 3.4 28.9 - - - +
132B MET* 1.3 77.6 - - - +
134B GLU* 1.3 65.7 + - - +
136B LEU* 3.8 1.2 - - - +
137B TYR* 2.9 62.4 + + + +
138B TYR* 4.2 20.9 + + - -
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Residues in contact with GLU 134 (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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130B GLN* 2.7 51.9 + - - +
131B ARG* 3.5 25.4 + - - +
132B MET 3.2 0.2 - - - -
133B TYR* 1.3 78.5 - - + +
135B GLU* 1.3 64.3 + - + +
138B TYR* 2.9 47.0 + - + -
139B HIS* 3.6 12.0 + - + -
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Residues in contact with GLU 135 (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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122B TYR* 2.6 42.9 + - - +
126B LYS* 5.9 0.9 - - - -
131B ARG* 3.3 45.1 + - - +
132B MET* 3.2 11.3 + - - +
134B GLU* 1.3 80.1 - - - +
136B LEU* 1.3 63.9 + - - +
139B HIS* 3.1 16.8 + - + +
140B ARG* 3.0 38.5 + - + +
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Residues in contact with LEU 136 (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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89B VAL* 3.8 29.4 - - + -
101B ALA* 4.0 14.1 - - + +
103B LEU* 3.5 34.0 - - + +
118B ASN* 2.8 36.4 + - + +
120B ARG* 3.6 31.6 - - + +
122B TYR* 3.8 13.9 - - + +
132B MET* 2.9 28.0 + - + +
133B TYR* 3.9 3.1 - - - +
135B GLU* 1.3 75.6 - - - +
137B TYR* 1.3 59.1 + - - +
140B ARG* 4.2 5.7 - - + +
142B PRO* 3.5 6.9 - - - +
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Residues in contact with TYR 137 (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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103B LEU* 3.8 13.7 - - + +
105B SER* 3.6 32.0 + - - -
107B PRO* 5.9 0.9 - - - +
113B TYR* 4.9 15.4 - - - +
114B SER 5.0 0.9 + - - -
116B TRP* 4.0 29.5 + + + -
133B TYR* 2.9 50.1 + + + +
134B GLU 4.3 0.4 - - - +
136B LEU* 1.3 77.8 - - - +
138B TYR* 1.3 92.7 + + + +
142B PRO* 3.5 19.7 - - + +
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Residues in contact with TYR 138 (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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53B ARG* 5.5 4.0 + - - -
133B TYR* 4.2 17.3 + + - -
134B GLU* 2.9 46.9 + - + -
137B TYR* 1.3 106.8 - + - +
139B HIS* 1.3 80.1 + + + +
140B ARG 3.4 1.2 + - - -
141B SER* 3.8 8.0 + - - -
142B PRO* 4.8 0.2 - - - +
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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