Contacts of the strand formed by residues 115 - 119 (chain A) in PDB entry 2YVL
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 GLU 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A LYS 3.2 4.5 + - - +
94A ARG* 2.9 50.7 + - + +
95A VAL* 3.0 25.8 + - - +
114A GLY* 1.3 79.3 - - - +
116A VAL* 1.3 66.6 + - - +
117A TRP* 2.9 22.4 + - + +
141A ASN* 3.3 17.5 - - + +
143A LYS* 4.6 12.1 + - + +
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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
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95A VAL* 3.3 28.3 - - + +
97A GLU* 4.4 12.3 - - + -
106A LEU* 3.8 19.7 - - + -
109A LEU* 3.8 23.8 - - + +
110A SER* 3.9 16.6 - - - +
113A ALA* 4.5 1.6 - - + -
115A GLU* 1.3 79.1 - - - +
117A TRP* 1.3 71.9 + - - +
141A ASN* 3.1 6.9 + - - +
142A VAL* 3.5 15.6 - - + +
143A LYS* 2.8 33.6 + - - +
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Residues in contact with TRP 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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94A ARG* 3.8 8.6 - - + +
95A VAL 2.9 7.3 + - - +
96A LEU* 3.6 1.9 - - - -
97A GLU 3.0 25.5 + - - +
115A GLU* 2.9 27.9 + - - -
116A VAL* 1.3 77.5 - - - +
118A THR* 1.3 61.2 + - - +
119A PHE* 3.9 19.3 - + + -
143A LYS* 3.5 33.4 - - + +
145A PHE* 3.7 27.4 - + + -
153A GLU 4.5 8.5 - - - -
154A VAL* 5.2 0.4 - - + -
155A PRO* 3.7 35.2 - - + -
158A ILE* 4.1 10.3 - - + -
159A PHE* 3.5 35.0 - + + -
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Residues in contact with THR 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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97A GLU* 2.6 34.8 + - - -
100A THR* 2.6 30.0 + - + +
106A LEU* 4.1 8.3 - - + -
116A VAL 3.9 0.4 - - - -
117A TRP* 1.3 74.5 - - - +
119A PHE* 1.3 63.1 + - - +
142A VAL* 3.8 11.7 - - + -
143A LYS 2.9 14.8 + - - +
144A PHE* 3.7 29.4 - - + -
145A PHE* 2.9 31.4 + - - -
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Residues in contact with PHE 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 LEU* 3.2 35.4 - - + -
97A GLU 3.0 10.0 + - - -
98A PHE* 3.4 12.6 - - + +
99A GLY* 3.2 11.1 - - - -
100A THR* 3.1 19.3 + - - -
117A TRP* 3.9 23.3 - + + -
118A THR* 1.3 72.7 + - - +
120A GLU* 1.3 60.7 + - - +
145A PHE* 3.5 44.2 - + + -
147A VAL* 3.9 12.6 - - + +
149A PHE* 4.1 12.8 - + + -
152A ALA* 3.4 31.9 - - + -
153A GLU 5.5 2.0 - - - -
154A VAL* 3.8 17.5 - - + -
601A SAM 3.7 5.0 - - + -
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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