Contacts of the strand formed by residues 114 - 120 (chain A) in PDB entry 5YVT
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 ASN 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A CYS 3.3 3.4 - - - -
101A VAL* 4.0 27.5 - - - +
112A ASP 3.6 5.3 + - - +
113A VAL* 1.3 74.5 - - - +
115A ILE* 1.3 62.2 + - - +
116A VAL* 5.1 0.2 - - - +
165A ARG* 2.8 52.7 + - - +
216A PRO 5.2 1.4 + - - -
217A SER* 5.8 0.6 - - - +
219A PHE 3.4 14.5 + - - +
220A ASP* 4.1 0.3 - - - -
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Residues in contact with ILE 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A ARG 3.8 0.5 - - - +
99A PRO* 3.4 0.9 - - - +
100A CYS* 2.6 46.5 + - + +
101A VAL* 5.4 0.3 - - - +
113A VAL* 3.8 20.6 - - + -
114A ASN* 1.3 77.4 + - - +
116A VAL* 1.3 72.6 + - - +
117A THR* 4.1 2.9 - - + -
212A MET* 3.5 30.7 - - - -
216A PRO* 3.6 17.7 - - + +
219A PHE* 3.5 20.9 - - + +
220A ASP 3.3 8.1 - - - +
222A LEU* 3.9 24.9 - - + -
236A CYS* 4.1 15.0 - - + -
239A LEU* 4.7 0.7 - - + -
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Residues in contact with VAL 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A VAL* 3.7 22.4 - - + -
98A ARG 3.8 4.7 - - - +
99A PRO* 4.3 12.6 - - + -
114A ASN* 5.1 0.4 - - - +
115A ILE* 1.3 78.6 - - - +
117A THR* 1.3 65.5 + - - +
118A ILE* 4.1 8.1 - - + -
159A TYR* 3.6 38.6 - - + +
165A ARG* 3.7 29.4 - - - +
220A ASP 2.9 7.3 + - - +
221A VAL* 3.3 11.2 - - + +
222A LEU 2.8 26.7 + - - +
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Residues in contact with THR 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ASN 3.6 1.0 - - - +
97A VAL* 3.5 3.8 - - - -
98A ARG* 2.9 45.6 + - - +
100A CYS* 5.8 0.5 - - - -
115A ILE* 4.1 8.0 - - + -
116A VAL* 1.3 73.7 - - - +
118A ILE* 1.3 63.3 + - - +
119A ARG* 4.1 1.6 - - - -
222A LEU* 3.5 29.8 - - + -
224A MET* 4.0 14.8 - - + -
232A LEU* 4.9 0.9 - - + -
233A SER* 2.7 34.5 + - - +
236A CYS* 4.2 13.9 - - + -
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Residues in contact with ILE 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ALA* 4.9 0.4 - - + -
96A ASN 3.3 5.8 - - - +
97A VAL* 4.3 8.7 - - + -
116A VAL* 4.1 8.7 - - + -
117A THR* 1.3 78.7 - - - +
119A ARG* 1.3 61.0 + - - +
152A ILE* 3.8 19.5 - - + -
155A PHE* 3.8 24.0 - - + -
156A ALA* 3.8 25.8 - - + -
159A TYR* 3.9 28.3 - - + -
221A VAL* 3.8 23.6 - - + -
222A LEU 2.7 14.2 + - - +
223A VAL* 3.3 9.4 - - + +
224A MET* 3.1 27.3 + - - +
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Residues in contact with ARG 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ASN* 2.9 68.5 + - + +
98A ARG* 5.4 0.6 - - - +
117A THR 4.1 0.9 - - - -
118A ILE* 1.3 75.5 - - - +
120A GLU* 1.3 81.7 + - - +
121A ASN* 2.9 25.2 + - - +
126A TYR* 3.7 12.7 + - - -
152A ILE* 3.7 6.9 - - - +
224A MET* 3.5 15.7 - - + -
225A PRO 3.9 14.8 - - - +
226A ASN* 3.1 21.8 + - - -
229A GLY* 3.3 27.4 - - - -
230A ASP* 3.5 29.1 + - - +
233A SER* 5.2 8.0 + - - +
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Residues in contact with GLU 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A TYR* 3.6 12.4 - - + +
119A ARG* 1.3 78.7 + - - +
121A ASN* 1.3 67.6 + - - +
122A THR* 2.6 33.3 + - - +
123A GLU* 2.9 39.3 + - - +
144A ILE* 5.8 1.4 - - + +
148A ALA* 3.8 29.4 - - + +
149A SER* 5.4 0.9 - - - -
152A ILE* 3.7 20.7 - - + +
184A PHE* 6.0 0.4 - - + -
224A MET 3.0 17.1 + - - +
225A PRO* 4.0 14.4 - - + -
226A ASN* 3.2 24.0 + - - +
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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