Contacts of the strand formed by residues 107 - 116 (chain A) in PDB entry 2VNE
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 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A LYS* 5.2 3.8 + - - -
96A ASP* 2.6 30.4 - - - +
97A MSE 3.1 13.7 - - - +
98A THR* 2.9 21.3 + - - +
99A PHE* 4.8 0.4 - - - -
105A PRO 3.5 0.4 - - - -
106A HIS* 1.3 94.0 + - + +
108A TYR* 1.3 67.8 + - - +
109A LYS* 5.9 1.6 - - + -
129A GLY* 3.8 4.2 - - - -
130A GLY* 3.0 20.0 + - - -
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Residues in contact with TYR 108 (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 LEU 3.7 0.7 - - - +
96A ASP* 3.8 0.3 - - - -
97A MSE 3.0 53.6 + - + -
99A PHE* 3.6 26.6 - + - -
105A PRO* 3.7 33.7 - - + -
107A GLU* 1.3 80.2 - - - +
109A LYS* 1.3 73.0 + - - +
110A GLU* 3.4 26.2 + - + -
126A MSE 4.0 23.8 - - + -
128A GLU 3.2 14.4 - - - +
129A GLY* 3.7 2.2 - - - -
130A GLY* 3.5 11.2 - - - +
131A TYR* 5.8 1.1 - + - -
179A PRO* 5.1 11.4 - - - +
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Residues in contact with LYS 109 (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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86A ILE* 5.3 8.3 - - - -
94A ILE* 4.3 15.3 - - + -
95A LEU 3.3 3.6 - - - +
96A ASP* 3.1 36.6 + - + +
107A GLU* 5.9 2.0 - - + -
108A TYR* 1.3 78.4 - - - +
110A GLU* 1.3 62.1 + - - +
126A MSE 3.6 5.9 - - - -
127A ILE* 3.3 38.9 + - + -
128A GLU* 2.7 46.4 + - + +
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Residues in contact with GLU 110 (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* 3.1 8.5 - - - +
95A LEU* 2.8 60.9 + - + +
97A MSE 3.5 11.0 - - - +
108A TYR* 3.4 31.2 + - + -
109A LYS* 1.3 76.8 - - - +
111A LYS* 1.3 63.5 + - - +
112A PHE* 4.7 5.0 - - + -
124A VAL* 4.1 25.1 - - + +
125A GLN 3.2 16.2 - - - +
126A MSE 4.7 3.7 - - + +
127A ILE* 4.5 2.0 - - - -
141A ASP* 4.8 4.7 - - - +
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Residues in contact with LYS 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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92A GLY* 3.9 22.4 - - - +
93A THR 3.4 9.4 - - - +
94A ILE* 4.0 15.5 - - + +
110A GLU* 1.3 76.2 - - - +
112A PHE* 1.3 70.5 + - - +
113A ILE* 3.3 24.5 + - + +
124A VAL* 3.3 5.6 - - - -
125A GLN* 2.8 33.2 + - - +
127A ILE* 3.9 27.1 - - + -
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Residues in contact with PHE 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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69A ALA* 4.9 9.9 - - + -
72A LEU* 6.3 0.2 - - + -
89A GLY* 3.3 29.6 - - - -
90A GLY 3.5 16.6 - - - +
91A VAL* 3.5 5.1 - - - -
92A GLY* 2.8 29.1 + - - -
93A THR* 2.9 29.2 + - + +
95A LEU* 3.8 33.9 - - + -
110A GLU* 4.7 3.8 - - + -
111A LYS* 1.3 73.8 - - - +
113A ILE* 1.3 64.5 + - - +
114A LEU 3.6 1.3 - - - -
115A VAL* 4.9 7.0 - - + -
122A LYS* 4.0 25.4 - - - -
123A LYS 4.0 3.6 - - - +
124A VAL* 3.6 27.8 - - + -
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Residues in contact with ILE 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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91A VAL* 3.8 10.4 - - - +
111A LYS* 3.3 37.5 - - + +
112A PHE* 1.3 72.9 - - - +
114A LEU* 1.3 69.4 + - + +
123A LYS* 3.0 25.2 + - + +
125A GLN* 3.4 30.5 - - + +
140A MSE 3.6 27.4 - - + -
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Residues in contact with LEU 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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91A VAL* 3.9 2.5 - - + -
112A PHE 3.6 0.8 - - - -
113A ILE* 1.3 86.1 - - + +
115A VAL* 1.3 77.9 + - - +
116A ASP* 3.8 30.7 - - + +
121A LEU* 4.3 23.8 - - + +
122A LYS* 3.2 7.8 - - - +
123A LYS* 3.0 54.4 + - + +
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Residues in contact with VAL 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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60A TRP* 4.1 8.1 - - + -
64A SER* 4.0 36.1 - - - +
89A GLY 5.6 0.9 - - - +
90A GLY* 4.8 4.9 - - - -
91A VAL* 3.5 33.8 - - + +
112A PHE* 4.9 6.3 - - + -
114A LEU* 1.3 83.1 - - - +
116A ASP* 1.3 59.2 + - - +
117A ASN* 3.6 11.3 + - - +
121A LEU 3.8 2.2 - - - -
122A LYS* 4.2 20.9 - - - +
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Residues in contact with ASP 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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60A TRP* 3.5 2.9 - - - -
114A LEU* 3.8 21.0 - - + +
115A VAL* 1.3 70.2 - - - +
117A ASN* 1.3 62.1 + - - +
118A GLU* 3.1 9.4 + - - +
119A HIS* 3.0 47.1 + - - +
120A ARG* 3.0 17.3 + - - -
121A LEU* 2.8 32.0 + - + +
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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