Contacts of the helix formed by residues 30 - 45 (chain A) in PDB entry 1P4V
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 LYS 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A VAL* 3.6 6.1 - - - +
29A GLY* 1.3 74.1 - - - -
31A ALA* 1.3 65.6 + - - +
32A LEU* 4.0 18.7 - - + +
33A ASP* 3.1 26.9 + - - +
34A ALA* 3.0 19.0 + - - +
72A GLU* 5.6 8.5 - - - -
93A ARG* 4.1 18.0 - - - +
159A ASP* 3.7 6.1 - - - +
161A GLN* 4.4 14.8 - - - +
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Residues in contact with ALA 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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25A LEU* 4.1 8.3 - - - -
30A LYS* 1.3 72.7 - - - +
32A LEU* 1.3 57.2 + - - +
34A ALA* 3.2 1.6 + - - +
35A VAL* 2.9 34.0 + - - +
157A ALA* 3.8 14.6 - - + +
159A ASP* 2.8 30.8 + - + +
163A ASN* 3.5 18.2 - - + +
164A LEU 4.1 0.7 - - - -
165A SER* 3.5 20.9 - - - +
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Residues in contact with LEU 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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30A LYS* 3.1 17.6 - - + +
31A ALA* 1.3 78.7 - - - +
33A ASP* 1.3 62.3 + - - +
35A VAL* 3.3 4.7 - - + +
36A GLU* 3.2 23.0 + - - +
69A ILE* 3.5 36.6 - - + -
70A MET 4.6 1.8 - - - +
71A ASP* 4.0 30.1 - - + +
72A GLU* 4.8 4.4 + - - +
93A ARG* 3.4 35.2 - - - +
96A MET* 4.0 18.2 - - + -
97A GLU* 4.2 2.7 - - - +
165A SER* 3.4 14.2 + - - +
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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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24A VAL* 4.1 16.6 - - + +
30A LYS* 3.1 38.8 + - - +
32A LEU* 1.3 76.3 - - - +
34A ALA* 1.3 63.6 + - - +
36A GLU* 3.4 3.2 + - - +
37A LYS* 3.0 27.2 + - - +
93A ARG* 2.7 36.3 + - - +
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Residues in contact with ALA 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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21A ALA* 3.4 25.4 - - + +
24A VAL* 3.7 14.5 - - + +
25A LEU* 3.4 42.4 - - + -
30A LYS 3.0 7.6 + - - +
31A ALA 3.5 6.3 - - - +
33A ASP* 1.3 77.4 - - - +
35A VAL* 1.3 59.5 + - + +
37A LYS* 3.8 0.3 - - - +
38A GLY 2.9 23.7 + - - -
157A ALA* 5.0 0.2 - - + -
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Residues in contact with VAL 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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31A ALA 2.9 18.6 + - - +
32A LEU* 3.3 17.7 - - - +
34A ALA* 1.3 72.2 - - - +
36A GLU* 1.3 69.4 + - - +
38A GLY* 3.8 0.2 - - - -
39A VAL* 3.1 28.9 + - - +
69A ILE* 4.5 4.9 - - + -
155A MET* 3.7 29.8 - - + +
157A ALA* 3.9 16.2 - - + +
165A SER* 3.7 20.0 - - - +
166A GLY 3.8 22.9 - - - +
167A ALA* 3.9 13.9 - - + +
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Residues in contact with GLU 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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32A LEU 3.2 12.8 + - - +
33A ASP* 3.8 4.2 - - - +
35A VAL* 1.3 82.3 - - - +
37A LYS* 1.3 65.4 + - - +
39A VAL* 3.5 6.9 - - - +
40A ARG* 3.0 43.5 + - + +
69A ILE* 4.3 8.7 - - + -
89A ILE* 4.3 11.2 - - + -
90A SER* 2.7 33.9 + - - +
93A ARG* 2.8 42.6 + - - +
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Residues in contact with LYS 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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20A GLU* 3.2 42.4 - - + +
23A LYS* 2.9 38.2 - - - +
24A VAL* 3.6 17.4 - - + +
33A ASP 3.0 17.6 + - - +
34A ALA 3.8 2.9 - - - +
36A GLU* 1.3 78.9 - - - +
38A GLY* 1.3 65.4 + - - +
40A ARG* 3.4 10.1 + - - +
41A LEU* 3.4 16.8 + - - +
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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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17A ALA* 3.3 42.4 - - - +
20A GLU* 4.2 3.6 - - - -
21A ALA 4.3 1.1 - - - +
34A ALA 2.9 17.8 + - - -
35A VAL 3.8 1.6 - - - -
36A GLU 3.2 0.4 - - - -
37A LYS* 1.3 79.5 - - - +
39A VAL* 1.3 62.2 + - - +
41A LEU* 3.4 12.8 - - - +
42A VAL 4.1 0.7 + - - -
155A MET* 3.9 7.9 - - - -
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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 VAL 3.1 17.2 + - - +
36A GLU 3.5 5.8 - - - +
38A GLY* 1.3 72.8 - - - +
40A ARG* 1.3 68.6 + - - +
41A LEU 3.0 2.0 - - - -
42A VAL* 2.9 15.6 + - - +
43A GLU* 3.0 14.2 + - - +
89A ILE* 3.6 34.1 - - + -
153A ILE* 4.2 23.6 - - + -
155A MET* 3.9 24.2 - - + -
167A ALA* 4.0 15.0 - - + +
169A THR* 3.7 16.8 - - + +
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Residues in contact with ARG 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 GLU* 3.0 36.4 + - - +
37A LYS* 3.7 10.1 - - - +
38A GLY 3.3 0.2 - - - -
39A VAL* 1.3 76.8 - - - +
41A LEU* 1.3 63.1 + - - +
43A GLU* 3.2 13.8 + - - +
44A ASP* 2.9 39.9 + - - +
87A ASN* 3.3 38.4 + - - +
89A ILE* 3.6 18.4 - - + -
90A SER* 2.7 36.1 + - - -
118A PHE* 4.8 3.6 - - - -
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Residues in contact with LEU 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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16A HIS* 3.2 46.9 - - + +
17A ALA* 3.8 3.6 - - + +
20A GLU* 3.6 29.2 - - + +
37A LYS 3.4 4.1 + - - +
38A GLY 3.4 12.2 + - - +
39A VAL 3.0 0.2 - - - -
40A ARG* 1.3 80.1 - - - +
42A VAL* 1.3 63.6 + - + +
44A ASP* 3.5 7.8 + - + +
45A ASP* 3.3 21.2 + - + +
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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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13A PHE* 4.3 18.8 - - + +
17A ALA* 4.1 13.0 - - + -
38A GLY 4.2 0.7 - - - +
39A VAL 2.9 7.9 + - - +
41A LEU* 1.3 79.9 - - + +
43A GLU* 1.3 66.0 + - - +
45A ASP* 3.3 21.6 + - - +
48A GLU* 3.6 25.1 - - + +
51A VAL* 3.6 31.3 - - + +
153A ILE* 3.4 37.2 - - + -
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Residues in contact with GLU 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 3.0 14.8 + - - +
40A ARG* 3.6 10.3 - - - +
42A VAL* 1.3 77.7 - - - +
44A ASP* 1.3 62.1 + - - +
45A ASP 3.4 0.2 + - - -
51A VAL* 3.6 25.6 - - + +
52A GLY* 4.6 1.1 - - - +
53A TYR* 3.0 29.6 + - - +
86A LYS* 3.4 14.6 - - - +
87A ASN* 3.1 27.2 - - - +
88A PRO* 3.2 12.2 - - + +
89A ILE* 3.0 38.5 + - - +
169A THR* 2.7 25.5 + - + +
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Residues in contact with ASP 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 ARG* 2.9 32.1 + - - +
41A LEU* 3.8 8.7 - - + +
43A GLU* 1.3 78.6 - - - +
45A ASP* 1.3 57.4 + - - +
46A PRO* 3.1 14.4 - - - +
53A TYR* 3.5 10.6 - - - -
86A LYS* 3.6 27.0 + - - +
87A ASN* 3.0 23.3 + - - +
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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 LEU* 3.3 13.6 + - + +
42A VAL* 3.3 9.5 + - - +
44A ASP* 1.3 78.0 - - - +
46A PRO* 1.3 62.0 - - - +
47A THR* 2.4 49.1 + - - +
48A GLU* 3.0 32.6 + - + +
53A TYR 3.2 10.8 - - - +
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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