Contacts of the strand formed by residues 44 - 51 (chain B) in PDB entry 3VKO
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 ASP 44 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42B ASP 3.3 4.0 + - - +
43B ALA* 1.3 74.5 - - - +
45B ARG* 1.3 103.9 + - + +
69B ARG* 3.9 1.7 - - - +
70B PHE* 3.3 24.0 + - - +
71B LYS* 4.4 7.0 + - - +
99B ARG* 5.0 3.6 - - - +
143B LYS* 3.4 19.7 + - - +
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Residues in contact with ARG 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ALA 3.6 1.2 - - - -
44B ASP* 1.3 104.8 + - + +
46B PHE* 1.3 64.4 + - - +
47B GLN* 2.7 30.9 + - - -
67B ASN* 3.1 35.6 + - - +
68B PRO 3.4 17.5 - - - +
69B ARG* 3.3 28.6 - - + +
70B PHE* 3.9 5.1 - - - -
142B GLY* 3.8 2.9 - - - -
143B LYS* 2.9 24.4 + - - +
2D GAL 3.1 32.5 + - - -
3D SIA 3.5 7.4 - - - +
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Residues in contact with PHE 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B VAL* 4.1 11.0 - - + -
45B ARG* 1.3 77.3 - - - +
47B GLN* 1.3 72.4 + - - +
48B VAL* 4.2 18.4 - - + -
67B ASN* 2.8 19.5 + - - -
68B PRO* 3.0 38.9 + - + +
70B PHE* 4.0 27.4 - + - -
97B PHE* 4.4 9.9 - + - -
103B PHE* 4.0 21.1 - + - -
105B ILE* 4.7 3.8 - - + -
140B ILE* 5.3 0.4 - - + -
141B TYR 3.2 14.6 - - - +
142B GLY* 4.0 2.7 - - - -
143B LYS 3.5 22.9 - - - +
144B VAL* 3.6 29.8 - - + -
146B ILE* 5.8 1.8 - - + -
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Residues in contact with GLN 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ARG* 2.7 26.0 + - - -
46B PHE* 1.3 79.0 - - - +
48B VAL* 1.3 64.4 + - - +
49B ASP* 2.8 24.0 + - - +
59B ARG* 3.8 3.0 - - - +
65B HIS* 3.0 30.8 - - + -
66B PHE 3.2 9.0 - - - +
67B ASN* 4.1 3.6 - - - +
139B GLY 3.7 0.2 - - - +
140B ILE* 3.3 7.3 - - - +
141B TYR* 2.9 60.5 + - + +
3D SIA 3.1 27.3 + - - +
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Residues in contact with VAL 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ILE* 3.9 32.8 - - + -
46B PHE* 4.2 18.4 - - + -
47B GLN* 1.3 76.3 - - - +
49B ASP* 1.3 62.2 + - - +
50B LEU* 4.7 3.4 - - + +
64B PHE* 3.3 3.7 - - + +
66B PHE* 2.9 49.2 + - + +
105B ILE* 4.6 7.0 - - + -
107B ILE* 4.3 19.5 - - + -
138B LEU* 4.0 15.7 - - + -
139B GLY 3.4 3.1 - - - -
140B ILE* 4.3 10.8 - - + -
146B ILE* 6.1 0.9 - - + -
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Residues in contact with ASP 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B GLN* 2.8 26.8 + - - +
48B VAL* 1.3 78.5 - - - +
50B LEU* 1.3 65.2 + - - +
51B GLN* 3.6 17.5 + - + +
59B ARG* 4.1 7.1 + - - -
62B VAL* 3.6 19.0 - - + +
64B PHE 3.3 3.1 - - - -
65B HIS* 2.5 32.4 + - - -
138B LEU* 3.6 3.9 - - - +
139B GLY 2.7 40.9 + - - +
141B TYR* 3.4 13.3 - - + -
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Residues in contact with LEU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ILE* 4.7 6.7 - - + -
27B LEU* 4.5 1.6 - - + -
33B ILE* 3.8 28.7 - - + -
48B VAL* 4.7 7.2 - - + -
49B ASP* 1.3 70.5 - - - +
51B GLN* 1.3 61.5 + - - +
62B VAL 3.6 1.4 - - - -
63B ALA* 2.9 27.9 + - - +
64B PHE* 3.0 40.9 + - + +
107B ILE* 4.5 8.7 - - + -
114B PHE* 3.8 24.2 - - + -
135B ILE* 3.9 22.7 - - + -
137B THR 3.6 3.4 - - - -
138B LEU* 3.8 27.1 - - + -
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Residues in contact with GLN 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B VAL* 5.0 1.2 - - - +
49B ASP* 3.8 20.1 - - + +
50B LEU* 1.3 77.7 - - - +
52B ASN* 1.3 60.3 + - - +
53B GLY 3.0 22.6 + - - +
54B SER* 4.0 11.7 - - - +
55B SER 5.6 0.4 + - - -
60B ALA* 4.5 6.5 - - + +
61B ASP 3.4 12.6 - - - +
62B VAL* 4.2 10.3 - - + +
63B ALA 5.2 0.2 - - - -
135B ILE* 3.5 5.8 - - - -
136B ASP 3.0 24.4 + - - -
137B THR* 2.7 28.2 + - - +
139B GLY* 3.9 7.6 - - - -
141B TYR* 2.6 39.2 + - - -
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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