Contacts of the strand formed by residues 110 - 117 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A GLU* 4.7 17.4 + - - +
180A ILE* 3.9 20.4 - - + -
181A VAL 3.2 4.5 - - - -
182A LEU* 3.4 19.3 - - + -
195A ILE* 5.4 0.9 - - + -
81C CYS 5.1 5.4 + - - -
83C GLY* 4.6 5.5 - - - +
86C ASP* 3.0 32.8 + - - -
103C PHE* 3.6 16.4 - - - +
104C GLU* 3.5 2.9 - - - -
105C SER* 3.1 32.7 + - - -
108C GLN 3.1 0.4 - - - -
109C ASP* 1.3 88.5 + - - +
111C ILE* 1.3 65.9 + - - +
112C ALA* 4.3 11.9 - - - +
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Residues in contact with ILE 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ASN* 3.9 1.7 - - - +
180A ILE* 3.6 0.3 - - - -
181A VAL* 2.8 47.8 + - + +
183A ARG* 3.6 36.8 - - - +
102C MET* 3.8 27.1 - - + -
103C PHE 3.5 2.2 - - - -
104C GLU* 3.6 33.0 - - + +
108C GLN* 4.2 13.0 - - + +
110C LYS* 1.3 81.7 - - - +
112C ALA* 1.3 61.5 + - - +
113C ASP* 5.9 0.2 - - + -
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Residues in contact with ALA 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ASN 3.2 7.0 - - - +
180A ILE* 4.0 12.8 - - + +
81C CYS 6.1 0.2 - - - +
101C PHE 4.4 0.4 - - - -
102C MET* 3.2 12.5 - - - +
103C PHE* 2.9 50.5 + - + +
110C LYS* 4.2 9.2 - - - -
111C ILE* 1.3 75.7 - - - +
113C ASP* 1.3 61.1 + - - +
114C PHE* 3.8 21.8 - - + -
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Residues in contact with ASP 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A THR 4.0 0.2 - - - +
178A ALA* 3.1 4.9 - - - -
179A ASN* 2.8 62.2 + - - +
100C THR* 3.3 13.0 - - - +
101C PHE 3.8 1.6 - - - -
102C MET* 3.9 17.7 - - + -
111C ILE* 5.5 0.9 - - + +
112C ALA* 1.3 75.0 - - - +
114C PHE* 1.3 62.9 + - - +
115C GLU* 2.7 33.7 + - - +
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Residues in contact with PHE 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ASP* 5.2 0.4 - - + -
151A LEU* 4.6 9.6 - - + -
154A ILE* 4.1 11.0 - - + -
177A THR 3.4 3.8 - - - -
178A ALA* 3.4 27.4 - - + -
179A ASN 4.8 0.2 - - - -
180A ILE* 4.6 11.2 - - + -
78C MET* 3.9 35.7 - - + -
81C CYS* 3.6 36.8 - - + -
99C VAL 3.8 1.0 - - - +
100C THR* 3.7 0.9 - - - -
101C PHE* 2.9 49.7 + - + +
103C PHE* 3.7 22.0 - + + -
112C ALA* 3.8 20.4 - - + -
113C ASP* 1.3 85.0 + - - +
115C GLU* 1.3 60.8 + - - +
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Residues in contact with GLU 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A GLY* 3.4 2.0 - - - -
177A THR* 2.9 50.7 + - - +
178A ALA 5.1 0.2 + - - -
179A ASN* 4.8 4.3 + - - -
78C MET* 3.3 9.5 - - - +
98C THR* 5.3 11.2 - - + -
99C VAL 3.6 4.3 - - - +
100C THR* 3.4 21.2 + - - +
113C ASP* 2.7 43.2 - - - +
114C PHE* 1.3 73.0 - - - +
116C MET* 1.3 61.2 + - - +
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Residues in contact with MET 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ILE 3.6 17.0 - - - +
176A GLY* 4.7 0.9 - - - -
70C MET* 3.5 36.3 - - + -
71C ASN* 3.8 23.1 - - + +
74C ASN* 4.1 13.5 - - + +
75C MET* 3.8 26.2 - - - +
78C MET* 3.8 16.4 - - - +
98C THR* 3.2 6.7 - - - -
99C VAL* 2.9 42.5 + - + +
101C PHE* 4.1 8.5 - - + -
115C GLU* 1.3 75.9 - - - +
117C LYS* 1.3 75.5 + - - +
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Residues in contact with LYS 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A ASP 5.9 3.1 - - - +
175A ILE 4.1 7.1 + - - +
176A GLY* 5.2 4.5 - - - -
70C MET* 5.7 0.5 - - - -
71C ASN 5.8 0.2 + - - -
97C ASP* 3.5 25.9 + - - +
98C THR* 3.5 25.9 - - + +
116C MET* 1.3 94.5 - - - +
118C LEU* 1.3 69.0 + - - +
119C MET* 5.7 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