Contacts of the helix formed by residues 38 - 51 (chain A) in PDB entry 2VL7
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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11A TRP* 3.8 1.7 - - - -
12A GLN* 2.8 25.1 + - - -
36A GLY 3.2 4.1 - - - -
37A LEU* 1.3 78.6 - - - +
39A LYS* 1.3 66.2 + - - +
40A THR 3.3 3.1 - - - -
41A VAL* 3.2 18.8 + - - +
42A PHE 3.3 0.2 + - - -
1541A PO4 3.0 16.9 + - - -
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Residues in contact with LYS 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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11A TRP* 4.3 8.1 - - - -
31A LEU* 4.6 8.3 - - + -
33A ALA* 3.2 41.7 - - + +
34A LYS 4.7 1.1 - - - -
35A PRO* 4.8 5.5 - - - +
37A LEU 3.7 0.6 - - - -
38A GLY* 1.3 75.7 - - - +
40A THR* 1.3 64.3 + - - +
42A PHE* 3.1 5.9 + - - +
43A VAL* 3.0 25.1 + - - +
182A ASP* 4.2 6.2 + - - -
183A GLU* 3.3 22.8 + - - -
325A MET* 3.9 21.1 - - + -
326A SER* 3.6 22.9 - - - +
327A GLY* 3.2 19.0 - - - +
1541A PO4 3.0 35.8 + - - +
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Residues in contact with THR 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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38A GLY 3.3 0.6 - - - -
39A LYS* 1.3 80.6 - - - +
41A VAL* 1.3 57.4 + - - +
43A VAL* 3.6 3.3 + - - +
44A GLU* 3.0 55.0 + - + +
56A ILE* 4.7 8.2 - - + +
67A ILE* 4.6 21.5 - - + +
70A ASN* 3.7 26.7 + - + +
182A ASP* 4.4 7.1 + - - -
325A MET* 4.0 17.5 - - - +
1541A PO4 3.9 12.7 + - - -
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Residues in contact with VAL 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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9A ARG* 6.5 0.4 - - - -
12A GLN* 3.9 13.2 - - - +
38A GLY* 3.2 16.6 + - - +
40A THR* 1.3 75.1 - - - +
42A PHE* 1.3 60.5 + - - +
44A GLU* 3.3 13.1 - - - +
45A VAL* 2.9 34.0 + - + +
70A ASN* 5.0 13.7 - - + +
73A LEU* 5.9 4.0 - - + -
74A LEU* 4.5 22.2 - - + -
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Residues in contact with PHE 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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11A TRP* 3.5 31.0 - + + -
12A GLN* 3.0 50.2 + - - +
15A LYS* 4.0 13.0 - - + -
16A LEU* 3.9 21.0 - - + +
19A ALA* 3.8 23.6 - - + -
29A LEU* 4.9 1.8 - - + -
31A LEU* 3.9 28.5 - - + -
38A GLY 3.3 1.6 + - - -
39A LYS 3.1 8.2 + - - +
41A VAL* 1.3 75.1 - - - +
43A VAL* 1.3 60.9 + - + +
44A GLU 3.1 1.8 - - - -
45A VAL* 3.2 5.5 + - + +
46A LEU* 2.7 52.9 + - + +
341A ILE* 5.5 0.4 - - + -
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Residues in contact with VAL 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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31A LEU* 4.4 2.5 - - + -
39A LYS 3.0 11.3 + - - +
40A THR* 4.2 3.4 - - - +
42A PHE* 1.3 87.6 - - + +
44A GLU* 1.3 57.8 + - - +
46A LEU* 3.3 11.8 - - + +
47A GLY* 3.1 21.0 + - - -
54A VAL* 4.3 9.1 - - + +
56A ILE* 5.2 5.4 - - + -
178A LEU* 3.7 11.6 - - + +
180A VAL* 3.0 33.2 - - + -
323A VAL* 4.2 17.0 - - + -
325A MET* 3.5 31.4 - - + -
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Residues in contact with GLU 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 THR* 3.0 42.3 + - + +
41A VAL* 3.3 11.8 - - - +
42A PHE 3.1 0.2 - - - -
43A VAL* 1.3 76.1 - - - +
45A VAL* 1.3 64.2 + - - +
47A GLY* 3.4 6.9 + - - -
48A MET* 3.3 24.6 + - - +
54A VAL* 4.7 8.9 - - + +
56A ILE* 5.2 5.6 - - + +
67A ILE* 4.0 5.0 - - - +
70A ASN* 3.8 7.7 - - - +
71A ALA* 3.4 29.6 + - - +
74A LEU* 3.0 32.4 - - + +
76A LEU* 4.4 11.9 - - + +
147A VAL* 4.7 10.1 - - + +
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Residues in contact with VAL 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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12A GLN* 4.8 6.3 - - - +
16A LEU* 3.9 28.0 - - + -
41A VAL* 2.9 27.1 + - + +
42A PHE* 3.6 7.6 - - + +
44A GLU* 1.3 73.9 - - - +
46A LEU* 1.3 64.3 + - - +
48A MET* 3.1 22.6 + - + +
49A GLN* 3.1 14.1 + - + +
74A LEU* 5.3 6.1 - - + -
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Residues in contact with LEU 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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16A LEU* 3.9 16.1 - - + +
19A ALA* 4.0 12.8 - - + -
20A ILE* 3.2 33.4 - - + +
23A LEU* 3.9 24.2 - - + -
29A LEU* 4.2 7.0 - - + -
42A PHE* 2.7 37.6 + - + +
43A VAL* 3.3 16.6 - - + +
45A VAL* 1.3 73.1 - - - +
47A GLY* 1.3 61.8 + - - +
49A GLN* 3.3 4.9 + - - +
50A LEU* 3.1 25.6 + - + +
178A LEU* 4.1 6.7 - - + -
323A VAL* 4.1 17.3 - - + -
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Residues in contact with GLY 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 VAL 3.1 10.9 + - - -
44A GLU 3.4 0.8 + - - -
45A VAL 3.3 0.6 - - - -
46A LEU* 1.3 75.7 - - - +
48A MET* 1.3 62.0 + - - +
50A LEU* 3.3 3.2 + - - -
51A LYS* 3.2 15.4 + - - -
52A LYS 3.0 23.5 + - - +
54A VAL* 3.9 18.6 - - - -
178A LEU* 3.7 19.3 - - - +
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Residues in contact with MET 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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44A GLU 3.3 21.8 - - - +
45A VAL* 3.1 13.3 + - + +
47A GLY* 1.3 76.6 - - - +
49A GLN* 1.3 61.2 + - - +
51A LYS* 3.7 12.2 + - - +
52A LYS 4.9 0.7 - - - -
54A VAL* 6.0 1.6 - - + -
74A LEU* 4.8 16.2 - - + +
76A LEU* 3.9 38.6 - - + -
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Residues in contact with GLN 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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16A LEU* 4.8 16.9 - - + +
20A ILE* 4.0 30.2 - - + +
24A LYS* 6.1 0.7 - - - -
45A VAL* 3.1 17.4 + - + +
46A LEU* 3.7 4.9 - - - +
47A GLY 3.3 0.4 - - - -
48A MET* 1.3 78.6 - - - +
50A LEU* 1.3 60.2 + - - +
51A LYS* 3.4 5.3 + - - +
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Residues in contact with LEU 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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20A ILE* 3.7 26.9 - - + +
23A LEU* 3.6 32.1 - - + -
24A LYS* 4.3 23.1 - - + -
46A LEU* 3.1 16.2 + - + +
47A GLY* 3.3 4.9 + - - +
49A GLN* 1.3 76.7 - - - +
51A LYS* 1.3 69.7 + - - +
52A LYS* 3.5 9.5 + - + +
178A LEU* 4.5 7.6 - - + -
321A PHE* 3.6 50.9 - - + -
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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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47A GLY 3.2 4.9 + - - -
48A MET* 3.7 10.9 + - - +
49A GLN 3.4 5.9 - - - +
50A LEU* 1.3 81.8 - - - +
52A LYS* 1.3 65.9 - - - +
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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