Contacts of the helix formed by residues 39 - 49 (chain A) in PDB entry 1X57
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 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ALA* 3.5 7.0 - - - +
38A GLU* 1.3 79.4 + - - +
40A PRO* 1.3 73.0 - - + +
41A GLN* 3.1 21.3 - - + +
42A VAL* 3.3 27.5 - - + +
43A ILE* 3.7 3.8 - - - +
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Residues in contact with PRO 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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1A GLY* 4.6 18.6 - - - +
2A SER 6.0 0.2 - - - +
3A SER* 4.3 8.5 + - - +
29A GLN* 4.5 4.2 - - - +
30A LYS* 3.4 42.0 - - + -
33A ALA* 3.5 18.3 - - + -
38A GLU 4.3 1.6 - - - +
39A LYS* 1.3 88.1 - - + +
41A GLN* 1.3 66.0 + - - +
43A ILE* 3.9 6.6 - - + +
44A ALA* 3.3 20.8 + - - +
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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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2A SER 3.8 18.7 + - - +
3A SER* 5.0 9.5 - - - +
39A LYS* 3.1 15.0 - - + -
40A PRO* 1.3 76.1 - - - +
42A VAL* 1.3 70.4 + - + +
44A ALA* 3.1 19.7 + - - +
45A ASP* 3.1 29.3 + - - +
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Residues in contact with VAL 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 GLU* 3.9 31.9 - - + +
39A LYS* 3.3 26.0 + - + +
41A GLN* 1.3 78.9 - - + +
43A ILE* 1.3 56.0 + - + +
45A ASP* 3.1 9.3 + - - +
46A TYR* 2.8 53.7 + - + +
51A ALA* 4.7 8.5 - - + -
57A VAL* 5.6 0.4 - - + -
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Residues in contact with ILE 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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18A ILE* 4.4 18.4 - - + -
22A ARG* 4.6 1.1 - - - +
29A GLN* 3.8 44.2 - - + +
32A LEU* 4.2 19.7 - - + -
33A ALA* 3.9 8.3 - - + +
36A ILE* 3.7 29.8 - - + -
39A LYS 3.7 14.8 - - - +
40A PRO* 3.9 6.1 - - + +
41A GLN 3.2 0.8 - - - -
42A VAL* 1.3 81.9 - - + +
44A ALA* 1.3 61.3 + - - +
46A TYR* 3.3 7.6 + - + +
47A GLU* 3.0 25.7 + - - +
61A ILE* 4.7 8.7 - - + -
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Residues in contact with ALA 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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3A SER* 4.4 16.4 - - - -
4A GLY* 4.9 13.0 - - - +
9A ARG* 4.5 6.1 + - - -
29A GLN* 3.9 21.7 - - - +
40A PRO 3.3 10.6 + - - +
41A GLN* 3.1 14.0 + - - +
43A ILE* 1.3 77.5 - - - +
45A ASP* 1.3 64.2 + - - +
47A GLU* 3.8 8.4 - - - +
48A SER* 3.7 14.4 + - - -
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Residues in contact with ASP 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* 3.1 31.9 + - - +
42A VAL* 3.1 9.2 + - - +
44A ALA* 1.3 78.0 - - - +
46A TYR* 1.3 58.3 + - - +
47A GLU 3.2 1.6 - - - -
48A SER* 3.2 6.0 + - - -
49A GLY 2.9 9.4 + - - -
50A ARG* 2.9 43.3 + - - +
51A ALA* 3.7 23.4 - - + +
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Residues in contact with TYR 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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14A VAL* 3.6 9.4 - - + +
15A GLY* 3.3 16.6 + - - -
18A ILE* 3.5 25.4 - - + -
42A VAL* 2.8 37.1 + - + +
43A ILE* 3.5 11.7 - - + +
45A ASP* 1.3 70.3 - - - +
47A GLU* 1.3 61.5 + - - +
49A GLY* 3.1 14.2 + - - +
51A ALA* 4.0 17.9 - - + +
52A ILE 4.3 5.1 + - - -
53A PRO* 3.8 16.8 - - + -
54A ASN 3.5 15.9 + - - -
57A VAL* 3.3 40.1 - - + +
58A LEU* 3.7 28.4 + - + +
61A ILE* 3.9 12.8 - - + -
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Residues in contact with GLU 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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9A ARG* 5.6 5.2 + - - +
11A THR* 3.2 27.7 - - + +
15A GLY* 3.4 29.6 - - - +
18A ILE* 4.3 9.8 - - + +
19A GLN* 3.9 23.1 + - + -
22A ARG* 2.7 34.2 + - - -
29A GLN* 2.8 26.5 + - - +
43A ILE* 3.0 14.7 + - - +
44A ALA 3.8 8.5 - - - +
46A TYR* 1.3 75.8 - - - +
48A SER* 1.3 60.5 + - - +
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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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9A ARG* 3.2 35.2 + - - -
10A VAL 3.4 23.0 - - - +
11A THR* 4.3 2.2 - - - +
12A LEU* 3.4 18.2 + - - +
44A ALA 3.7 7.1 + - - -
45A ASP* 3.2 8.5 + - - -
47A GLU* 1.3 76.7 - - - +
49A GLY* 1.3 59.8 + - - +
50A ARG* 4.0 29.0 + - - +
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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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12A LEU* 4.1 31.7 - - - +
45A ASP 2.9 4.3 + - - -
46A TYR* 3.1 13.9 + - - -
48A SER* 1.3 79.0 - - - +
50A ARG* 1.3 62.4 + - - +
51A ALA 3.8 6.9 - - - +
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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