Contacts of the strand formed by residues 110 - 117 (chain A) in PDB entry 3QEV
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 VAL 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A HIS 5.5 1.3 - - - +
108A ILE* 3.8 21.1 - - + +
109A ARG* 1.3 74.5 - - - +
111A ALA* 1.3 61.7 + - - +
112A ASN* 3.9 19.7 + - - +
139A TYR* 3.8 2.1 - - - +
141A SER* 2.9 47.1 + - - +
212A ILE* 3.5 33.0 - - + +
214A THR* 4.5 5.4 - - + -
341A ILE* 4.5 21.5 - - + -
345A LEU* 5.3 4.0 - - + -
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Residues in contact with ALA 111 (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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109A ARG* 3.8 3.5 + - + -
110A VAL* 1.3 73.0 - - - +
112A ASN* 1.3 58.9 + - - +
113A PHE 4.1 0.4 - - - -
138A HIS* 3.4 31.4 - - + +
139A TYR 3.3 4.9 - - - +
140A ASP* 5.2 1.8 - - - +
210A PRO* 3.7 27.6 - - + -
212A ILE 2.8 9.5 + - - +
213A LEU* 3.5 5.6 - - + +
214A THR* 2.8 34.5 + - - +
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Residues in contact with ASN 112 (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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110A VAL* 3.9 15.2 + - - +
111A ALA* 1.3 75.9 - - - +
113A PHE* 1.3 59.9 + - - +
139A TYR* 2.7 45.6 + - + -
141A SER* 6.2 0.2 - - - -
214A THR* 3.2 32.3 - - - +
215A GLY* 4.6 1.5 + - - +
273A TYR* 5.5 0.2 - - - -
328A VAL* 3.4 21.5 - - + +
331A VAL* 3.5 24.7 - - + +
332A LEU* 3.6 27.4 - - + +
335A ASP* 6.1 0.3 - - - +
341A ILE* 6.1 0.4 - - - +
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Residues in contact with PHE 113 (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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112A ASN* 1.3 74.5 - - - +
114A ASP* 1.3 65.2 + - - +
115A ILE* 3.8 28.3 - - + -
136A ILE* 4.1 4.0 - - + -
137A THR 3.2 13.0 - - - +
138A HIS* 3.9 17.7 - - + +
201A TYR* 3.6 21.8 - + - -
205A TRP* 5.2 5.2 - + - -
213A LEU* 3.7 30.5 - - + -
214A THR 3.2 12.0 + - - -
215A GLY* 3.8 8.4 - - - -
216A TRP 4.5 1.0 + - - -
218A VAL* 3.5 36.7 - - + +
222A ALA* 3.6 21.1 - - + -
223A ILE* 3.9 18.2 - - + -
226A VAL* 4.2 11.9 - - + -
328A VAL* 4.1 4.0 - - - -
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Residues in contact with ASP 114 (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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113A PHE* 1.3 78.2 - - - +
115A ILE* 1.3 70.3 + - - +
116A GLU* 3.3 12.5 - - - +
136A ILE* 3.5 2.8 - - - +
137A THR 3.0 30.1 + - - -
216A TRP* 4.6 14.9 + - - +
218A VAL* 6.1 0.2 - - - +
222A ALA* 5.3 3.1 - - - -
290A LEU* 6.1 0.6 - - - +
324A ASN* 2.9 22.9 + - - +
327A ALA* 4.0 18.2 - - + +
328A VAL* 3.6 20.2 - - + +
909A CA 4.1 2.4 - - - -
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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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113A PHE* 3.8 25.1 - - + -
114A ASP* 1.3 87.7 + - - +
116A GLU* 1.3 71.5 + - - +
117A VAL* 3.8 19.1 - - + -
133A ILE* 4.3 8.1 - - + -
135A ALA 3.3 8.3 - - - +
136A ILE* 3.9 16.8 - - + -
221A PHE* 3.8 22.2 - - + -
222A ALA* 4.1 11.4 - - + +
225A TYR* 3.8 32.8 - - + -
226A VAL* 3.8 18.8 - - + -
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Residues in contact with GLU 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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114A ASP* 3.3 4.7 - - - +
115A ILE* 1.3 76.3 - - - +
117A VAL* 1.3 67.5 + - - +
133A ILE* 3.7 2.8 - - - +
134A ASP* 3.0 30.0 + - - +
135A ALA* 2.8 24.0 + - + +
309A ILE* 4.1 15.9 - - - +
320A TYR* 3.2 31.4 + - + +
323A TYR 5.0 0.5 - - - -
324A ASN* 3.3 39.2 + - + +
327A ALA* 5.6 0.2 - - - +
909A CA 2.6 29.6 - - - -
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Residues in contact with VAL 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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115A ILE* 3.8 19.1 - - + -
116A GLU* 1.3 82.3 + - - +
118A THR* 1.3 63.1 + - - +
119A SER* 3.4 2.4 + - - -
124A PRO* 3.8 24.5 - - + +
131A HIS* 3.7 13.2 - - + -
132A PRO 3.6 15.3 - - - +
133A ILE* 4.2 5.6 - - + -
221A PHE* 4.2 9.5 - - + -
225A TYR* 3.3 46.2 - - + +
309A ILE* 5.9 3.7 - - - +
320A TYR* 3.7 2.9 + - - -
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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