Contacts of the helix formed by residues 28 - 45 (chain A) in PDB entry 1HOV
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 ASP 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A LEU* 1.3 81.7 - - - +
29A PRO* 1.3 72.7 - - - +
30A GLU* 3.2 25.2 - - - +
31A THR* 2.6 26.2 + - - +
32A VAL 2.7 29.8 + - - -
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Residues in contact with PRO 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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23A TYR* 3.1 40.9 - - + -
24A THR 4.8 4.7 - - - +
27A LEU 3.4 4.0 - - - +
28A ASP* 1.3 98.3 - - - +
30A GLU* 1.3 70.5 + - + +
31A THR 3.0 1.1 - - - -
32A VAL* 3.3 1.4 - - + +
33A ASP 3.1 9.5 + - - -
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Residues in contact with GLU 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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23A TYR* 5.3 0.2 - - - -
28A ASP* 3.2 25.6 - - - +
29A PRO* 1.3 84.9 - - + +
31A THR* 1.3 70.6 + - - +
33A ASP* 3.2 11.7 - - - +
34A ASP* 3.1 21.8 + - - +
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Residues in contact with THR 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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27A LEU* 3.7 11.4 - - + -
28A ASP* 2.6 37.3 + - - +
29A PRO 3.0 0.6 - - - -
30A GLU* 1.3 84.1 + - - +
32A VAL* 1.3 67.3 + - - +
33A ASP 2.9 1.3 - - - -
34A ASP* 2.7 17.1 + - + +
35A ALA* 2.7 12.1 + - - +
107A ASN* 3.2 40.8 - - + +
108A THR* 5.6 3.8 - - + +
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Residues in contact with VAL 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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23A TYR* 2.8 52.7 - - + -
24A THR* 3.8 10.3 - - + +
27A LEU* 3.2 31.8 - - + +
28A ASP 2.7 9.9 + - - +
29A PRO 3.3 2.5 - - - +
31A THR* 1.3 73.2 - - - +
33A ASP* 1.3 61.8 + - - +
35A ALA* 3.8 2.9 - - - +
36A PHE* 3.1 38.1 + - + -
114A LEU* 3.4 33.7 - - + -
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Residues in contact with ASP 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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20A ILE* 5.2 1.0 - - - +
23A TYR* 2.6 33.0 + - + -
29A PRO 3.1 9.4 + - - +
30A GLU* 3.2 17.9 - - - +
32A VAL* 1.3 83.9 - - - +
34A ASP* 1.3 59.9 + - - +
36A PHE* 3.6 5.3 + - - +
37A ALA* 3.2 21.7 + - - +
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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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30A GLU 3.1 9.7 + - - +
31A THR* 2.7 18.7 + - + +
33A ASP* 1.3 72.3 - - - +
35A ALA* 1.3 66.4 + - - +
36A PHE 2.9 2.4 + - - -
37A ALA* 2.9 10.1 + - - +
38A ARG* 2.7 62.3 + - - +
107A ASN* 6.3 1.8 - - - -
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Residues in contact with ALA 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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27A LEU* 4.8 2.0 - - + -
31A THR* 2.7 18.4 + - - +
32A VAL* 3.8 4.3 - - - +
34A ASP* 1.3 72.8 - - - +
36A PHE* 1.3 58.9 + - - +
38A ARG* 4.6 3.8 - - - +
39A ALA* 3.2 26.3 + - - +
107A ASN* 4.8 13.1 - - + +
114A LEU* 3.4 34.3 - - + +
115A PHE* 3.5 25.1 - - + +
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Residues in contact with PHE 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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18A TYR* 5.3 12.8 - + + +
20A ILE* 3.8 41.1 - - + -
32A VAL* 3.1 32.0 + - + +
33A ASP* 3.8 6.1 - - - +
34A ASP 2.9 0.4 - - - -
35A ALA* 1.3 76.1 - - - +
37A ALA* 1.3 54.3 + - - +
39A ALA* 3.3 2.7 + - - +
40A PHE* 2.7 35.4 + - - +
63A ILE* 4.0 27.1 - - + -
99A PHE* 4.1 9.0 - + - -
114A LEU* 3.7 20.4 - - + -
118A ALA* 3.4 25.6 - - + -
122A PHE* 3.4 31.1 - + + -
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Residues in contact with ALA 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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18A TYR* 5.3 5.8 + - - +
33A ASP 3.2 11.9 + - - +
34A ASP* 2.9 14.9 + - - +
36A PHE* 1.3 79.2 - - - +
38A ARG* 1.3 69.0 + - - +
40A PHE* 2.8 27.8 + - + +
41A GLN* 2.9 10.4 + - - +
53A ARG* 5.7 6.7 - - - +
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Residues in contact with ARG 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 ASP* 2.7 47.8 + - - +
35A ALA* 4.2 5.6 - - - +
37A ALA* 1.3 70.3 - - - +
39A ALA* 1.3 66.8 + - - +
41A GLN* 2.6 21.3 + - + +
42A VAL* 2.6 12.8 + - - +
107A ASN* 5.6 5.4 - - - -
115A PHE* 4.6 13.2 - - + -
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Residues in contact with ALA 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 ALA 3.2 19.3 + - - +
36A PHE* 3.4 7.4 - - - +
38A ARG* 1.3 76.9 - - - +
40A PHE* 1.3 67.6 + - - +
42A VAL* 2.6 36.5 + - + +
43A TRP* 3.0 3.8 + - - +
115A PHE* 3.6 22.9 - - + +
118A ALA* 4.5 4.3 - - + -
119A ALA 4.6 0.9 - - - +
122A PHE* 4.2 22.6 - - + -
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Residues in contact with PHE 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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18A TYR* 5.2 9.0 - - + +
36A PHE 2.7 17.5 + - - +
37A ALA* 3.0 26.0 - - + +
39A ALA* 1.3 71.9 - - - +
41A GLN* 1.3 78.1 + - + +
43A TRP* 3.3 2.3 + - - +
44A SER* 2.7 56.0 + - - -
49A LEU 4.3 2.9 - - - -
50A ARG* 5.8 0.2 - - - -
51A PHE* 3.1 51.5 - + + -
53A ARG* 5.5 10.1 - - - -
122A PHE* 3.8 17.6 - - + -
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Residues in contact with GLN 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 ALA 2.9 8.4 + - - +
38A ARG* 2.6 18.1 + - + +
40A PHE* 1.3 92.7 - - + +
42A VAL* 1.3 59.1 + - - +
44A SER* 3.9 9.5 - - - -
45A ASP* 2.8 44.8 + - + +
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Residues in contact with VAL 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 ARG 2.6 7.6 + - - +
39A ALA* 2.6 32.4 + - + +
41A GLN* 1.3 73.5 - - - +
43A TRP* 1.3 78.9 + - + +
45A ASP* 4.2 9.0 + - - +
46A VAL* 4.5 4.0 - - - +
115A PHE* 3.3 33.7 - - + -
119A ALA* 4.4 6.1 - - + -
148A PHE* 3.0 42.4 - - + -
150A LEU* 4.2 17.7 - - + +
800A I52 5.1 1.6 - - + -
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Residues in contact with TRP 43 (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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39A ALA 3.0 3.4 + - - +
40A PHE 4.1 4.0 - - - +
42A VAL* 1.3 102.0 - - + +
44A SER* 1.3 62.3 + - - +
45A ASP 3.1 1.8 - - - -
46A VAL* 2.6 34.2 - - + +
47A THR* 3.5 8.2 - - - +
49A LEU* 6.5 0.2 - - - -
51A PHE* 5.4 7.9 - - + -
119A ALA* 3.5 14.8 + - - +
122A PHE* 3.9 30.1 - - + +
123A GLY* 3.2 33.9 - - - -
126A MET* 4.9 5.8 - - + -
128A LEU* 5.2 6.1 - - + -
137A LEU* 3.6 22.2 - - + +
138A MET* 4.2 4.9 - - + -
150A LEU* 6.2 1.9 - - + +
154A ASP* 3.2 37.0 - - + -
158A ILE* 4.1 38.6 - - + -
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Residues in contact with SER 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 PHE* 2.7 40.1 + - - -
41A GLN* 3.9 9.6 - - - -
43A TRP* 1.3 73.7 - - - +
45A ASP* 1.3 59.7 + - - +
46A VAL 3.0 5.8 - - - -
47A THR* 2.3 31.3 + - - +
49A LEU* 3.0 29.0 + - - +
51A PHE* 3.6 9.5 - - - -
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Residues in contact with ASP 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 GLN* 2.8 28.6 + - + +
42A VAL* 4.2 7.6 - - - +
43A TRP 3.1 0.8 - - - -
44A SER* 1.3 78.6 - - - +
46A VAL* 1.3 56.0 + - - +
47A THR 3.3 1.5 + - - -
150A LEU* 5.4 10.9 - - + +
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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