Contacts of the helix formed by residues 27 - 41 (chain A) in PDB entry 1VEP
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 ASN 27 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A ILE* 4.7 2.7 - - - -
23A PRO* 5.6 0.7 - - - -
26A THR* 1.3 87.2 + - - +
28A TRP* 1.3 65.7 + - - +
29A GLU* 2.9 43.7 + - - +
30A THR* 2.8 21.6 + - - +
31A PHE* 3.0 21.6 + - - +
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Residues in contact with TRP 28 (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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22A ILE* 3.7 29.6 - - + -
23A PRO* 3.6 29.9 - - + +
27A ASN* 1.3 75.6 - - - +
29A GLU* 1.3 56.6 + - - +
31A PHE* 3.2 24.7 + + - +
32A GLU* 2.8 37.0 + - - +
67A TYR* 3.8 20.9 - + - -
70A ARG* 3.3 59.0 - - + +
71A PHE* 3.9 24.0 - + - -
74A SER* 3.4 17.5 - - - +
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Residues in contact with GLU 29 (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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27A ASN* 2.9 16.9 + - - +
28A TRP* 1.3 76.1 - - - +
30A THR* 1.3 62.4 + - - +
32A GLU* 3.2 14.0 + - - +
33A ASN* 3.1 35.4 + - - +
36A ARG* 5.0 1.2 + - - +
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Residues in contact with THR 30 (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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26A THR* 3.3 24.2 + - + +
27A ASN* 2.8 22.1 + - - +
29A GLU* 1.3 78.7 + - - +
31A PHE* 1.3 57.7 + - - +
33A ASN* 3.1 12.2 + - + +
34A ASP* 2.8 42.5 + - - +
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Residues in contact with PHE 31 (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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22A ILE* 3.5 38.6 - - + -
26A THR* 4.3 4.0 - - + +
27A ASN 3.0 14.5 + - - +
28A TRP* 3.3 31.9 - + - +
29A GLU 3.2 0.2 - - - -
30A THR* 1.3 76.4 - - - +
32A GLU* 1.3 61.8 - - - +
34A ASP* 3.0 5.2 + - - +
35A LEU* 2.9 52.3 + - + +
46A ILE* 4.1 15.3 - - + -
71A PHE* 3.7 29.4 - + - -
74A SER* 3.8 19.5 - - - -
75A VAL* 4.5 4.5 - - + -
398A TYR* 3.5 26.0 - + - -
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Residues in contact with GLU 32 (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 TRP* 2.8 23.4 + - - +
29A GLU* 3.6 10.4 - - - +
31A PHE* 1.3 74.5 - - - +
33A ASN* 1.3 59.5 + - - +
35A LEU* 3.3 6.2 + - - +
36A ARG* 3.0 48.8 + - - +
70A ARG* 4.7 3.5 + - - -
74A SER* 2.8 37.0 + - - +
77A ASN* 2.8 37.7 + - - +
78A ALA* 3.7 12.6 - - + +
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Residues in contact with ASN 33 (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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29A GLU* 3.1 34.6 + - - +
30A THR* 3.1 11.7 + - + +
32A GLU* 1.3 74.4 - - - +
34A ASP* 1.3 69.5 + - - +
36A ARG* 3.3 31.5 + - - +
37A TRP* 3.1 22.2 + - - +
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Residues in contact with ASP 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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26A THR* 5.0 3.8 - - - +
30A THR* 2.8 31.6 + - - +
31A PHE* 3.0 5.7 + - - +
33A ASN* 1.3 77.5 - - - +
35A LEU* 1.3 59.0 + - - +
37A TRP* 3.2 7.4 + - - +
38A ALA* 2.9 28.6 + - - +
398A TYR* 2.7 36.5 + - + +
402A MET* 3.6 32.3 - - - +
403A TYR* 4.7 8.6 + - - -
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Residues in contact with LEU 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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15A LEU* 5.9 2.0 - - + -
31A PHE* 2.9 47.7 + - + +
32A GLU* 3.5 8.1 - - - +
34A ASP* 1.3 76.3 - - - +
36A ARG* 1.3 59.4 + - - +
38A ALA* 3.1 7.9 + - + +
39A LYS* 2.9 30.5 + - - +
46A ILE* 4.0 33.4 - - + -
74A SER 4.3 0.9 - - - +
75A VAL* 3.9 29.2 - - + -
78A ALA* 3.7 14.6 - - + -
80A MET* 3.9 23.1 - - + +
398A TYR* 4.8 5.6 - - + -
402A MET* 5.9 0.2 - - + -
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Residues in contact with ARG 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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29A GLU* 5.0 1.8 + - - +
32A GLU* 3.0 38.3 + - - +
33A ASN* 3.3 32.0 + - - +
34A ASP 3.3 0.2 - - - -
35A LEU* 1.3 76.9 - - - +
37A TRP* 1.3 61.4 + - - +
39A LYS* 3.6 9.3 + - + +
40A GLN* 3.2 24.1 + - - +
77A ASN* 3.2 26.7 + - - +
78A ALA* 3.6 22.2 - - - +
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Residues in contact with TRP 37 (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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33A ASN 3.1 14.4 + - - +
34A ASP* 3.3 9.9 - - - +
35A LEU 3.1 0.2 - - - -
36A ARG* 1.3 76.0 - - - +
38A ALA* 1.3 63.0 + - - +
40A GLN* 3.0 39.4 + - + +
41A ASN* 2.8 49.7 - - - +
401A VAL 5.0 0.2 + - - -
402A MET* 3.7 30.5 + - - -
405A ASN* 4.6 24.4 - - + +
408A MET* 3.7 27.8 - - + +
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Residues in contact with ALA 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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15A LEU* 4.4 5.8 - - + -
34A ASP 2.9 13.4 + - - +
35A LEU* 3.5 12.6 - - + +
37A TRP* 1.3 77.4 - - - +
39A LYS* 1.3 58.0 + - - +
41A ASN* 2.9 15.8 + - - -
42A GLY 3.4 0.3 + - - -
43A PHE* 3.1 46.6 + - + -
80A MET* 4.7 5.8 - - + -
402A MET* 4.1 15.7 - - + -
408A MET* 4.3 7.9 - - - -
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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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35A LEU 2.9 16.8 + - - +
36A ARG* 3.7 8.1 - - + +
38A ALA* 1.3 77.3 - - - +
40A GLN* 1.3 61.9 + - - +
42A GLY* 3.3 12.3 + - - -
43A PHE 3.5 15.4 + - - +
44A TYR* 6.1 0.2 - - - -
78A ALA 4.6 6.0 + - - +
79A GLY* 2.5 38.9 + - - +
80A MET* 3.7 20.6 - - + -
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Residues in contact with GLN 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 ARG 3.2 13.0 + - - +
37A TRP* 3.0 39.4 + - + +
39A LYS* 1.3 79.9 - - - +
41A ASN* 1.3 60.5 + - - +
42A GLY 3.4 1.8 + - - -
412A LYS* 3.6 17.7 - - - -
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Residues in contact with ASN 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 TRP* 2.8 49.9 - - - +
38A ALA 2.9 9.6 + - - +
40A GLN* 1.3 80.1 - - - +
42A GLY* 1.3 57.1 + - - +
43A PHE* 3.6 2.0 + - + -
408A MET* 3.3 48.9 + - - +
409A GLY* 4.6 2.8 - - - -
411A PHE* 4.2 5.4 - - + -
412A LYS* 3.4 48.8 - - + +
416A GLY* 3.8 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