Contacts of the helix formed by residues 41 - 59 (chain B) in PDB entry 1PV7
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 SER 41 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B HIS 3.6 3.2 + - - -
40B ILE* 1.3 79.8 - - - +
42B LYS* 1.3 58.2 + - - +
43B SER* 4.0 6.7 + - - -
44B ASP* 2.7 32.5 + - - -
45B THR* 2.7 32.8 + - - +
374B GLU* 4.9 11.4 - - - -
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Residues in contact with LYS 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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35B HIS* 6.6 0.4 - - - -
40B ILE 5.2 2.5 - - - +
41B SER* 1.3 75.4 - - - +
43B SER* 1.3 62.8 + - - +
45B THR* 3.0 7.2 - - + +
46B GLY* 2.5 35.2 + - - -
242B GLN* 3.6 12.7 + - - +
245B ASN* 6.3 0.7 - - - +
370B GLY* 2.9 28.7 - - - +
373B TYR* 2.9 33.1 + - - +
374B GLU* 3.2 31.8 + - + +
378B PHE* 3.2 39.9 - - - -
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Residues in contact with SER 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B SER* 3.4 7.4 - - - -
42B LYS* 1.3 81.3 - - - +
44B ASP* 1.3 65.5 + - - +
46B GLY* 3.9 0.8 - - - -
47B ILE* 3.1 32.5 + - - +
104B LEU* 4.6 2.2 - - - -
371B ASN* 3.6 21.9 + - - +
374B GLU* 2.8 23.7 + - - -
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Residues in contact with ASP 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B HIS 4.9 1.4 - - - +
40B ILE* 3.1 24.0 - - + +
41B SER* 2.7 28.4 + - - +
42B LYS 3.1 0.4 - - - -
43B SER* 1.3 77.4 - - - +
45B THR* 1.3 54.9 + - - +
47B ILE* 3.8 1.0 - - - +
48B ILE* 2.7 39.5 + - - +
104B LEU* 2.7 50.6 - - + +
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Residues in contact with THR 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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31B PRO* 6.1 0.7 - - + -
34B LEU* 4.0 8.5 - - + -
40B ILE* 3.1 33.1 - - + +
41B SER 2.7 21.2 + - - +
42B LYS* 2.7 14.6 + - + -
44B ASP* 1.3 71.0 - - - +
46B GLY* 1.3 66.0 + - - +
48B ILE* 2.4 30.6 + - - -
49B PHE* 2.7 22.1 + - + +
242B GLN* 2.7 36.6 + - + +
245B ASN* 5.0 7.4 - - - +
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Residues in contact with GLY 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 LYS 2.5 21.1 + - - -
43B SER* 3.9 0.9 - - - -
45B THR* 1.3 74.6 + - - +
47B ILE* 1.3 56.7 + - - -
49B PHE* 5.0 2.0 - - - -
50B ALA* 2.9 31.9 + - - +
241B GLN* 5.8 0.4 - - - -
242B GLN* 4.7 5.6 - - - -
366B SER* 3.6 13.1 - - - -
367B VAL* 4.2 8.1 - - - -
370B GLY* 4.2 15.5 - - - -
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Residues in contact with ILE 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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43B SER* 3.1 21.7 + - - +
44B ASP 3.8 2.2 - - - +
45B THR 2.7 3.6 + - - -
46B GLY* 1.3 72.0 - - - +
48B ILE* 1.3 60.2 + - - +
50B ALA* 4.2 0.9 - - - -
51B ALA* 2.5 40.8 + - + +
104B LEU* 4.7 10.1 - - + -
105B VAL* 5.7 13.7 - - + -
108B ILE* 3.5 25.4 - - + -
109B VAL* 6.4 1.3 - - + -
367B VAL* 4.0 25.4 - - + -
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Residues in contact with ILE 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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30B PHE* 3.4 33.2 - - + -
34B LEU* 3.7 18.6 - - + -
40B ILE* 3.3 26.7 - - + -
44B ASP 2.7 22.0 + - - +
45B THR* 2.4 17.2 + - - +
47B ILE* 1.3 72.9 - - - +
49B PHE* 1.3 68.6 + - + +
51B ALA* 3.4 1.9 - - - +
52B ILE* 3.0 21.4 + - + +
95B PHE* 5.6 6.5 - - + -
99B LEU* 4.6 12.8 - - + -
104B LEU* 4.4 8.5 - - + -
108B ILE* 3.2 30.5 - - + +
112B ILE* 6.1 0.4 - - + -
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Residues in contact with PHE 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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27B PHE* 5.4 12.3 - + - -
30B PHE* 3.9 21.1 - + - -
31B PRO* 3.5 28.9 - - + -
34B LEU* 4.5 11.2 - - + -
45B THR* 2.7 31.1 + - + +
46B GLY* 4.2 2.2 - - - +
48B ILE* 1.3 78.4 - - + +
50B ALA* 1.3 67.5 + - - +
52B ILE* 2.6 34.1 + - + +
53B SER* 3.3 2.1 + - - -
241B GLN* 2.8 70.4 - - + +
242B GLN* 5.3 3.1 - - + +
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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 GLY 2.9 22.2 + - - +
47B ILE* 3.7 1.6 - - - +
49B PHE* 1.3 74.2 - - - +
51B ALA* 1.3 67.3 + - - +
53B SER* 2.6 27.3 + - - -
54B LEU 3.5 0.7 + - - -
241B GLN* 4.2 0.4 + - - -
362B MET* 5.7 0.9 - - - -
363B ILE* 3.4 30.2 - - + +
366B SER* 3.2 28.7 - - - +
367B VAL* 3.9 7.4 - - + -
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Residues in contact with ALA 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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47B ILE* 2.5 31.7 + - + +
50B ALA* 1.3 69.6 - - - +
52B ILE* 1.3 55.1 + - - +
54B LEU* 2.5 42.5 + - - +
55B PHE 3.7 1.0 + - - -
108B ILE* 3.3 12.1 - - + -
109B VAL* 4.9 6.1 - - + +
112B ILE* 3.1 25.5 - - + +
363B ILE* 5.3 4.0 - - - -
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Residues in contact with ILE 52 (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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26B TYR* 3.4 17.3 - - - +
30B PHE* 3.3 36.6 - - + -
48B ILE* 3.0 18.6 + - + +
49B PHE* 2.6 24.9 + - + +
51B ALA* 1.3 74.2 - - - +
53B SER* 1.3 61.2 + - - +
55B PHE 3.2 4.2 + - - -
56B SER* 3.1 14.2 + - - -
112B ILE* 3.2 36.1 - - + +
115B GLY* 5.2 5.8 - - - +
116B PHE* 6.4 0.2 - - - -
119B ASN* 4.8 15.9 - - + +
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Residues in contact with SER 53 (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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49B PHE 3.3 1.4 + - - -
50B ALA* 2.6 17.5 + - - -
51B ALA 2.6 4.0 + - - -
52B ILE* 1.3 73.6 - - - +
54B LEU* 1.3 50.5 + - - -
56B SER* 2.5 31.8 + - - -
57B LEU* 2.6 17.8 + - - +
359B GLN* 2.9 26.8 + - - +
362B MET* 4.5 11.4 - - - -
363B ILE* 2.7 30.4 - - - +
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Residues in contact with LEU 54 (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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50B ALA 3.5 0.6 + - - -
51B ALA* 2.5 21.4 + - - +
53B SER* 1.3 74.3 + - - +
55B PHE* 1.3 78.7 + - + +
57B LEU* 2.9 8.5 + - + +
58B LEU* 2.6 60.3 + - + +
109B VAL* 5.9 3.1 - - + -
363B ILE* 3.8 27.3 - - + +
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Residues in contact with PHE 55 (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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51B ALA 3.7 1.3 + - - -
52B ILE 3.2 7.6 + - - +
53B SER 3.1 0.4 - - - -
54B LEU* 1.3 100.1 - - + +
56B SER* 1.3 55.7 + - - +
57B LEU 3.1 5.2 - - - -
58B LEU* 4.2 6.1 - - + +
59B PHE* 2.7 51.5 + + + +
60B GLN* 3.8 1.4 + - - +
109B VAL* 3.5 33.4 - - + -
112B ILE* 3.0 44.6 - - + +
113B TYR* 2.7 45.3 - + - -
116B PHE* 4.8 8.6 - - + +
120B ALA* 5.9 0.5 - - - +
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Residues in contact with SER 56 (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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52B ILE 3.1 5.7 + - - -
53B SER* 2.5 29.0 + - - -
55B PHE* 1.3 71.7 - - - +
57B LEU* 1.3 60.6 + - - +
60B GLN* 3.6 22.0 + - - +
119B ASN* 2.8 47.3 + - - -
355B CYS* 4.2 4.2 - - - -
359B GLN* 3.6 27.3 + - - +
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Residues in contact with LEU 57 (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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53B SER 2.6 7.4 + - - +
54B LEU* 3.2 11.7 - - + +
56B SER* 1.3 83.2 - - - +
58B LEU* 1.3 75.9 + - + +
59B PHE 3.5 0.4 - - - -
61B PRO* 3.2 23.4 - - - +
355B CYS* 3.1 23.7 - - - +
356B PHE* 3.9 21.3 - - + +
359B GLN* 3.7 11.0 - - + -
360B LEU* 4.2 32.1 - - + +
363B ILE* 4.3 15.0 - - + -
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Residues in contact with LEU 58 (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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54B LEU* 2.6 54.8 + - + +
55B PHE* 5.0 7.0 - - + -
57B LEU* 1.3 89.4 - - + +
59B PHE* 1.3 64.2 + - + +
61B PRO* 4.3 3.1 - - - +
62B LEU* 4.4 16.5 + - - +
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Residues in contact with PHE 59 (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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55B PHE* 2.7 38.7 + + + +
58B LEU* 1.3 84.3 - - + +
60B GLN* 1.3 59.0 + - - +
61B PRO 3.4 0.9 - - - -
62B LEU* 3.7 14.2 + - + +
63B PHE* 3.0 31.6 + + + +
113B TYR* 3.9 34.3 - + - -
116B PHE* 3.5 55.9 - + + -
120B ALA* 5.1 0.7 - - + -
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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
------------------------------------------------------------
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