Contacts of the helix formed by residues 30 - 41 (chain A) in PDB entry 4XXL
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 ASP 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A ALA 3.4 3.1 + - - +
29A VAL* 1.3 70.7 - - - +
31A VAL* 1.3 56.7 + - - +
32A ASP* 3.4 11.4 + - - +
33A ALA* 3.1 28.8 + - + +
34A ALA* 3.0 13.5 + - - +
109A ASN* 2.9 35.8 + - - +
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Residues in contact with VAL 31 (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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29A VAL* 3.5 17.4 + - + +
30A ASP* 1.3 68.7 + - - +
32A ASP* 1.3 72.0 + - - +
34A ALA* 3.2 4.0 + - - +
35A LYS* 2.9 39.1 + - + +
113A TRP* 3.9 31.2 - - + +
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Residues in contact with ASP 32 (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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30A ASP* 3.4 7.9 + - - +
31A VAL* 1.3 82.8 - - - +
33A ALA* 1.3 59.5 + - - +
35A LYS* 3.5 6.2 + - - +
36A SER* 2.9 30.7 + - - -
39A ARG* 4.8 1.7 + - - -
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Residues in contact with ALA 33 (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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30A ASP* 3.1 31.9 + - + +
31A VAL 3.2 0.2 - - - -
32A ASP* 1.3 73.8 - - - +
34A ALA* 1.3 68.0 + - - +
36A SER* 3.6 6.7 - - - -
37A LEU* 3.0 24.4 + - - +
106A ALA* 6.6 0.4 - - + -
109A ASN* 4.0 8.7 - - - +
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Residues in contact with ALA 34 (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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30A ASP 3.0 14.0 + - - +
31A VAL 3.5 7.2 - - - +
33A ALA* 1.3 78.4 - - - +
35A LYS* 1.3 56.5 + - - +
37A LEU* 3.2 2.9 + - - +
38A ALA* 3.0 28.6 + - - +
106A ALA 5.8 0.4 - - - -
109A ASN* 3.5 11.5 - - - +
110A LEU* 3.7 21.0 - - - +
113A TRP* 3.6 36.6 - - + -
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Residues in contact with LYS 35 (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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31A VAL* 2.9 34.8 + - + +
32A ASP* 4.1 5.4 - - - +
34A ALA* 1.3 72.1 - - - +
36A SER* 1.3 57.6 + - - +
38A ALA* 3.3 3.6 + - - +
39A ARG* 2.9 49.9 + - - +
44A PHE* 3.8 19.6 - - + -
49A VAL* 5.2 6.0 - - - +
113A TRP* 3.9 34.5 - - + -
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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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32A ASP 2.9 19.9 + - - -
33A ALA* 3.6 7.9 - - - -
35A LYS* 1.3 77.6 - - - +
37A LEU* 1.3 64.2 + - - +
39A ARG* 3.3 24.3 + - - +
40A GLU* 3.0 45.7 + - - +
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Residues in contact with LEU 37 (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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33A ALA 3.0 18.2 + - - +
34A ALA* 3.2 5.8 + - - +
36A SER* 1.3 75.3 + - - +
38A ALA* 1.3 61.4 + - - +
40A GLU* 3.4 13.1 + - - +
41A ASN* 3.0 51.2 + - - +
43A CYS* 4.6 0.2 - - - -
98A ILE* 4.7 4.5 - - + -
101A LYS 5.4 0.2 - - - +
102A ALA* 3.7 24.0 - - + -
106A ALA* 3.6 42.0 - - + +
107A ILE* 4.1 7.6 - - + +
110A LEU* 4.0 20.0 - - + -
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Residues in contact with ALA 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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34A ALA 3.0 16.3 + - - +
35A LYS 3.6 0.2 - - - +
37A LEU* 1.3 77.8 - - - +
39A ARG* 1.3 61.6 + - - +
41A ASN 3.4 0.9 + - - -
42A ASN 3.3 3.3 + - - -
43A CYS* 3.0 49.9 + - + +
44A PHE* 3.6 32.1 + - + -
58A TYR* 5.4 1.3 - - + +
110A LEU* 4.3 14.7 - - + +
113A TRP* 5.1 0.9 - - + -
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Residues in contact with ARG 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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32A ASP 4.8 1.8 + - - -
35A LYS* 2.9 36.8 + - - +
36A SER* 3.5 32.1 + - - +
38A ALA* 1.3 75.6 - - - +
40A GLU* 1.3 65.0 + - + +
41A ASN 3.3 0.9 + - - -
42A ASN* 3.4 13.9 + - - +
44A PHE* 3.9 21.7 - - + -
45A LYS* 4.9 5.2 + - - -
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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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36A SER* 3.0 35.3 + - - +
37A LEU* 3.8 19.6 - - - +
38A ALA 3.3 0.2 - - - -
39A ARG* 1.3 78.8 - - + +
41A ASN* 1.3 66.7 + - - +
42A ASN* 3.5 3.4 + - - +
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Residues in contact with ASN 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 LEU* 3.0 49.9 + - - +
39A ARG 3.2 0.2 - - - -
40A GLU* 1.3 83.0 + - - +
42A ASN* 1.3 64.2 + - - +
43A CYS* 3.2 9.1 + - - -
96A LYS* 3.4 26.0 + - - +
98A ILE* 3.7 31.2 - - + +
101A LYS* 4.3 17.6 + - - +
102A ALA* 5.3 0.8 - - - +
201A HEC 3.9 13.9 - - + +
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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