Contacts of the helix formed by residues 40 - 51 (chain B) in PDB entry 1V2E
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 PRO 40 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B PRO 3.8 0.2 - - - -
39B PRO* 1.3 89.9 - - + +
41B PRO* 1.3 76.0 - - + +
42B PHE* 3.6 40.2 - - + -
43B LEU* 3.1 20.0 + - + +
44B LEU* 3.4 9.7 + - - +
224B LEU* 3.2 21.3 - - + +
225B GLU* 4.5 3.1 - - + -
275B PHE* 3.7 28.5 - - + -
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Residues in contact with PRO 41 (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 PRO 4.2 2.0 - - - +
40B PRO* 1.3 87.2 - - + +
42B PHE* 1.3 58.9 + - + +
44B LEU* 3.4 10.3 + - + +
45B GLU* 3.0 36.3 + - + +
48B ARG* 5.0 0.9 + - - +
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Residues in contact with PHE 42 (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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40B PRO* 3.6 28.9 - - + -
41B PRO* 1.3 79.8 - - + +
43B LEU* 1.3 61.3 + - - +
45B GLU* 4.1 6.2 - - - +
46B ALA* 3.4 22.5 + - - +
49B ARG* 5.0 1.6 + - - -
224B LEU* 4.3 4.3 - - + -
266B ALA* 3.7 35.0 - - + +
269B LEU* 3.9 22.4 - - + +
270B ALA* 4.1 7.2 - - - -
273B GLU* 3.8 34.3 - - + +
275B PHE* 3.7 41.7 - + + -
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Residues in contact with LEU 43 (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 PRO* 3.9 11.4 - - + -
40B PRO* 3.1 19.3 + - + +
42B PHE* 1.3 82.6 - - - +
44B LEU* 1.3 63.5 + - - +
46B ALA* 3.6 1.7 + - - +
47B VAL* 3.1 33.3 + - + +
224B LEU* 3.8 28.0 - - + -
226B ALA* 3.9 10.5 - - + -
229B TYR* 3.7 27.4 - - + -
262B GLY 3.6 17.3 - - - +
263B VAL* 4.0 13.0 - - + +
266B ALA* 3.4 26.7 - - + -
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Residues in contact with LEU 44 (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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51A LEU* 4.5 6.8 - - + +
52A GLY* 3.8 32.5 - - - +
38B PRO* 5.1 3.8 - - + -
39B PRO* 3.4 31.9 - - + +
40B PRO 3.4 11.1 + - - +
41B PRO* 3.4 9.4 + - + +
43B LEU* 1.3 73.0 - - - +
45B GLU* 1.3 65.5 + - - +
47B VAL* 3.3 5.0 + - - +
48B ARG* 3.0 54.5 + - - +
229B TYR* 3.3 25.6 - - - +
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Residues in contact with GLU 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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41B PRO* 3.0 20.0 + - + +
42B PHE* 4.3 5.6 - - - +
44B LEU* 1.3 78.4 - - - +
46B ALA* 1.3 61.0 + - - +
48B ARG* 3.3 35.4 + - - +
49B ARG* 3.0 48.9 + - - +
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Residues in contact with ALA 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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42B PHE 3.4 18.1 + - - +
43B LEU 3.9 2.0 - - - +
44B LEU 3.3 0.4 - - - -
45B GLU* 1.3 76.7 - - - +
47B VAL* 1.3 66.9 + - - +
49B ARG* 3.3 24.4 + - - +
50B ALA* 3.4 11.1 + - - +
261B ALA 5.3 0.3 - - - -
262B GLY* 3.8 28.8 - - - +
265B GLU* 3.6 25.8 - - + +
269B LEU* 5.8 0.4 - - + -
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Residues in contact with VAL 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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47A VAL* 5.9 0.9 - - + -
51A LEU* 3.8 23.6 - - + -
259A LEU* 6.3 0.7 - - + -
43B LEU* 3.1 22.0 + - + +
44B LEU* 3.8 5.2 - - - +
46B ALA* 1.3 74.8 - - - +
48B ARG* 1.3 57.3 + - - +
50B ALA* 2.8 24.6 + - - +
51B LEU* 3.1 19.7 + - + +
229B TYR* 4.2 16.8 - - + +
258B PRO* 4.3 11.2 - - + +
259B LEU* 3.8 32.5 - - + +
262B GLY* 4.2 16.2 - - - -
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Residues in contact with ARG 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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48A ARG* 3.2 54.8 + - + +
51A LEU* 4.2 26.9 + - + +
52A GLY* 5.7 0.4 - - - -
41B PRO* 5.0 1.0 + - - +
44B LEU* 3.0 39.2 + - - +
45B GLU* 3.3 47.2 + - - +
47B VAL* 1.3 77.1 - - - +
49B ARG* 1.3 61.7 + - + +
50B ALA 3.2 0.7 + - - -
51B LEU* 3.4 21.3 + - - +
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Residues in contact with ARG 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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42B PHE 5.0 1.8 + - - -
45B GLU* 3.0 33.6 + - - +
46B ALA* 3.5 27.1 + - - +
47B VAL 3.1 0.4 - - - -
48B ARG* 1.3 77.4 - - + +
50B ALA* 1.3 59.1 + - - +
51B LEU 4.1 3.3 - - - +
53B ARG* 3.6 28.9 + - - +
265B GLU* 2.4 42.7 + - - +
269B LEU* 5.3 6.1 - - - +
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Residues in contact with ALA 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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46B ALA 3.4 8.8 + - - +
47B VAL 2.8 12.7 + - - +
49B ARG* 1.3 78.5 - - - +
51B LEU* 1.3 66.3 + - - +
53B ARG* 2.9 20.8 + - - +
54B GLN* 2.9 21.1 + - + +
55B ASP* 4.1 1.1 - - - +
258B PRO* 3.9 17.5 - - + +
261B ALA* 3.9 27.4 - - + -
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Residues in contact with LEU 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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44A LEU* 4.1 13.2 - - + +
47A VAL* 3.6 35.7 - - + -
48A ARG* 4.2 29.6 + - + +
51A LEU* 4.1 20.2 - - + -
229A TYR* 3.5 24.9 - - + +
259A LEU* 5.7 0.4 - - + -
47B VAL* 3.1 15.0 + - + +
48B ARG* 3.4 15.6 + - - +
49B ARG 4.1 3.8 - - - +
50B ALA* 1.3 77.8 - - - +
52B GLY* 1.3 58.0 + - - +
53B ARG* 3.3 2.9 + - - +
55B ASP* 3.7 4.3 - - - +
258B PRO* 4.0 17.0 - - + -
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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