Contacts of the helix formed by residues 26 - 39 (chain A) in PDB entry 6H1D
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 ALA 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A TYR* 3.6 12.8 - - + +
24A GLU 3.2 4.6 + - - +
25A PRO* 1.3 74.4 - - - +
27A GLU* 1.3 73.6 + - - +
28A ASP* 3.3 13.0 - - - +
29A THR* 3.0 9.5 + - - -
30A PHE* 2.9 37.0 + - - -
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Residues in contact with GLU 27 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A ALA* 1.3 87.4 - - - +
28A ASP* 1.3 61.1 + - - +
30A PHE* 4.1 11.7 - - + +
31A LEU* 3.0 28.8 + - - +
199A ARG* 5.0 2.0 + - - +
201A ALA* 3.5 29.6 - - + +
202A GLY* 3.7 22.8 + - - -
206A LEU* 3.9 6.1 - - + +
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Residues in contact with ASP 28 (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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23A TYR* 2.8 31.2 + - - -
26A ALA* 3.6 8.8 - - - +
27A GLU* 1.3 70.2 - - - +
29A THR* 1.3 71.9 + - - -
31A LEU* 3.4 3.7 + - - +
32A LEU* 3.0 23.0 + - - +
122A ASN* 3.1 26.9 + - - +
125A TYR* 3.3 33.0 + - + +
172A VAL* 4.1 9.3 - - + +
204A GLU* 5.9 0.2 + - - -
206A LEU* 3.9 20.1 - - + +
301A SAH 5.4 0.7 - - - +
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Residues in contact with THR 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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23A TYR* 3.6 3.3 - - - -
25A PRO* 3.5 8.8 - - + +
26A ALA 3.2 24.1 + - - -
28A ASP* 1.3 85.1 + - - +
30A PHE* 1.3 57.1 + - + +
32A LEU* 3.2 7.3 + - - +
33A LEU* 3.0 36.3 + - + +
58A VAL* 3.7 26.0 - - + -
59A VAL* 4.1 6.9 - - + +
122A ASN* 4.0 1.1 + - - +
301A SAH 2.8 39.8 + - - +
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Residues in contact with PHE 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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8A THR* 4.2 25.1 - - + -
11A HIS* 5.1 6.7 - + - -
25A PRO* 3.9 32.1 - - + -
26A ALA* 2.9 33.1 + - - +
27A GLU* 4.1 10.1 - - + +
28A ASP 3.3 0.2 - - - -
29A THR* 1.3 73.9 - - - +
31A LEU* 1.3 64.6 + - - +
33A LEU* 3.8 19.8 - - + +
34A ASP* 3.1 32.7 + - - +
58A VAL* 6.2 0.2 - - + -
199A ARG* 4.2 5.8 - - - +
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Residues in contact with LEU 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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27A GLU 3.0 18.9 + - - +
28A ASP* 3.8 5.4 - - - +
30A PHE* 1.3 75.0 - - - +
32A LEU* 1.3 65.2 + - - +
34A ASP* 3.2 3.3 + - - +
35A ALA* 3.0 22.3 + - - +
172A VAL* 6.0 1.6 - - + -
197A LEU* 3.5 34.5 - - + +
199A ARG* 3.4 54.6 - - + +
206A LEU* 3.6 33.9 - - + -
207A SER 4.5 0.2 - - - +
208A VAL* 3.9 20.2 - - + -
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Residues in contact with LEU 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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28A ASP 3.0 14.2 + - - +
29A THR* 3.2 9.6 + - - +
31A LEU* 1.3 76.8 - - - +
33A LEU* 1.3 56.8 + - - +
35A ALA* 3.3 1.6 + - - +
36A LEU* 3.0 54.1 + - + +
51A GLU* 5.2 0.4 - - - +
59A VAL* 3.9 21.8 - - + -
120A VAL* 3.6 23.8 - - + -
122A ASN* 4.1 14.6 - - + +
170A TYR* 4.3 22.2 - - + -
172A VAL* 4.0 24.7 - - + -
208A VAL* 4.1 17.6 - - + +
301A SAH 4.7 0.7 - - - +
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Residues in contact with LEU 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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8A THR* 4.5 19.3 - - + +
9A PRO* 4.8 5.6 - - + -
29A THR* 3.0 23.4 + - + +
30A PHE* 3.8 28.3 - - + +
31A LEU 3.3 0.2 - - - -
32A LEU* 1.3 75.3 - - - +
34A ASP* 1.3 60.7 + - - +
36A LEU* 3.3 3.7 + - + +
37A GLU* 2.8 34.4 + - - +
58A VAL* 4.3 4.9 - - + +
59A VAL* 4.0 29.4 - - + -
62A PHE* 3.7 46.1 - - + -
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Residues in contact with ASP 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 PHE* 3.1 13.4 + - - +
31A LEU 3.5 7.2 - - - +
33A LEU* 1.3 79.1 - - - +
35A ALA* 1.3 55.7 - - - +
37A GLU* 3.8 12.3 - - - +
38A ALA* 3.0 29.8 + - - +
197A LEU* 3.6 16.2 - - + -
199A ARG* 2.7 36.8 + - - +
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Residues in contact with ALA 35 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A LEU 3.0 13.1 + - - +
32A LEU 3.7 6.3 - - - +
34A ASP* 1.3 76.0 - - - +
36A LEU* 1.3 61.5 + - - +
38A ALA* 3.3 7.2 + - - +
39A ALA* 3.2 21.7 + - - +
170A TYR* 4.6 8.0 - - + -
196A ALA* 4.5 9.9 - - + +
197A LEU* 3.7 20.5 - - + +
208A VAL* 3.7 28.5 - - + -
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Residues in contact with LEU 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 LEU* 3.0 36.6 + - + +
33A LEU* 3.9 7.6 - - + +
35A ALA* 1.3 73.4 - - - +
37A GLU* 1.3 66.4 + - - +
39A ALA* 2.9 18.3 + - - +
40A ALA 3.4 6.6 + - - -
43A LEU* 3.9 6.9 - - + +
59A VAL* 3.8 29.6 - - + -
62A PHE* 4.3 4.9 - - + -
63A LEU* 3.8 31.4 - - + -
66A MET* 3.8 9.6 - - + +
118A LEU* 4.5 1.3 - - + -
120A VAL* 4.4 9.2 - - + -
170A TYR* 3.9 37.5 - - + -
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Residues in contact with GLU 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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7A SER* 4.5 9.8 + - - -
33A LEU* 2.8 22.6 + - - +
34A ASP* 3.8 13.1 - - - +
36A LEU* 1.3 71.7 - - - +
38A ALA* 1.3 62.3 + - - +
39A ALA 3.1 1.2 + - - -
40A ALA* 3.2 18.9 + - + +
62A PHE* 3.7 27.3 - - + -
66A MET* 3.9 12.8 - - + -
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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 ASP 3.0 18.5 + - - +
35A ALA* 3.7 8.1 - - - +
36A LEU 3.2 0.2 - - - -
37A GLU* 1.3 76.2 - - - +
39A ALA* 1.3 57.1 + - - +
40A ALA 3.4 1.4 + - - -
41A ALA 5.3 0.2 + - - -
197A LEU* 6.0 4.3 - - + -
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Residues in contact with ALA 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 ALA 3.2 8.6 + - - +
36A LEU 2.9 11.8 + - - +
38A ALA* 1.3 78.2 - - - +
40A ALA* 1.3 62.4 - - - -
41A ALA* 3.3 3.1 - - - -
42A GLU* 2.8 31.5 + - + +
43A LEU* 3.2 16.2 + - + +
170A TYR* 3.2 27.6 - - + +
210A LYS* 5.6 0.2 - - + -
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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