Contacts of the helix formed by residues 42 - 52 (chain D) in PDB entry 3MLQ
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 VAL 42 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28D LYS* 4.2 42.0 - - + +
29D ALA* 4.4 2.3 - - - +
31D GLN* 4.1 7.4 - - - +
40D GLU* 3.2 26.5 + - + +
41D ASN* 1.3 85.0 - - - +
43D GLY* 1.3 76.1 + - - +
44D ILE 3.3 0.3 + - - -
45D GLN* 3.1 18.4 + - - +
46D ALA* 3.1 9.0 + - - +
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Residues in contact with GLY 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D ALA* 3.5 19.5 - - - +
42D VAL* 1.3 82.0 - - - +
44D ILE* 1.3 62.5 + - - -
46D ALA* 3.7 3.2 - - - +
47D ALA* 3.2 18.6 + - - +
341D ALA* 3.5 30.4 - - - +
345D ARG* 4.1 7.0 + - - +
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Residues in contact with ILE 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D ALA* 3.0 20.2 + - - +
30D LEU* 4.5 9.6 - - + -
43D GLY* 1.3 69.1 - - - -
45D GLN* 1.3 56.6 + - - +
47D ALA* 2.8 11.7 + - - +
48D PHE* 2.6 70.1 + - + -
71D TYR* 4.2 16.6 - - + -
94D LEU* 4.5 7.0 - - + -
118D LEU* 3.4 35.2 - - + -
340D MET* 4.7 8.5 - - + -
341D ALA* 4.5 1.0 - - - +
344D PHE* 3.8 30.1 - - + -
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Residues in contact with GLN 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D ALA 4.7 0.6 + - - -
31D GLN* 4.0 7.4 - - - +
36D PRO 4.5 5.9 + - - -
39D ARG* 4.1 22.2 + - + +
40D GLU 3.1 26.2 - - - +
41D ASN* 4.3 2.9 - - - -
42D VAL 3.1 9.6 + - - +
44D ILE* 1.3 78.4 - - - +
46D ALA* 1.3 63.2 + - - +
48D PHE* 3.0 5.5 + - - +
49D LYS* 2.9 56.7 + - + +
68D PHE* 3.8 15.3 - - - -
71D TYR* 3.4 30.2 + - + +
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Residues in contact with ALA 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D ASN* 4.0 15.9 - - + +
42D VAL* 3.1 23.2 + - - +
43D GLY 3.7 8.1 - - - +
45D GLN* 1.3 77.4 - - - +
47D ALA* 1.3 65.8 + - - +
49D LYS* 3.0 5.6 + - - +
50D GLU* 2.9 43.0 + - - +
345D ARG* 3.9 9.6 - - - +
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Residues in contact with ALA 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D GLY 3.2 11.3 + - - +
44D ILE* 2.8 16.4 + - - +
46D ALA* 1.3 75.0 - - - +
48D PHE* 1.3 53.2 + - - +
50D GLU* 3.8 11.5 - - - +
51D THR* 2.3 34.9 + - - -
341D ALA 4.6 1.6 - - - +
344D PHE* 3.7 26.9 - - + -
345D ARG* 3.8 23.2 - - + +
348D LEU* 3.5 5.2 - - + -
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Residues in contact with PHE 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D ILE* 2.6 47.0 + - + -
45D GLN 3.4 7.2 - - - +
47D ALA* 1.3 74.5 - - - +
49D LYS* 1.3 61.9 + - - +
52D PHE* 3.1 48.2 + + - +
68D PHE* 3.7 31.3 - + + -
71D TYR* 3.5 31.6 - + + -
94D LEU* 4.3 3.6 - - + -
96D ALA* 4.1 8.5 - - + -
98D LEU* 6.0 0.4 - - + -
115D LEU* 3.3 34.3 - - + -
344D PHE* 3.9 12.3 - + - -
348D LEU* 3.8 19.5 - - + -
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Residues in contact with LYS 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D ARG 4.8 6.7 + - - -
41D ASN* 3.8 36.8 + - - +
45D GLN* 2.9 42.1 + - - +
46D ALA 3.9 1.8 - - - +
48D PHE* 1.3 78.9 - - - +
50D GLU* 1.3 57.5 + - - +
52D PHE 2.4 30.3 - - - +
68D PHE* 4.4 17.9 - - + -
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Residues in contact with GLU 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D ASN* 5.9 0.7 + - - -
46D ALA* 2.9 38.7 + - - +
47D ALA* 3.8 6.0 + - - +
49D LYS* 1.3 73.2 - - - +
51D THR* 1.3 64.4 + - - +
52D PHE 4.5 0.3 - - - +
345D ARG* 2.5 41.8 + - + -
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Residues in contact with THR 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D ALA 2.3 28.2 + - - -
48D PHE 3.7 3.6 - - - -
49D LYS 3.2 0.6 - - - -
50D GLU* 1.3 81.9 - - - +
52D PHE* 1.3 75.2 + - + +
53D PRO 3.5 11.6 - - - +
54D ILE* 4.2 5.9 - - + +
345D ARG* 5.2 2.4 + - - +
348D LEU* 3.1 26.3 - - + +
349D ALA* 4.7 4.0 + - - +
352D ALA* 3.9 27.8 - - + -
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Residues in contact with PHE 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D PHE* 3.1 47.7 + + - +
49D LYS* 2.4 26.5 - - - +
50D GLU 4.3 1.0 - - - -
51D THR* 1.3 94.3 - - + +
53D PRO* 1.3 67.6 - - + +
54D ILE* 4.0 25.1 - - + -
66D LEU* 3.8 34.1 - - + -
67D ASP* 4.7 2.2 - - - +
68D PHE* 3.7 31.4 - - + +
98D LEU* 4.8 16.8 - - + -
348D LEU* 4.6 7.9 - - + -
351D LEU* 6.3 4.0 - - + -
352D ALA* 6.0 0.9 - - + -
355D VAL* 6.1 0.2 - - + -
373D VAL* 5.8 2.5 - - + -
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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