Contacts of the helix formed by residues 33 - 46 (chain A) in PDB entry 5VXA
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 ILE 33 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A ALA* 4.4 3.6 - - - +
15A ALA* 3.7 18.8 - - + +
16A ALA* 3.5 43.5 - - + +
19A HIS* 4.2 15.2 + - + +
20A ARG* 6.5 0.2 - - - -
31A PRO* 4.2 8.3 - - + -
32A TYR* 1.3 76.7 - - - +
34A ASN* 1.3 68.8 + - - +
35A HIS 3.2 0.5 + - - -
36A PRO* 3.3 11.5 - - + +
37A ILE* 3.2 41.7 + - + +
59A LEU* 6.0 0.9 - - + -
31B PRO* 5.0 3.1 - - + -
33B ILE* 3.6 30.3 - - + -
34B ASN* 4.5 5.6 - - - +
37B ILE* 4.8 1.8 - - + -
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Residues in contact with ASN 34 (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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24A ARG* 5.9 0.7 - - + -
30A THR* 3.5 27.7 - - + +
31A PRO* 3.4 17.8 - - - +
32A TYR 2.9 1.0 + - - -
33A ILE* 1.3 86.1 - - - +
35A HIS* 1.3 56.4 + - - +
37A ILE* 3.9 5.3 - - - +
38A GLY* 2.9 24.3 + - - -
125A TYR* 3.6 14.8 + - - +
13B ASP* 5.0 1.4 - - - +
16B ALA* 3.1 45.5 + - + +
17B ARG* 4.1 7.2 - - + +
20B ARG* 3.7 10.5 - - - +
33B ILE* 4.3 3.5 - - - +
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Residues in contact with HIS 35 (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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24A ARG* 3.5 26.8 + - - +
31A PRO 4.5 0.4 + - - -
32A TYR* 2.8 21.2 + - + +
34A ASN* 1.3 75.4 - - - +
36A PRO* 1.3 73.6 - - + +
38A GLY* 3.0 2.9 + - - -
39A VAL* 2.8 37.4 + - + +
61A HIS* 3.3 2.8 + + - -
62A ASP* 3.1 11.9 - - - -
122A ASP* 2.7 18.8 - - - -
125A TYR* 3.2 32.3 + + + -
126A ASN* 3.3 20.0 - - - -
201A ZN 1.9 32.6 - - - -
202A NDP 3.3 2.9 + - - -
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Residues in contact with PRO 36 (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 HIS* 4.1 23.3 - - + +
32A TYR* 3.0 29.4 - - + +
33A ILE* 3.3 15.5 - - + +
35A HIS* 1.3 89.0 - - + +
37A ILE* 1.3 60.6 + - - +
39A VAL* 3.4 2.1 + - + +
40A ALA* 3.0 25.1 + - - +
58A ALA 3.8 12.3 - - - +
59A LEU* 3.2 31.9 - - + +
61A HIS* 4.2 11.2 - - + -
62A ASP* 4.6 2.9 - - + +
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Residues in contact with ILE 37 (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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12A ALA* 5.5 4.0 - - + -
33A ILE* 3.2 37.3 + - + +
34A ASN* 3.9 4.3 - - - +
36A PRO* 1.3 75.7 - - - +
38A GLY* 1.3 58.9 + - - +
40A ALA* 3.3 2.9 + - - +
41A ARG* 2.9 26.5 + - - +
59A LEU* 3.9 20.4 - - + -
9B LEU* 5.0 5.3 - - + +
12B ALA* 4.0 14.8 - - + +
13B ASP* 3.7 35.2 - - + +
16B ALA* 4.1 19.5 - - + -
33B ILE* 4.8 1.3 - - + -
37B ILE* 3.9 22.0 - - + -
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Residues in contact with GLY 38 (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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34A ASN 2.9 17.1 + - - -
35A HIS 3.5 2.5 - - - -
37A ILE* 1.3 74.9 - - - +
39A VAL* 1.3 58.6 + - - +
41A ARG* 3.3 2.9 + - - +
42A ILE* 2.9 33.1 + - - +
125A TYR* 3.8 19.3 - - - -
13B ASP* 3.7 16.6 - - - -
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Residues in contact with VAL 39 (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 HIS* 2.8 50.3 + - + +
36A PRO 3.7 4.9 - - - +
38A GLY* 1.3 71.8 - - - +
40A ALA* 1.3 62.7 + - - +
42A ILE* 3.3 13.2 + - - +
43A LEU* 3.2 21.5 + - + +
58A ALA* 4.2 15.0 - - + -
61A HIS* 3.9 15.3 - - + +
118A VAL* 4.3 6.5 - - + +
121A ALA* 3.7 19.6 - - + +
122A ASP* 3.8 21.5 - - - +
125A TYR* 3.9 7.2 - - + -
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Residues in contact with ALA 40 (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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36A PRO 3.0 17.1 + - - +
37A ILE 3.7 3.6 - - - +
39A VAL* 1.3 77.1 - - - +
41A ARG* 1.3 61.0 + - - +
43A LEU* 3.1 15.5 + - - +
44A THR 3.2 9.0 + - - -
55A LEU* 4.0 6.8 - - + +
58A ALA* 3.9 20.8 - - + +
59A LEU* 3.8 22.2 - - + -
9B LEU* 3.5 23.4 - - + +
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Residues in contact with ARG 41 (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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37A ILE 2.9 17.9 + - - +
38A GLY* 3.8 4.3 - - - +
40A ALA* 1.3 72.8 - - - +
42A ILE* 1.3 60.6 + - + +
44A THR* 3.7 7.6 - - - -
45A HIS* 2.7 71.3 + - + +
46A GLU* 5.5 3.8 + - - -
9B LEU* 4.2 12.3 - - + +
10B GLU* 2.7 40.1 + - - +
13B ASP* 3.3 42.9 + - + -
17B ARG* 4.6 8.0 - - - +
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Residues in contact with ILE 42 (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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38A GLY 2.9 18.3 + - - +
39A VAL* 3.4 7.4 - - - +
41A ARG* 1.3 78.1 - - + +
43A LEU* 1.3 58.2 + - - +
46A GLU* 2.9 45.6 + - - +
47A ALA 3.2 6.4 + - - -
121A ALA* 3.7 31.6 - - + +
124A LEU* 3.9 10.1 - - + -
125A TYR* 3.8 28.5 - - + +
128A ARG* 3.9 13.9 - - - +
164A LEU* 3.4 27.8 - - + -
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Residues in contact with LEU 43 (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 VAL 3.2 10.5 + - - +
40A ALA 3.1 8.2 + - - +
41A ARG 3.1 0.8 - - - -
42A ILE* 1.3 77.5 - - - +
44A THR* 1.3 57.8 + - - +
47A ALA* 3.3 5.3 - - - +
48A GLY 3.1 9.9 + - - -
49A ILE* 2.9 35.5 + - + -
54A VAL* 4.2 18.8 - - + -
55A LEU* 3.7 13.5 - - + -
58A ALA* 3.7 30.7 - - + -
117A LEU* 3.5 31.6 - - + +
118A VAL* 4.4 8.1 - - + -
121A ALA* 3.7 13.5 - - + -
164A LEU* 4.0 14.6 - - + -
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Residues in contact with THR 44 (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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40A ALA 3.2 5.2 + - - -
41A ARG* 3.2 11.6 + - - -
43A LEU* 1.3 75.6 - - - +
45A HIS* 1.3 66.5 + - - +
48A GLY* 3.6 14.7 + - - -
49A ILE 3.4 21.5 - - - +
55A LEU* 3.6 25.4 - - + -
5B ALA* 4.6 0.2 - - + -
6B ALA* 3.7 36.3 + - + +
9B LEU* 3.6 24.2 - - + +
10B GLU* 4.6 1.9 + - - -
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Residues in contact with HIS 45 (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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41A ARG* 2.7 58.6 + - + +
42A ILE* 5.0 0.2 - - - -
44A THR* 1.3 75.6 + - - +
46A GLU* 1.3 74.2 + - + +
48A GLY 4.8 0.2 - - - -
6B ALA* 5.9 0.9 - - - -
10B GLU* 3.4 23.8 + - - +
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Residues in contact with GLU 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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41A ARG* 5.5 3.6 + - - -
42A ILE* 2.9 24.0 + - - +
45A HIS* 1.3 99.9 - - + +
47A ALA* 1.3 61.1 + - - +
48A GLY 3.5 1.3 - - - -
124A LEU* 4.0 8.8 - - - +
128A ARG* 2.6 47.7 + - - -
163A GLN* 3.2 29.9 + - + +
164A LEU* 4.5 9.0 - - + -
167A ALA* 4.6 5.2 - - - +
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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