Contacts of the helix formed by residues 37 - 49 (chain A) in PDB entry 2L1R
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 SER 37 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A ALA* 4.5 4.3 - - - -
32A GLU* 3.0 37.6 + - - -
35A CYS 3.0 2.4 + - - -
36A ILE* 1.3 77.1 - - - +
38A THR* 1.3 72.7 + - - +
39A LYS* 3.3 7.2 - - - -
40A GLU* 3.3 8.9 + - - +
41A LEU* 3.0 21.8 + - - +
61A ILE* 3.7 9.0 - - - -
70A GLY 4.5 5.2 + - - -
71A THR* 3.3 7.2 + - - +
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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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37A SER* 1.3 77.2 + - - +
39A LYS* 1.3 63.1 + - - +
41A LEU* 3.9 1.3 - - - +
42A GLY* 2.9 27.7 + - - -
54A PRO* 3.4 27.1 - - + +
57A LEU* 3.8 18.6 - - - +
58A GLN* 3.4 41.3 - - + +
61A ILE* 4.1 8.4 - - + +
70A GLY 5.9 0.2 - - - +
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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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37A SER* 3.3 4.4 - - - -
38A THR* 1.3 84.4 + - - +
40A GLU* 1.3 66.7 + - + +
42A GLY* 3.4 1.7 + - - -
43A LYS* 3.1 41.0 + - - +
54A PRO* 6.4 0.2 - - - -
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Residues in contact with GLU 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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27A PHE* 3.2 25.4 - - - +
28A VAL* 3.2 2.4 - - - -
29A LEU* 3.0 32.6 + - - +
30A GLY 3.6 9.7 + - - +
31A ALA* 3.2 31.9 - - + -
36A ILE* 4.2 4.7 - - + -
37A SER* 3.3 17.0 + - - +
39A LYS* 1.3 81.4 - - + +
41A LEU* 1.3 64.8 + - - +
43A LYS* 2.8 53.5 + - - +
44A VAL* 3.6 8.7 + - - +
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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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27A PHE* 4.4 9.0 - - - -
36A ILE* 4.4 6.2 - - + +
37A SER 3.0 16.3 + - - +
38A THR* 3.9 2.5 - - - +
40A GLU* 1.3 77.4 - - - +
42A GLY* 1.3 65.1 + - - +
43A LYS 3.2 0.3 + - - -
44A VAL* 3.2 4.0 + - - +
45A MET* 3.0 34.1 + - + +
57A LEU* 3.4 39.5 - - + +
60A MET* 3.7 4.5 - - + -
61A ILE* 6.2 3.1 - - + -
91A SXK 3.0 48.5 - - + -
153B MET* 3.8 13.0 - - + -
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Residues in contact with GLY 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 2.9 17.3 + - - -
39A LYS* 3.4 2.9 + - - -
40A GLU 3.2 0.2 - - - -
41A LEU* 1.3 78.5 - - - +
43A LYS* 1.3 61.8 + - - +
45A MET* 3.1 21.5 + - - +
46A ARG* 3.1 14.0 + - - +
51A ASN* 5.0 4.5 + - - -
52A PRO* 5.7 2.6 - - - +
57A LEU* 4.5 9.4 - - - -
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Residues in contact with LYS 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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27A PHE 5.7 0.4 - - - +
29A LEU* 5.2 11.2 - - + -
39A LYS* 3.1 36.1 + - - +
40A GLU* 2.8 41.8 + - - +
41A LEU 3.1 0.2 - - - -
42A GLY* 1.3 79.0 - - - +
44A VAL* 1.3 64.3 + - + +
46A ARG* 3.4 19.5 + - - +
47A MET* 3.7 9.2 + - - +
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Residues in contact with VAL 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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27A PHE* 3.1 38.4 - - + -
40A GLU 3.6 3.6 + - - +
41A LEU 3.2 4.8 + - - +
43A LYS* 1.3 75.8 - - + +
45A MET* 1.3 65.7 + - - +
47A MET* 3.0 30.5 + - + +
48A LEU* 3.5 6.6 + - + +
153B MET* 3.6 34.9 - - + +
156B ALA* 5.2 7.8 - - + +
157B LEU* 3.6 22.4 - - + +
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Residues in contact with MET 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* 3.0 41.3 + - + +
42A GLY* 3.2 17.3 - - - +
44A VAL* 1.3 77.4 - - - +
46A ARG* 1.3 62.3 + - - +
48A LEU* 3.2 19.0 + - - +
49A GLY 3.4 0.5 + - - -
50A GLN* 3.0 32.2 + - - +
52A PRO* 4.1 23.6 - - + -
57A LEU* 3.7 16.8 - - + -
60A MET* 4.0 9.6 - - + -
91A SXK 4.8 0.2 - - + -
146B VAL* 5.4 6.5 - - + -
148B ILE* 3.3 36.1 - - + -
153B MET* 4.8 2.2 - - + -
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Residues in contact with ARG 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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42A GLY 3.1 5.1 + - - +
43A LYS* 3.5 14.5 + - - +
44A VAL 3.2 0.2 - - - -
45A MET* 1.3 79.2 - - - +
47A MET* 1.3 104.9 + - - +
49A GLY* 3.2 14.0 + - - -
50A GLN 3.5 9.6 + - - +
51A ASN* 3.1 33.6 - - - +
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Residues in contact with MET 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 LYS 3.8 8.5 - - - +
44A VAL* 3.0 23.1 + - + +
46A ARG* 1.3 108.4 - - - +
48A LEU* 1.3 62.9 + - - +
49A GLY* 4.5 0.3 - - - -
156B ALA* 3.6 22.2 - - + +
157B LEU* 5.1 2.7 - - + +
160B ALA* 2.9 40.7 - - + +
161B ARG* 4.4 15.0 - - - +
162B ALA* 4.8 4.7 - - + -
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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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44A VAL* 3.5 4.6 + - + +
45A MET* 3.2 15.2 + - - +
46A ARG 3.2 0.2 - - - -
47A MET* 1.3 80.2 - - - +
49A GLY* 1.3 58.7 + - - +
50A GLN* 3.5 34.1 - - - +
147B ARG 5.0 11.2 - - - +
148B ILE* 5.4 8.7 - - + -
152B ALA* 5.8 7.2 - - + +
153B MET* 5.4 12.1 - - - -
156B ALA* 5.1 15.9 - - + +
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Residues in contact with GLY 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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46A ARG* 3.2 12.9 + - - -
47A MET 4.5 0.7 - - - -
48A LEU* 1.3 80.1 - - - +
50A GLN* 1.3 71.8 + - - +
51A ASN* 5.5 1.8 - - - -
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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