Contacts of the strand formed by residues 121 - 129 (chain A) in PDB entry 2VQ5
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 LEU 121 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A TRP* 3.4 4.9 - - - -
114A LEU* 3.8 24.9 - - + +
115A VAL* 3.8 0.9 - - - -
116A ASP* 2.8 49.8 + - + +
119A HIS* 4.1 14.6 - - + -
120A ARG* 1.3 76.3 - - - +
122A LYS* 1.3 58.2 + - - +
123A LYS* 4.5 10.5 - - + -
142A THR* 3.6 29.6 - - + -
143A ILE 3.3 0.7 - - - +
144A HIS* 3.6 28.3 - - + +
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Residues in contact with LYS 122 (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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60A TRP* 3.8 15.2 - - + -
63A TYR* 3.2 32.8 + - + +
64A SER* 5.8 0.2 - - - +
65A TRP 5.7 0.6 + - - -
68A LEU* 4.7 7.7 - - - +
112A PHE* 3.7 36.1 - - - -
114A LEU 3.3 10.5 - - - +
115A VAL* 4.4 14.4 - - + -
121A LEU* 1.3 74.3 - - - +
123A LYS* 1.3 65.2 + - - +
124A VAL* 4.1 7.6 - - + -
141A ASP 3.9 0.2 - - - +
142A THR* 3.4 4.0 - - - +
143A ILE* 2.7 52.1 + - + +
1203A HBA 3.3 37.6 + - - +
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Residues in contact with LYS 123 (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 PHE* 3.8 1.0 - - - -
113A ILE* 2.9 33.6 + - + -
114A LEU* 2.8 49.0 + - + +
121A LEU* 4.5 9.0 - - + -
122A LYS* 1.3 78.2 - - - +
124A VAL* 1.3 65.1 + - - +
140A MSE 4.0 21.3 - - + +
141A ASP 3.3 4.5 - - - +
142A THR* 2.8 40.7 + - + +
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Residues in contact with VAL 124 (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 GLU* 3.7 38.9 - - + +
111A LYS 3.4 6.7 - - - +
112A PHE* 3.6 31.4 - - + -
122A LYS* 4.1 9.9 - - + -
123A LYS* 1.3 79.4 - - - +
125A GLN* 1.3 62.6 + - - +
126A MSE 4.1 0.7 + - - -
139A TYR* 5.5 0.2 - - - -
140A MSE 3.7 2.2 - - - +
141A ASP* 2.8 46.9 + - + +
143A ILE* 4.7 3.4 - - + -
1203A HBA 4.0 26.5 - - + -
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Residues in contact with GLN 125 (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 GLU* 3.1 5.0 - - - -
111A LYS* 2.8 35.5 + - - +
113A ILE* 3.6 31.9 - - + +
124A VAL* 1.3 73.9 - - - +
126A MSE 1.3 69.7 + - - +
127A ILE* 3.4 16.6 + - + +
138A TYR* 4.0 19.0 - - - -
139A TYR 3.3 18.6 + - - +
140A MSE 3.6 23.7 - - + +
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Residues in contact with MSE 126 (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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108A TYR* 4.0 24.2 - - + -
109A LYS 3.5 11.0 - - - +
110A GLU* 3.8 10.4 - - + +
124A VAL 4.1 1.4 + - - -
125A GLN* 1.3 81.3 - - - +
127A ILE* 1.3 61.2 + - - +
128A GLU 4.1 8.5 - - - +
129A GLY 3.6 13.7 - - - +
130A GLY* 4.3 0.4 - - - -
131A TYR* 3.6 35.4 - - + -
132A LEU* 3.6 33.2 - - + +
136A VAL* 4.7 0.2 - - + -
138A TYR* 5.7 0.2 - - - -
139A TYR* 3.0 63.1 + - + +
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Residues in contact with ILE 127 (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 ILE* 4.1 32.5 - - + -
109A LYS* 2.8 36.9 + - + +
110A GLU* 4.4 1.6 - - - +
111A LYS* 3.9 22.7 - - + -
125A GLN* 3.6 32.5 - - + +
126A MSE 1.3 74.1 - - - +
128A GLU* 1.3 64.6 + - + +
132A LEU* 3.4 12.7 - - - +
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Residues in contact with GLU 128 (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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107A GLU* 5.2 3.4 - - - +
108A TYR* 3.2 7.8 - - - +
109A LYS* 2.9 66.5 + - + +
126A MSE 4.1 0.9 - - - +
127A ILE* 1.3 82.9 - - + +
129A GLY* 1.3 65.1 + - - +
132A LEU* 3.5 6.8 - - - +
101B PRO* 4.7 20.0 - - + +
106B HIS* 5.7 4.3 - - - -
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Residues in contact with GLY 129 (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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107A GLU* 3.8 13.5 - - - -
108A TYR* 3.8 2.0 - - - -
126A MSE 3.6 3.6 - - - +
128A GLU* 1.3 85.0 - - - +
130A GLY* 1.3 67.7 + - - -
131A TYR 3.4 0.5 + - - -
132A LEU* 3.2 24.4 + - - +
133A ASP* 3.8 19.0 + - - -
106B HIS* 6.1 2.2 - - - -
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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