Contacts of the strand formed by residues 45 - 52 (chain A) in PDB entry 3VTV
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 LYS 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A ILE* 5.8 0.7 - - - +
39A ARG* 2.9 20.6 + - - -
42A HIS* 3.0 44.1 + - + +
44A THR* 1.3 90.8 + - - +
46A ILE* 1.3 63.6 + - - +
47A PRO* 3.8 3.8 - - - +
68A LEU* 4.1 31.3 - - + +
69A VAL 3.4 6.1 - - - +
70A PRO* 4.0 32.8 - - + -
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Residues in contact with ILE 46 (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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39A ARG* 3.6 21.3 - - - +
45A LYS* 1.3 73.9 - - - +
47A PRO* 1.4 62.1 - - - +
48A VAL* 3.5 23.5 + - + +
68A LEU* 3.5 4.2 - - - -
69A VAL 2.7 35.8 + - - +
71A ASP* 3.8 31.9 - - + -
110A ILE* 4.0 21.1 - - + -
111A SER* 4.3 9.4 - - - +
114A TYR* 3.5 48.0 - - + -
124A LEU* 4.5 1.8 - - + -
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Residues in contact with PRO 47 (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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35A VAL* 4.2 8.5 - - + -
38A ILE* 4.0 20.0 - - + -
39A ARG* 3.9 13.9 - - - -
45A LYS 3.8 7.6 - - - +
46A ILE* 1.4 82.2 - - - +
48A VAL* 1.3 60.5 + - - +
67A PHE 3.6 7.0 - - - +
68A LEU* 4.2 4.7 - - + -
114A TYR* 3.8 20.6 - - + +
122A GLY 3.6 19.5 - - - +
123A PHE* 3.7 23.5 - - + -
124A LEU* 3.0 23.7 + - - +
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Residues in contact with VAL 48 (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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46A ILE* 3.6 27.6 - - + +
47A PRO* 1.3 80.0 - - - +
49A ILE* 1.3 66.0 + - - +
50A ILE* 3.7 22.4 - - + -
65A THR 3.6 1.2 - - - +
66A LYS* 3.7 1.9 - - - +
67A PHE* 2.8 36.7 + - + +
69A VAL* 3.8 22.7 - - + -
78A LEU* 5.3 0.2 - - + -
110A ILE* 3.9 9.2 - - + -
123A PHE* 4.3 0.4 - - - -
124A LEU* 3.2 15.9 - - + +
126A MET* 3.7 24.9 - - + -
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Residues in contact with ILE 49 (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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22A PHE* 3.7 31.2 - - + -
48A VAL* 1.3 77.0 - - - +
50A ILE* 1.4 59.2 + - - +
51A GLU* 3.7 19.3 - - - +
65A THR* 3.3 15.9 - - + +
66A LYS* 3.8 17.9 - - + -
123A PHE* 3.6 37.7 - - + -
124A LEU 2.8 8.5 + - - +
125A TYR* 3.4 34.0 - - + -
126A MET* 2.7 33.5 + - - +
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Residues in contact with ILE 50 (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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48A VAL* 3.7 20.6 - - + -
49A ILE* 1.4 77.6 - - - +
51A GLU* 1.4 68.0 + - - +
62A LEU* 3.8 22.7 - - + +
64A LYS 4.2 1.0 - - - +
65A THR* 3.0 22.9 + - - +
67A PHE* 3.5 33.4 - - + -
69A VAL* 5.4 1.3 - - + -
78A LEU* 4.7 9.9 - - + -
82A ILE* 3.8 35.7 - - + -
96A LEU* 4.6 8.3 - - + -
126A MET* 3.6 11.4 - - + +
128A TYR* 4.0 16.4 - - + -
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Residues in contact with GLU 51 (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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20A LYS 4.8 0.2 - - - +
21A THR* 3.5 15.9 - - - +
22A PHE* 2.8 32.7 + - - +
23A LYS 5.4 0.2 + - - -
25A ARG* 4.3 3.1 + - - -
49A ILE* 3.7 25.3 - - + +
50A ILE* 1.4 81.2 - - - +
52A ARG* 1.3 66.6 + - - +
62A LEU* 6.1 0.4 - - - -
65A THR* 4.0 9.2 - - + +
125A TYR* 4.4 9.0 - - - -
126A MET 3.1 11.3 + - - +
127A VAL* 3.0 17.1 - - + +
128A TYR* 2.9 29.5 + - - -
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Residues in contact with ARG 52 (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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19A GLU* 2.9 37.9 + - - +
51A GLU* 1.3 79.0 - - - +
53A TYR* 1.3 77.8 + - - +
54A LYS* 3.4 3.1 + - - -
56A GLU* 3.6 27.5 + - + +
59A LEU 2.9 29.6 + - - -
60A PRO* 3.5 9.2 - - - +
61A VAL* 3.4 32.6 - - + +
62A LEU* 5.9 0.4 - - - +
127A VAL* 4.0 1.4 - - - +
128A TYR* 3.5 31.6 + - + +
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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