Contacts of the helix formed by residues 28 - 41 (chain A) in PDB entry 1X6Q
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 PHE 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A THR 4.2 12.6 - - - -
27A GLU* 1.3 74.0 - - - +
29A ALA* 1.3 63.7 + - - +
30A ARG 3.2 3.0 + - - -
31A SER* 3.3 20.0 + - - +
32A GLU* 2.9 31.6 + - + +
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Residues in contact with ALA 29 (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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27A GLU* 3.0 23.2 + - + +
28A PHE* 1.3 75.6 - - - +
30A ARG* 1.3 62.4 + - - +
32A GLU* 3.7 4.3 - - - -
33A GLY* 3.4 9.7 + - - -
110A LYS* 4.3 4.9 - - + -
111A ASN* 2.9 33.8 + - - +
137A PHE* 3.6 39.8 - - + +
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Residues in contact with ARG 30 (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 PHE 3.3 0.6 - - - -
29A ALA* 1.3 78.5 - - - +
31A SER* 1.3 64.1 + - - +
33A GLY* 3.3 4.3 + - - -
34A ALA* 3.2 19.6 + - + +
136A GLN* 3.1 45.1 + - - +
137A PHE* 4.0 31.1 + - + +
138A ILE 5.3 2.8 + - - -
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Residues in contact with SER 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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28A PHE* 3.3 29.4 + - - +
30A ARG* 1.3 77.1 - - - +
32A GLU* 1.3 60.0 + - - +
34A ALA* 3.3 8.1 + - - +
35A SER* 2.9 31.4 + - - -
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Residues in contact with GLU 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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27A GLU* 2.7 30.7 - - - +
28A PHE* 2.9 25.4 + - + +
29A ALA* 3.7 1.2 - - - -
31A SER* 1.3 78.9 - - - +
33A GLY* 1.3 57.2 + - - +
35A SER 3.3 0.9 + - - -
36A ALA* 2.9 30.7 + - - +
82A LEU* 3.6 33.0 - - + +
104A MET* 4.5 3.5 - - - +
107A ALA* 3.6 11.8 - - + -
108A GLY* 2.9 26.1 + - - -
111A ASN* 2.9 23.8 + - + +
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Residues in contact with GLY 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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29A ALA 3.4 5.6 + - - -
30A ARG 3.3 7.5 + - - -
32A GLU* 1.3 77.8 - - - +
34A ALA* 1.3 64.1 + - - +
36A ALA* 3.4 2.3 + - - +
37A LEU* 3.0 25.5 + - - +
104A MET* 4.7 1.8 - - - -
111A ASN* 4.3 0.8 - - - +
116A ILE* 3.8 5.4 - - - +
133A GLN* 4.0 22.4 - - - -
137A PHE 4.6 2.2 - - - -
139A PRO* 3.7 14.7 - - - +
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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 ARG* 3.2 13.6 + - + +
31A SER* 3.7 11.2 - - - +
32A GLU 3.3 0.2 - - - -
33A GLY* 1.3 75.7 - - - +
35A SER* 1.3 58.6 + - - +
37A LEU* 3.4 5.3 + - - +
38A ALA* 2.9 30.6 + - - +
139A PRO* 4.6 7.1 - - + +
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Residues in contact with SER 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 SER 2.9 18.6 + - - -
32A GLU 3.6 3.4 - - - -
34A ALA* 1.3 77.3 - - - +
36A ALA* 1.3 61.7 + - - +
38A ALA* 3.2 8.9 + - - +
39A SER* 3.2 17.2 + - - -
80A ASN* 3.0 27.2 + - - -
82A LEU* 3.7 13.8 - - - +
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Residues in contact with ALA 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 GLU 2.9 17.6 + - - +
33A GLY 3.7 4.0 - - - +
35A SER* 1.3 75.7 - - - +
37A LEU* 1.3 62.3 + - - +
39A SER* 3.1 14.4 + - - -
40A VAL* 3.5 12.6 + - - +
80A ASN* 4.1 2.6 - - - +
82A LEU* 4.5 1.5 - - + +
102A PHE* 3.4 44.1 - - + -
104A MET* 3.9 9.2 - - - -
116A ILE* 3.8 15.7 - - + -
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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 GLY 3.0 17.3 + - - +
34A ALA* 3.8 4.7 - - - +
36A ALA* 1.3 75.8 - - - +
38A ALA* 1.3 59.3 + - - +
40A VAL* 3.1 8.5 + - + -
41A ASN* 2.8 48.5 + - + +
116A ILE* 4.2 8.4 - - + +
118A LEU* 3.9 27.6 - - + -
129A CYS* 4.3 13.7 - - + -
139A PRO* 3.8 28.5 - - + -
140A LYS 4.1 13.9 - - - +
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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 2.9 18.8 + - - +
35A SER* 3.5 9.4 - - - +
36A ALA 3.2 0.4 - - - -
37A LEU* 1.3 77.0 - - - +
39A SER* 1.3 57.3 + - - +
41A ASN* 4.7 2.9 - - - -
42A PRO* 3.1 28.0 - - - +
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Residues in contact with SER 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 SER 3.2 3.3 + - - -
36A ALA 3.1 11.4 + - - -
38A ALA* 1.3 78.2 - - - +
40A VAL* 1.3 60.6 + - - +
42A PRO* 4.1 3.6 - - - +
43A LEU* 3.8 17.3 - - - +
75A VAL* 5.2 3.3 - - - +
79A ALA* 5.9 1.1 - - - +
80A ASN* 2.9 30.1 + - - +
85A ILE* 4.0 14.8 - - - +
102A PHE* 3.9 19.5 - - - -
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Residues in contact with VAL 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 ALA 3.7 9.0 - - - +
37A LEU* 3.5 16.2 - - + +
39A SER* 1.3 81.7 - - - +
41A ASN* 1.3 67.6 + - - +
42A PRO* 3.3 2.7 - - - -
43A LEU* 3.0 25.1 + - + +
44A LYS 3.9 1.2 + - - -
85A ILE* 4.1 19.3 - - + -
100A LEU* 4.0 10.6 - - + +
101A THR 4.0 23.3 - - - +
102A PHE* 4.1 17.5 - - + +
116A ILE* 4.9 4.5 - - + -
118A LEU* 3.6 31.4 - - + +
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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* 2.8 39.8 + - + +
38A ALA* 4.7 2.5 - - - -
40A VAL* 1.3 73.6 - - - +
42A PRO* 1.3 67.2 - - + +
43A LEU 3.1 0.9 + - - -
44A LYS* 2.9 52.9 + - - +
45A THR* 4.5 1.0 + - - -
118A LEU* 3.9 8.6 - - - +
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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