Contacts of the helix formed by residues 35 - 46 (chain A) in PDB entry 5UM9
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 ALA 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ILE 3.3 1.8 + - - -
34A ASP* 1.3 72.5 + - - +
36A SER* 1.3 67.6 + - - +
38A SER* 3.0 6.2 + - - -
39A ILE* 2.9 27.8 + - + +
67A MET* 5.0 2.2 - - + -
83A TYR* 3.9 25.6 - - + -
84A VAL 3.2 17.4 + - - +
85A PHE* 3.7 35.7 - - + -
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Residues in contact with SER 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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34A ASP* 3.5 5.3 + - - -
35A ALA* 1.3 77.6 - - - +
37A MET* 1.3 57.0 + - - +
39A ILE* 3.2 12.0 + - - +
40A TYR* 2.9 39.5 + - - -
84A VAL 4.7 0.8 + - - -
85A PHE* 5.0 1.1 - - - -
86A ASN* 3.5 39.4 + - - +
133A VAL* 5.3 4.3 - - - +
138A ASN* 4.3 12.3 + - - +
5E C 5.7 4.2 + - - -
6E T 4.0 13.7 - - - -
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Residues in contact with MET 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASP* 3.8 25.9 + - + +
35A ALA 3.2 0.6 - - - -
36A SER* 1.3 76.9 - - - +
38A SER* 1.3 65.0 + - - +
40A TYR* 3.3 2.6 + - - +
41A GLN* 2.9 40.8 + - + +
177A THR* 4.7 2.7 - - - -
178A GLU* 3.6 39.5 - - - +
179A ASP* 3.8 30.7 - - + +
12D A 5.0 3.6 - - + -
6E T 3.4 31.3 + - + +
7E T 3.8 22.9 - - - +
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Residues in contact with SER 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ILE* 3.7 15.1 - - - +
34A ASP 3.3 13.7 + - - -
35A ALA* 3.0 10.8 + - - -
37A MET* 1.3 77.2 - - - +
39A ILE* 1.3 57.7 + - - +
41A GLN* 3.2 13.3 + - - +
42A PHE* 2.9 51.4 + - - -
67A MET* 4.8 7.4 - - - -
70A ARG* 4.2 12.7 + - - -
83A TYR* 4.6 4.2 - - - -
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Residues in contact with ILE 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ALA 2.9 19.5 + - - +
36A SER* 3.6 7.6 - - - +
38A SER* 1.3 76.4 - - - +
40A TYR* 1.3 62.3 + - - +
42A PHE* 3.3 7.0 + - - +
43A LEU* 2.9 35.6 + - + +
63A HIS* 4.0 15.7 - - + -
67A MET* 4.1 8.7 - - + -
85A PHE* 4.3 10.5 - - + -
133A VAL* 3.7 22.4 - - + -
137A HIS* 4.3 5.8 - - + +
138A ASN* 3.5 31.2 - - - +
141A CYS* 3.7 28.9 - - + -
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Residues in contact with TYR 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A SER* 2.9 28.3 + - - -
37A MET 3.3 7.2 + - - +
39A ILE* 1.3 76.8 - - - +
41A GLN* 1.3 63.2 + - - +
43A LEU* 3.8 2.5 - - - +
44A ILE* 2.9 36.2 + - + +
104A ARG* 5.5 0.2 + - - -
131A VAL* 3.5 31.0 - - + -
132A LYS* 4.0 10.3 - - - +
133A VAL* 3.4 42.4 + - + +
12D A 4.4 4.0 - - + +
5E C 4.8 0.6 - - + +
6E T 2.9 93.7 + + + +
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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 MET* 2.9 32.1 + - - +
38A SER* 3.2 9.4 + - - +
40A TYR* 1.3 76.1 - - - +
42A PHE* 1.3 66.0 + - + +
44A ILE* 3.2 1.4 + - - +
45A ALA* 2.9 28.9 + - - +
70A ARG* 3.1 28.7 + - - -
178A GLU* 4.6 14.8 + - - +
195A THR* 5.8 0.3 - - - +
12D A 3.8 48.2 + - + +
13D G 4.6 7.0 - - - -
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Residues in contact with PHE 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 SER* 2.9 35.0 + - - +
39A ILE* 3.9 6.5 - - - +
41A GLN* 1.3 74.4 - - + +
43A LEU* 1.3 58.5 + - - +
46A VAL* 2.9 41.4 + - + +
62A SER* 3.9 17.3 - - - +
63A HIS* 4.0 11.7 - - + -
66A GLY* 3.3 30.7 - - - -
67A MET* 3.3 32.8 - - + -
70A ARG* 3.5 49.6 - - + -
83A TYR* 6.1 0.2 - - - -
13D G 4.0 19.3 - - - -
14D A 5.1 1.1 - - - -
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Residues in contact with LEU 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 ILE* 2.9 35.3 + - + +
40A TYR 3.9 1.1 - - - +
42A PHE* 1.3 77.7 - - - +
44A ILE* 1.3 59.8 + - - +
46A VAL 4.7 2.4 - - - +
47A ARG* 3.2 22.5 + - - -
52A VAL* 4.3 8.8 - - + +
60A THR* 3.7 30.5 - - + -
62A SER* 4.4 4.3 - - - -
63A HIS* 3.9 20.6 - - + +
131A VAL* 3.7 24.0 - - + +
132A LYS 4.5 1.8 - - - +
133A VAL* 4.0 11.9 - - + -
137A HIS* 3.7 30.3 - - + +
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Residues in contact with ILE 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 TYR* 2.9 28.3 + - + +
41A GLN* 3.8 3.4 - - - +
43A LEU* 1.3 79.2 - - - +
45A ALA* 1.3 61.4 + - - +
47A ARG* 3.0 30.1 + - - +
128A LYS* 3.7 46.9 - - + +
131A VAL* 4.1 11.7 - - + -
12D A 3.3 70.2 - - + +
6E T 4.9 0.2 - - - +
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Residues in contact with ALA 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 2.9 15.0 + - - +
44A ILE* 1.3 79.2 - - - +
46A VAL* 1.3 60.4 + - - +
47A ARG* 2.8 18.8 + - - +
128A LYS* 5.4 4.5 + - - +
12D A 4.4 12.1 - - + +
13D G 3.5 53.3 - - + +
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Residues in contact with VAL 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 PHE* 2.9 33.9 + - + +
43A LEU 4.7 1.0 - - - +
44A ILE 5.2 0.2 - - - -
45A ALA* 1.3 71.1 - - - +
47A ARG* 1.3 60.1 + - - +
52A VAL* 3.9 4.7 - - - +
53A LEU* 3.7 24.3 + - + -
62A SER* 2.7 47.3 + - - +
65A MET* 4.2 7.6 - - + -
66A GLY* 5.2 1.6 - - - +
13D G 3.6 52.9 - - + +
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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