Contacts of the strand formed by residues 158 - 164 (chain E) 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 LEU 158 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41E SER* 3.4 44.9 - - - +
43E LYS* 4.7 9.4 - - + -
94E MET* 3.7 37.2 - - + -
100E LEU* 5.4 0.4 - - + -
121E VAL* 4.4 11.7 - - + -
153E GLY* 3.9 1.4 - - - -
154E LEU* 2.9 32.0 + - + -
155E GLY 2.8 10.4 + - - +
156E TYR* 3.6 13.2 - - + +
157E GLY* 1.3 85.0 - - - +
159E LYS* 1.3 62.3 + - - +
176E VAL* 4.3 9.9 - - + -
177E THR 3.5 7.9 - - - +
178E LYS* 4.6 1.8 - - + -
179E ALA* 3.6 7.0 - - - +
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Residues in contact with LYS 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151E SER* 5.3 12.3 - - - -
152E ARG 3.7 12.3 - - - +
153E GLY* 3.9 9.2 - - - +
154E LEU* 3.9 6.3 - - - +
158E LEU* 1.3 76.0 - - - +
160E SER* 1.3 64.8 + - - +
161E ARG* 6.1 4.7 - - + +
175E HIS 3.8 0.9 - - - +
176E VAL* 3.6 2.9 - - - +
177E THR* 3.0 53.5 + - - +
178E LYS 3.9 4.8 + - - -
179E ALA* 3.7 28.6 + - + +
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Residues in contact with SER 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E TRP* 4.9 4.2 - - - -
119E VAL* 3.6 42.7 + - - +
143E PHE* 5.1 3.6 - - - -
150E HIS 3.6 1.4 - - - +
151E SER* 3.1 7.1 - - - -
152E ARG* 2.9 44.8 + - - +
154E LEU* 3.8 11.7 - - - +
159E LYS* 1.3 76.0 - - - +
161E ARG* 1.3 60.9 + - - +
174E ILE* 4.8 2.0 - - - -
175E HIS 3.7 4.0 - - - -
176E VAL* 4.6 5.6 - - - +
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Residues in contact with ARG 161 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E TRP* 4.6 0.7 - - - -
149E TRP* 3.4 28.7 - - + -
150E HIS 3.5 4.3 - - - +
151E SER* 3.6 17.9 - - - +
159E LYS* 6.1 5.6 - - + +
160E SER* 1.3 74.3 - - - +
162E GLY* 1.3 59.9 + - - +
173E GLU 3.8 0.3 - - - +
174E ILE* 3.2 3.5 - - - +
175E HIS* 2.6 88.9 + - + +
177E THR* 5.8 3.9 - - + +
63F HIS* 2.7 63.7 + - + +
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Residues in contact with GLY 162 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E TRP* 3.4 26.4 - - - -
148E GLY 3.8 0.7 - - - +
149E TRP* 3.3 8.4 - - - -
150E HIS 2.9 33.1 + - - -
161E ARG* 1.3 78.0 - - - +
163E PHE* 1.3 59.8 + - - -
173E GLU 3.0 10.8 - - - -
174E ILE* 4.0 4.3 - - - -
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Residues in contact with PHE 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E TRP* 4.2 1.7 - - - -
147E ASN* 3.3 44.6 - - - -
148E GLY* 3.4 20.9 - - - -
149E TRP* 3.5 40.2 - + + -
162E GLY* 1.3 74.1 - - - -
164E MET* 1.3 74.6 + - - +
165E ASN* 4.3 3.8 - - + -
171E ILE* 3.5 3.0 - - - +
172E LEU* 3.3 9.1 - - - +
173E GLU* 2.8 34.2 + - + +
48F MET 5.0 0.2 - - - -
59F ILE 3.6 25.1 - - - -
60F VAL* 3.8 21.3 - - + -
61F LEU* 3.9 17.9 - - + -
73F TYR* 5.0 1.8 - - - -
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Residues in contact with MET 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E ILE* 3.8 28.9 - - + -
104E PHE* 4.8 2.0 - - + -
105E SER 4.1 5.6 - - - +
106E VAL* 3.8 17.9 - - + -
115E ASN* 4.1 10.5 - - - -
116E TRP 3.6 39.3 - - - +
117E TRP* 3.5 28.6 - - + +
145E GLY* 3.3 9.9 - - - -
146E ASP* 3.5 0.9 + - - +
147E ASN* 3.1 23.7 + - - -
148E GLY 4.4 3.1 + - - -
163E PHE* 1.3 82.5 - - - +
165E ASN* 1.3 69.7 + - - +
170E ALA* 4.0 7.9 - - + -
171E ILE 3.3 11.4 - - - +
172E LEU* 4.0 7.0 - - + -
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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