Contacts of the helix formed by residues 38 - 48 (chain A) in PDB entry 1U61
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 GLN 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A VAL* 4.0 15.8 - - + +
35A ARG* 2.9 44.6 + - - +
37A ASN* 1.3 89.2 - - - +
39A LEU* 1.3 62.5 + - - +
40A HIS 3.3 2.7 - - - -
41A ARG* 3.2 37.6 + - - +
42A LEU* 2.9 33.0 + - + +
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Residues in contact with LEU 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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28A LEU* 4.0 31.3 - - + +
29A LEU* 4.0 27.8 - - + -
34A VAL* 3.7 23.3 - - + +
35A ARG 4.3 1.6 - - - +
36A PRO* 3.2 35.1 + - + +
38A GLN* 1.3 75.8 - - - +
40A HIS* 1.3 64.0 + - - +
42A LEU* 3.2 5.3 + - + +
43A GLY* 2.9 21.7 + - - -
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Residues in contact with HIS 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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25A ARG* 5.7 5.1 + - - -
36A PRO 4.6 1.2 + - - -
37A ASN 4.6 5.9 + - - +
38A GLN 3.3 1.0 - - - -
39A LEU* 1.3 78.0 - - - +
41A ARG* 1.3 68.2 + - + +
43A GLY* 3.1 2.3 + - - -
44A THR* 3.1 36.5 + - - -
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Residues in contact with ARG 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 ASN 5.1 1.9 + - - +
38A GLN* 3.2 48.1 + - - +
40A HIS* 1.3 83.9 - - + +
42A LEU* 1.3 87.7 + - - +
44A THR* 3.3 20.5 + - - -
45A SER* 3.7 5.0 + - - -
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Residues in contact with LEU 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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28A LEU* 4.0 24.0 - - + -
34A VAL* 3.7 41.5 - - + -
38A GLN* 2.9 27.2 + - + +
39A LEU* 3.7 5.4 - - + +
41A ARG* 1.3 100.9 - - - +
43A GLY* 1.3 58.9 + - - +
45A SER* 2.8 28.6 + - - +
46A PHE* 3.5 8.0 - - + -
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Residues in contact with GLY 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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21A GLU* 5.7 3.1 - - - -
24A ILE* 4.4 8.3 - - - -
25A ARG* 6.4 0.9 - - - -
28A LEU* 3.5 17.6 - - - +
39A LEU 2.9 16.2 + - - -
40A HIS* 3.1 4.0 + - - -
42A LEU* 1.3 73.0 - - - +
44A THR* 1.3 51.9 + - - +
46A PHE* 2.8 26.1 + - - +
47A VAL* 3.0 21.6 + - - +
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Residues in contact with THR 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 HIS* 3.1 29.4 + - - -
41A ARG* 3.4 14.1 - - - -
42A LEU 3.2 0.2 - - - -
43A GLY* 1.3 75.5 - - - +
45A SER* 1.3 58.4 + - - +
46A PHE 3.1 0.2 - - - -
47A VAL* 4.1 10.1 - - - +
48A SER* 3.0 47.1 + - - -
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Residues in contact with SER 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 ARG 3.7 3.8 + - - -
42A LEU* 2.8 24.8 + - - +
44A THR* 1.3 78.3 - - - +
46A PHE* 1.3 69.1 + - - +
48A SER* 5.0 1.1 - - - -
51A ALA* 3.4 16.1 - - - +
126A LEU* 3.9 12.3 - - - +
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Residues in contact with PHE 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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20A TYR* 2.8 23.6 + - - -
24A ILE* 3.7 42.6 - - + -
27A HIS* 4.2 7.2 - + - -
28A LEU* 3.9 22.0 - - + -
42A LEU* 3.5 14.4 - - + -
43A GLY 2.8 8.7 + - - +
45A SER* 1.3 90.3 - - - +
47A VAL* 1.3 56.3 + - - +
48A SER 3.7 1.1 - - - -
51A ALA* 3.8 6.8 - - - +
52A GLN* 3.9 3.3 - - - +
123A ILE* 4.1 23.3 - - + -
126A LEU* 3.6 28.0 - - + +
127A GLU* 3.5 39.7 - - + -
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Residues in contact with VAL 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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17A ASP* 6.0 1.1 - - - +
20A TYR* 3.8 19.7 - - + -
21A GLU* 3.7 32.3 - - - +
24A ILE* 4.0 18.6 - - + -
43A GLY 3.0 23.6 + - - +
44A THR* 4.1 6.5 - - - +
46A PHE* 1.3 79.8 - - - +
48A SER* 1.3 69.7 + - - +
52A GLN* 3.3 21.0 + - - +
100A GLU* 5.2 1.0 - - - +
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Residues in contact with SER 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 THR* 3.0 32.5 + - - -
45A SER* 5.0 0.5 - - - -
46A PHE 3.7 0.4 - - - -
47A VAL* 1.3 83.9 - - - +
49A ALA* 1.3 63.8 + - - +
50A LYS* 3.5 8.4 + - - +
51A ALA* 3.0 20.6 + - - +
52A GLN* 3.0 22.6 + - - +
96A SER* 4.5 0.4 - - - -
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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