Contacts of the strand formed by residues 110 - 117 (chain D) in PDB entry 2ZVW
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 LYS 110 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81D CYS 5.1 5.6 + - - -
83D GLY* 4.5 5.1 - - - +
86D ASP* 2.7 33.3 + - - -
103D PHE* 3.8 20.4 - - - -
104D GLU* 3.6 1.2 - - - +
105D SER* 3.1 31.7 + - - -
108D GLN 3.0 0.6 - - - -
109D ASP* 1.3 90.3 + - - +
111D ILE* 1.3 67.9 + - - +
112D ALA* 4.1 12.6 - - - -
143E GLU* 4.6 14.9 + - - +
180E ILE* 4.0 21.5 - - + -
181E VAL 3.3 4.0 - - - -
182E LEU* 3.3 18.8 - - + -
195E ILE* 5.7 0.2 - - + -
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Residues in contact with ILE 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102D MET* 3.9 26.5 - - + -
103D PHE 3.4 5.8 - - - +
104D GLU* 4.3 26.7 - - + +
108D GLN* 4.0 17.3 - - - +
110D LYS* 1.3 81.7 - - - +
112D ALA* 1.3 61.0 + - - +
113D ASP 4.3 0.2 + - - -
179E ASN* 4.1 0.9 - - - +
180E ILE* 3.5 0.3 - - - -
181E VAL* 2.8 42.9 + - + +
183E ARG* 3.1 40.8 - - - +
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Residues in contact with ALA 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D CYS 5.7 1.1 - - - +
101D PHE 3.6 0.4 - - - +
102D MET* 3.2 13.7 - - - +
103D PHE* 2.7 52.7 + - + +
110D LYS* 4.1 9.4 - - - -
111D ILE* 1.3 73.6 - - - +
113D ASP* 1.3 62.3 + - - +
114D PHE* 3.8 22.2 - - + -
179E ASN 3.3 6.5 - - - +
180E ILE* 4.0 11.4 - - + +
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Residues in contact with ASP 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D THR* 3.4 7.6 - - - +
101D PHE 3.8 2.0 - - - -
102D MET* 3.4 25.9 - - + +
112D ALA* 1.3 73.8 - - - +
114D PHE* 1.3 60.2 + - - +
115D GLU* 3.1 30.9 + - - +
177E THR 4.0 0.5 - - - +
178E ALA* 3.4 3.6 - - - -
179E ASN* 2.7 56.2 + - - +
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Residues in contact with PHE 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D MET* 3.7 36.8 - - + -
81D CYS* 3.5 39.3 - - + -
99D VAL 3.6 2.3 - - - +
100D THR* 3.5 1.0 - - - -
101D PHE* 2.8 52.2 + - + +
103D PHE* 3.8 20.6 - + + -
112D ALA* 3.8 22.0 - - + -
113D ASP* 1.3 77.4 + - - +
115D GLU* 1.3 62.4 + - - +
116D MET 3.9 0.2 + - - -
150E ASP* 5.1 0.4 - - + -
151E LEU* 4.7 3.8 - - + -
154E ILE* 4.1 11.7 - - + -
177E THR 3.6 2.5 - - - -
178E ALA* 3.5 26.9 - - + -
179E ASN 4.6 0.4 - - - -
180E ILE* 4.3 17.9 - - + -
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Residues in contact with GLU 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D MET* 3.4 2.6 - - - +
98D THR* 4.4 19.6 + - + +
99D VAL 3.6 3.8 - - - +
100D THR* 2.7 27.3 + - - +
113D ASP* 3.1 25.5 - - - +
114D PHE* 1.3 71.4 - - - +
116D MET* 1.3 60.4 + - - +
117D LYS* 4.8 4.6 + - - +
176E GLY* 3.3 6.4 - - - -
177E THR* 2.9 53.0 + - + +
179E ASN* 6.2 0.7 - - - +
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Residues in contact with MET 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D MET* 3.7 42.4 - - + -
71D ASN* 4.3 11.7 - - + +
74D ASN* 3.7 16.8 - - + +
75D MET* 3.6 32.3 - - - +
78D MET* 3.5 17.9 - - - +
98D THR* 3.4 4.6 - - - -
99D VAL* 2.9 44.5 + - + +
101D PHE* 4.4 4.0 - - + -
114D PHE 3.9 0.2 + - - -
115D GLU* 1.3 75.6 - - - +
117D LYS* 1.3 78.9 + - - +
175E ILE 3.4 17.9 - - - +
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Residues in contact with LYS 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D MET* 5.7 0.9 - - - -
71D ASN 5.8 0.3 + - - -
97D ASP* 3.7 12.1 - - - +
98D THR* 4.3 13.7 - - + +
115D GLU* 4.8 4.4 + - - +
116D MET* 1.3 90.7 - - - +
118D LEU* 1.3 68.2 + - - +
119D MET* 5.2 1.0 - - - +
173E GLY 5.0 2.7 - - - -
174E ASP 4.6 8.7 - - - +
175E ILE 4.0 10.8 - - - +
176E GLY* 3.4 28.9 - - - +
177E THR* 4.3 17.4 + - - +
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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