Contacts of the helix formed by residues 31 - 42 (chain A) in PDB entry 3CFW
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 ASN 31 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A ILE* 3.6 11.5 - - - +
30A GLN* 1.3 89.2 + - - +
32A LYS* 1.3 62.4 + - - +
33A ALA* 3.0 14.3 + - - +
34A GLU* 2.9 57.7 + - - +
35A ILE* 3.5 9.7 + - - +
72A GLU* 3.6 23.5 + - + +
73A ALA* 4.1 1.6 - - - +
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Residues in contact with LYS 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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31A ASN* 1.3 73.8 - - - +
33A ALA* 1.3 65.4 + - - +
35A ILE* 3.2 22.2 + - + +
36A GLU* 2.9 49.9 + - - +
72A GLU 3.8 9.2 + - - +
75A ASN* 3.8 28.7 + - - +
102A GLY* 6.2 0.2 - - - -
103A LYS* 4.6 8.5 - - - +
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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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31A ASN* 3.0 13.2 + - - +
32A LYS* 1.3 77.6 - - - +
34A GLU* 1.3 57.7 + - - +
36A GLU* 3.1 15.8 + - - +
37A TYR* 2.8 29.3 + - - +
137A ILE* 4.1 11.1 - - + +
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Residues in contact with GLU 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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1A TRP* 3.6 10.1 + - - -
3A TYR* 3.6 21.9 + - - +
28A ALA 4.1 0.5 - - - +
29A ILE* 3.4 11.4 - - + -
30A GLN* 2.6 62.1 + - - +
31A ASN* 2.9 26.6 + - - +
32A LYS 3.2 0.2 - - - -
33A ALA* 1.3 76.3 - - - +
35A ILE* 1.3 61.7 + - - +
37A TYR* 3.2 3.3 + - - +
38A LEU* 2.9 31.4 + - + +
135A GLU 4.3 1.9 - - - +
136A ILE* 5.0 3.5 - - - -
137A ILE* 4.0 20.4 - - + -
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Residues in contact with ILE 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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29A ILE* 3.5 34.8 - - + -
31A ASN 3.5 5.4 + - - +
32A LYS* 3.2 24.1 + - + +
34A GLU* 1.3 76.4 - - - +
36A GLU* 1.3 57.9 + - - +
38A LEU* 3.3 9.6 + - - +
39A GLU* 2.9 29.4 + - + +
73A ALA 3.9 6.7 - - - +
75A ASN* 3.6 38.4 - - + +
93A ILE* 4.4 5.2 - - + -
95A ILE* 5.2 0.3 - - - +
102A GLY* 3.8 27.8 - - - +
104A TRP* 4.1 8.1 - - - +
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Residues in contact with GLU 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 LYS* 2.9 47.7 + - - +
33A ALA* 3.4 16.0 - - - +
35A ILE* 1.3 75.6 - - - +
37A TYR* 1.3 63.0 + - - +
39A GLU* 3.4 8.0 + - + +
40A LYS* 3.2 25.3 + - - +
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Residues in contact with TYR 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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3A TYR* 3.6 39.0 - + + -
33A ALA 2.8 6.6 + - - +
34A GLU 3.2 6.7 + - - +
36A GLU* 1.3 78.0 - - - +
38A LEU* 1.3 61.2 + - + +
40A LYS* 3.4 12.7 - - + +
41A THR* 2.9 67.0 + - + +
137A ILE* 3.6 37.2 - - + -
138A ASN* 3.1 24.8 + - - -
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Residues in contact with LEU 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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3A TYR* 3.7 53.6 - - + +
27A VAL* 4.7 2.0 - - + -
29A ILE* 4.7 21.8 - - + -
34A GLU* 2.9 25.3 + - + +
35A ILE* 3.6 9.6 - - - +
37A TYR* 1.3 77.5 - - + +
39A GLU* 1.3 58.6 + - - +
41A THR* 4.6 0.9 - - + -
42A LEU* 2.9 59.5 + - + +
93A ILE* 4.9 4.7 - - + -
95A ILE* 4.0 8.9 - - + +
116A LEU* 4.6 17.0 - - + -
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Residues in contact with GLU 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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35A ILE* 2.9 18.2 + - + +
36A GLU* 3.6 9.0 - - + +
37A TYR 3.3 0.2 - - - -
38A LEU* 1.3 77.3 - - - +
40A LYS* 1.3 58.2 + - + +
42A LEU 4.4 0.2 - - - +
95A ILE* 3.7 11.3 - - + +
96A LYS* 2.9 63.6 + - - +
101A ALA* 3.4 26.3 - - + +
102A GLY* 3.7 13.2 + - - +
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Residues in contact with LYS 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 GLU 3.2 11.0 + - - +
37A TYR* 3.4 21.3 - - + +
39A GLU* 1.3 81.6 - - + +
41A THR* 1.3 67.3 + - - +
96A LYS* 3.3 13.5 + - - +
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Residues in contact with THR 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 TYR* 2.9 56.1 + - + +
38A LEU* 4.1 2.2 - - + -
40A LYS* 1.3 88.2 - - - +
42A LEU* 1.3 71.8 + - + +
43A PRO* 3.8 4.0 - - - +
96A LYS* 4.0 0.4 - - - -
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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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3A TYR* 5.4 6.3 - - + -
5A TYR* 3.6 32.3 - - + -
38A LEU* 2.9 38.4 + - + +
41A THR* 1.3 79.6 - - + +
43A PRO* 1.3 68.9 - - + +
49A TYR* 3.8 13.0 - - + +
95A ILE* 3.9 28.4 - - + +
96A LYS* 2.5 29.5 + - - +
116A LEU* 3.9 39.9 - - + -
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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