Contacts of the helix formed by residues 38 - 54 (chain A) in PDB entry 3V6A
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 GLY 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A GLY* 1.3 74.6 - - - -
39A THR* 1.3 57.4 + - - -
41A GLU* 2.9 20.5 + - - -
42A LYS* 2.7 40.6 + - - +
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Residues in contact with THR 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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38A GLY* 1.3 70.8 - - - +
40A LYS* 1.3 69.8 + - + +
41A GLU* 3.7 0.4 + - - -
42A LYS* 3.0 13.6 + - - +
43A ARG* 2.8 53.1 + - - +
75A ASP* 4.2 15.6 + - - +
78A ILE* 3.7 6.1 - - + +
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Residues in contact with LYS 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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4A VAL* 3.9 20.6 - - + -
38A GLY 3.5 0.4 - - - -
39A THR* 1.3 79.2 - - + +
41A GLU* 1.3 66.6 + - - +
43A ARG* 3.5 17.5 + - - +
44A LEU* 3.3 27.2 + - - +
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Residues in contact with GLU 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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2A PRO 3.5 23.9 - - - +
3A THR* 4.1 4.3 - - - +
4A VAL* 3.8 31.4 + - + +
7A LEU* 3.8 18.5 - - + +
34A GLY* 4.0 5.5 - - - +
37A GLY* 4.1 7.6 - - - -
38A GLY* 2.9 36.4 + - - +
39A THR 3.7 0.7 + - - -
40A LYS* 1.3 80.7 + - - +
42A LYS* 1.3 66.1 + - - +
44A LEU* 3.1 5.2 + - - +
45A ALA* 3.1 19.9 + - - +
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Residues in contact with LYS 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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34A GLY 4.1 7.4 - - - +
35A VAL 3.6 23.3 - - - +
37A GLY 3.5 21.3 - - - +
38A GLY* 2.7 26.2 + - - +
39A THR* 3.7 10.1 + - - +
41A GLU* 1.3 68.8 - - - +
43A ARG* 1.3 65.6 + - - +
45A ALA* 3.1 5.6 + - - +
46A ALA* 3.0 24.8 + - - +
70A LEU* 3.9 19.6 - - + +
73A ASP* 2.9 38.7 + - - +
74A GLU* 4.0 8.1 + - - -
75A ASP* 5.6 0.4 - - - +
78A ILE* 4.1 12.4 - - + +
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Residues in contact with ARG 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 THR* 2.8 46.6 + - - +
40A LYS* 3.7 16.4 - - - +
41A GLU 3.2 0.2 - - - -
42A LYS* 1.3 78.5 - - - +
44A LEU* 1.3 60.2 + - + +
46A ALA* 3.8 9.4 - - - +
47A GLN* 2.9 32.4 + - - +
75A ASP* 4.2 3.6 + - - -
77A SER* 2.7 35.8 + - - -
78A ILE* 3.7 14.3 - - + +
81A GLN* 4.0 14.4 - - + +
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Residues in contact with LEU 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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4A VAL* 4.0 22.7 - - + -
7A LEU* 4.1 23.1 - - + -
8A TYR* 3.7 40.6 - - + +
40A LYS 3.3 10.9 + - - +
41A GLU 3.1 8.7 + - - +
42A LYS 3.1 0.4 - - - -
43A ARG* 1.3 78.9 - - + +
45A ALA* 1.3 65.4 + - - +
46A ALA 3.2 0.2 - - - -
47A GLN* 3.0 18.6 + - - +
48A PHE* 2.9 53.6 + - + -
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Residues in contact with ALA 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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7A LEU* 5.1 3.0 - - + +
31A ILE* 4.0 8.7 - - - +
34A GLY* 4.0 23.3 - - - -
35A VAL* 4.1 6.3 - - + +
41A GLU 3.1 12.9 + - - +
42A LYS* 3.1 8.0 + - - +
44A LEU* 1.3 76.2 - - - +
46A ALA* 1.3 59.3 + - - +
48A PHE* 4.3 4.5 - - - +
49A ILE* 2.9 56.6 + - + +
70A LEU* 4.3 1.1 - - + -
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Residues in contact with ALA 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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42A LYS 3.0 14.9 + - - +
43A ARG* 3.8 4.5 - - - +
45A ALA* 1.3 77.3 - - - +
47A GLN* 1.3 58.2 + - - +
50A PRO* 3.3 18.5 - - - +
67A GLN* 3.4 12.1 + - - +
70A LEU* 3.8 17.4 - - + +
78A ILE* 4.6 4.3 - - + +
81A GLN* 3.6 25.4 - - + +
82A ALA* 3.9 16.4 - - + +
85A GLU* 3.9 6.4 - - - +
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Residues in contact with GLN 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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43A ARG* 2.9 34.2 + - - +
44A LEU* 3.0 22.1 + - - +
46A ALA* 1.3 77.1 - - - +
48A PHE* 1.3 77.9 + - + +
49A ILE 3.5 0.7 - - - -
50A PRO* 3.1 17.6 - - - +
51A LYS* 3.5 13.0 + - - +
81A GLN* 3.6 31.0 + - - +
85A GLU* 4.9 3.9 - - + +
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Residues in contact with PHE 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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7A LEU* 4.0 15.5 - - + -
8A TYR* 4.2 13.2 - + - -
11A TYR* 3.4 57.0 - + + -
28A TYR* 4.1 2.3 - - - -
31A ILE* 3.7 27.8 - - + +
44A LEU* 2.9 56.4 + - + +
45A ALA* 4.6 0.4 - - - -
47A GLN* 1.3 96.3 - - + +
49A ILE* 1.3 67.7 + - - +
51A LYS* 3.3 10.8 + - + -
52A PHE* 3.4 19.3 - - - -
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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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28A TYR* 2.7 38.0 + - - +
31A ILE* 3.6 17.5 - - + -
32A LEU* 3.5 25.8 - - + -
35A VAL* 3.8 29.4 - - + -
45A ALA* 2.9 24.3 + - + +
48A PHE* 1.3 77.3 - - - +
50A PRO* 1.3 69.6 - - + +
53A PHE* 3.0 9.9 + - - +
63A ALA* 4.0 8.7 - - + +
66A ALA* 4.0 6.3 - - + -
67A GLN* 3.8 9.2 - - - +
70A LEU* 4.4 2.0 - - + -
89A PHE* 3.9 18.8 - - + -
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Residues in contact with PRO 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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46A ALA 3.3 24.0 - - - +
47A GLN 3.1 17.0 - - - +
49A ILE* 1.3 95.9 - - + +
51A LYS* 1.3 61.1 + - - +
52A PHE 3.3 0.5 + - - -
53A PHE* 3.4 14.0 + - + +
54A LYS 4.7 1.2 + - - -
67A GLN* 3.6 9.4 - - - +
85A GLU* 3.5 27.1 - - + +
88A GLN* 3.5 26.2 - - + +
89A PHE* 3.6 26.2 - - + -
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Residues in contact with LYS 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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11A TYR* 3.2 43.4 + - + +
15A ALA* 5.5 3.6 - - - -
47A GLN 3.6 14.1 - - - +
48A PHE* 3.3 7.3 + - + +
49A ILE 3.2 1.2 - - - -
50A PRO* 1.3 83.7 - - - +
52A PHE* 1.3 80.9 + - + +
54A LYS* 4.9 8.8 - - - +
55A HIS* 4.8 5.0 + - - -
88A GLN* 4.5 11.3 - - - +
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Residues in contact with PHE 52 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A TYR* 3.6 39.7 - + - -
14A LEU* 3.6 51.1 - - + -
15A ALA* 4.0 7.9 - - + -
21A VAL* 4.7 1.1 - - + -
28A TYR* 3.9 18.2 - + + -
31A ILE* 4.4 4.7 - - + -
48A PHE* 3.4 21.3 + - + -
49A ILE 4.0 0.2 - - - -
51A LYS* 1.3 106.8 - - + +
53A PHE* 1.3 67.4 + - - +
54A LYS 3.2 3.4 - - - -
55A HIS* 2.9 36.0 + + + -
56A PHE* 3.5 14.8 - - + -
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Residues in contact with PHE 53 (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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28A TYR* 3.3 11.3 - + - -
49A ILE 3.0 15.9 + - - +
50A PRO* 3.4 15.8 + - + +
52A PHE* 1.3 75.3 - - - +
54A LYS* 1.3 66.3 + - + +
55A HIS 2.9 7.3 + - - -
56A PHE* 3.1 18.7 + - - +
60A ALA* 3.7 38.1 - - + -
63A ALA* 3.6 12.3 - - + -
64A ILE* 4.0 2.0 - - + -
88A GLN 3.8 15.5 - - - +
89A PHE* 3.4 38.4 - + + -
91A THR* 3.7 22.0 - - - -
94A ASN* 3.9 22.7 - - - -
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Residues in contact with LYS 54 (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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50A PRO 4.7 1.2 + - - -
51A LYS 4.9 9.4 - - - +
52A PHE 3.0 1.0 + - - +
53A PHE* 1.3 87.2 - - + +
55A HIS* 1.3 88.3 + - + +
56A PHE 3.4 0.4 - - - -
57A PRO* 5.0 3.5 - - - +
88A GLN 6.0 0.2 - - - +
91A THR* 5.9 3.8 - - + +
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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