Contacts of the helix formed by residues 37 - 50 (chain A) in PDB entry 1PJR
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 37 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ALA* 3.6 29.2 - - + +
32A GLY 6.0 0.2 - - - +
35A SER* 3.7 2.4 + - - +
36A GLY* 1.3 74.5 - - - +
38A THR* 1.3 69.7 + - - +
40A VAL* 3.4 8.6 + - - +
41A LEU* 3.0 31.1 + - + +
223A ASP* 3.0 34.5 + - - +
224A GLU* 3.2 31.3 + - - +
249A VAL* 4.0 19.9 - - + +
250A GLY* 5.8 2.9 - - - +
282A LEU* 4.7 2.5 - - - -
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Residues in contact with THR 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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36A GLY* 3.3 1.0 - - - -
37A LYS* 1.3 87.8 + - - +
39A ARG* 1.3 59.4 + - - +
41A LEU* 3.2 7.7 + - - +
42A THR* 2.8 42.5 + - + +
71A GLU* 4.1 11.1 + - + +
72A MET* 5.3 10.3 - - + -
75A ARG* 3.8 39.9 - - + +
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Residues in contact with ARG 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 HIS* 2.7 53.6 + - - -
12A LEU* 4.0 14.7 - - + +
16A GLN* 3.8 22.0 + - - +
36A GLY* 3.3 16.4 - - - +
38A THR* 1.3 79.6 - - - +
40A VAL* 1.3 55.9 + - + +
42A THR* 3.8 5.2 - - - -
43A HIS* 2.9 48.6 + - - +
75A ARG* 6.4 0.4 - - - -
286A TYR* 6.0 2.4 - - - -
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Residues in contact with VAL 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 4.9 1.8 - - + -
16A GLN* 3.6 39.5 - - + +
19A ALA* 3.7 30.7 - - + -
20A VAL* 3.7 12.0 - - + +
29A ILE* 4.1 15.5 - - + -
36A GLY 3.3 14.5 + - - +
37A LYS* 3.6 9.0 - - - +
38A THR 3.3 0.2 - - - -
39A ARG* 1.3 76.7 - - + +
41A LEU* 1.3 56.9 + - + +
44A ARG* 2.9 30.7 + - + +
249A VAL* 6.2 1.3 - - + -
282A LEU* 3.9 15.3 - - + -
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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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29A ILE* 5.7 1.3 - - + -
37A LYS* 3.0 20.0 + - + +
38A THR* 3.7 6.1 - - - +
40A VAL* 1.3 77.1 - - + +
42A THR* 1.3 64.1 + - + +
44A ARG* 3.4 5.1 + - + +
45A ILE* 3.2 30.1 + - + +
72A MET* 4.2 21.1 - - + -
221A HIS* 4.2 33.2 - - + -
222A ILE 5.6 0.4 - - - +
223A ASP* 3.6 40.2 - - + +
247A CYS* 4.8 3.8 - - - -
249A VAL* 3.6 29.8 - - + -
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Residues in contact with THR 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 THR* 2.8 29.1 + - + +
39A ARG* 3.3 7.8 + - - -
41A LEU* 1.3 70.9 - - + +
43A HIS* 1.3 72.4 + - - +
45A ILE* 3.4 5.4 + - - +
46A ALA* 3.0 23.1 + - - +
72A MET* 3.7 29.6 - - + +
75A ARG* 3.5 38.7 - - + +
76A VAL* 4.1 14.8 - - + +
79A LEU* 4.3 5.0 - - - +
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Residues in contact with HIS 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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7A GLN 5.1 0.4 - - - -
8A LEU* 2.9 48.1 + - + +
11A HIS* 4.6 18.6 - + + -
12A LEU* 4.4 5.5 - - + +
20A VAL* 3.8 21.5 - - + -
39A ARG* 2.9 45.2 + - + +
42A THR* 1.3 87.4 + - - +
44A ARG* 1.3 51.9 + - - +
46A ALA* 3.6 6.3 - - - +
47A TYR* 2.8 34.8 + - - +
79A LEU* 4.3 19.8 - - + +
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Residues in contact with ARG 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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19A ALA 3.6 10.9 + - - -
20A VAL* 3.7 29.3 - - - +
22A THR 2.6 30.7 + - - -
23A THR* 3.1 26.6 + - + +
25A GLY 4.7 5.3 + - - -
27A LEU* 4.1 9.6 - - - +
29A ILE* 5.3 2.7 - - - -
40A VAL* 2.9 20.3 + - + +
41A LEU* 3.4 6.9 + - - +
43A HIS* 1.3 70.5 - - - +
45A ILE* 1.3 67.1 + - - +
47A TYR* 3.7 1.8 - - - +
48A LEU* 3.0 34.5 + - + +
219A TYR* 5.2 3.6 - - - +
220A ILE 4.5 2.2 + - - -
221A HIS* 3.3 29.1 + - + +
245A ASN 5.5 2.8 + - - -
246A ILE 5.7 0.4 - - - -
247A CYS* 3.2 39.1 - - - +
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Residues in contact with ILE 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* 3.2 17.9 + - + +
42A THR 3.7 6.5 - - - +
44A ARG* 1.3 78.2 - - - +
46A ALA* 1.3 63.4 + - - +
48A LEU* 3.2 17.0 + - - +
49A MET* 3.4 34.4 + - + +
59A ILE* 4.3 8.6 - - + +
61A ALA* 3.9 28.5 - - + -
72A MET* 4.7 9.6 - - - -
76A VAL* 4.2 24.5 - - + -
87A VAL* 4.4 16.6 - - + -
89A ILE* 5.1 2.2 - - + -
221A HIS* 3.7 25.8 - - + +
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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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8A LEU* 3.8 16.8 - - + -
42A THR 3.0 17.1 + - - +
43A HIS* 3.7 4.0 - - - +
45A ILE* 1.3 77.5 - - - +
47A TYR* 1.3 61.8 + - - +
49A MET* 3.3 2.4 + - - +
50A ALA* 2.9 26.9 + - - +
76A VAL* 5.2 1.5 - - + +
79A LEU* 3.8 23.1 - - + -
80A LEU* 3.8 27.3 - - + +
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Residues in contact with TYR 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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1A MET* 4.9 4.2 - - - +
5A SER* 4.6 11.9 - - - -
8A LEU* 3.9 14.8 - - + +
9A LEU* 4.5 22.9 - - + -
20A VAL* 3.3 36.1 - - + -
21A ARG* 4.0 31.1 + - + +
23A THR* 3.8 22.9 - - + -
43A HIS 2.8 21.2 + - - +
44A ARG 3.7 3.8 - - - +
45A ILE 3.3 0.2 - - - -
46A ALA* 1.3 72.5 - - - +
48A LEU* 1.3 63.3 + - - +
51A GLU* 2.9 61.6 + - + +
52A LYS* 3.2 15.3 + - + +
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Residues in contact with LEU 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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23A THR* 3.6 32.8 - - + -
44A ARG* 3.0 22.8 + - + +
45A ILE* 3.5 9.2 - - - +
47A TYR* 1.3 77.1 - - - +
49A MET* 1.3 58.1 + - - +
52A LYS* 3.1 13.0 - - + +
53A HIS 2.8 23.7 + - - -
54A VAL* 3.0 23.7 + - + -
59A ILE* 4.5 12.6 - - + -
219A TYR* 3.9 44.6 - - + -
221A HIS* 3.9 20.9 - - + +
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Residues in contact with MET 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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45A ILE* 3.4 24.0 + - + +
46A ALA 3.3 5.0 + - - +
47A TYR 3.3 0.2 - - - -
48A LEU* 1.3 73.9 - - - +
50A ALA* 1.4 66.5 + - - +
53A HIS* 3.0 26.7 + - - -
54A VAL 3.6 21.5 - - - +
56A PRO* 3.8 27.6 - - + -
59A ILE* 3.7 13.9 - - + -
76A VAL* 4.5 4.7 - - + -
80A LEU* 3.5 31.9 - - + -
83A ALA* 4.2 12.3 - - - +
84A ALA* 5.0 0.7 - - - -
87A VAL* 3.7 23.6 - - + -
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Residues in contact with ALA 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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2A ASN* 3.8 11.4 + - - +
4A LEU* 3.9 35.2 - - + -
5A SER* 3.9 9.0 - - - +
8A LEU* 4.4 9.4 - - + -
46A ALA 2.9 18.8 + - - +
49A MET* 1.4 70.9 - - - +
51A GLU* 1.3 58.9 + - - +
53A HIS* 3.2 22.6 + - - -
80A LEU* 5.0 6.3 - - + +
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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