Contacts of the helix formed by residues 24 - 37 (chain M) in PDB entry 1T6V
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 SER 24 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18M ASP* 4.2 2.0 - - - -
19M ASN* 3.5 22.1 + - - +
22M GLY 3.8 4.2 + - - -
23M TYR* 1.3 76.8 - - - +
25M LEU* 1.3 65.7 + - - +
26M GLY 4.2 2.1 + - - -
27M ASN* 3.0 35.6 + - - +
28M TRP* 3.5 2.8 - - - -
120M VAL* 3.6 14.4 - - - +
121M GLN* 5.8 4.0 - - - +
124M ILE* 6.6 0.2 - - - -
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Residues in contact with LEU 25 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9M ALA 3.7 27.6 - - - +
12M MET* 3.8 23.1 - - + -
13M LYS* 3.8 21.5 - - + +
17M LEU* 4.7 2.9 - - + -
18M ASP* 3.0 34.7 + - + +
23M TYR 3.8 0.2 + - - -
24M SER* 1.3 71.5 - - - +
26M GLY* 1.3 62.4 + - - +
28M TRP* 3.0 20.8 + - + +
29M VAL* 3.1 14.3 + - + +
124M ILE* 3.6 28.9 - - + +
129M LEU* 3.9 19.3 - - + -
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Residues in contact with GLY 26 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24M SER* 3.2 4.0 + - - -
25M LEU* 1.3 77.0 - - - +
27M ASN* 1.3 56.8 + - - +
29M VAL* 4.5 0.7 - - - -
30M CYS* 2.9 32.2 + - - +
120M VAL* 3.3 30.5 - - - +
121M GLN* 5.2 0.4 - - - -
123M TRP* 3.7 7.3 - - - +
124M ILE* 3.9 19.2 - - - +
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Residues in contact with ASN 27 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23M TYR* 4.0 14.4 - - + +
24M SER* 3.0 44.9 + - - +
26M GLY* 1.3 75.4 - - - +
28M TRP* 1.3 58.0 + - - +
30M CYS* 3.8 0.8 - - - +
31M ALA* 2.9 29.5 + - - +
105M MET* 3.7 18.4 - - - -
111M TRP* 2.9 34.0 + - - +
115M CYS 5.0 0.5 - - - +
116M LYS* 5.5 0.2 - - - -
120M VAL* 3.7 25.4 - - - +
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Residues in contact with TRP 28 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12M MET* 3.4 29.6 - - + +
17M LEU* 3.2 57.9 + - + -
20M TYR* 4.3 6.0 + - + -
23M TYR* 3.2 19.5 + - + +
24M SER 3.5 21.1 - - - -
25M LEU* 3.0 10.4 + - + +
27M ASN* 1.3 74.7 - - - +
29M VAL* 1.3 65.7 + - - +
31M ALA* 3.5 3.4 + - - +
32M ALA 3.1 17.5 + - - -
56M LEU* 4.4 14.1 - - + +
95M ALA* 4.1 12.6 - - + -
99M VAL* 3.8 42.4 - - + -
105M MET* 3.8 28.3 - - + -
108M TRP* 4.0 20.4 - + - -
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Residues in contact with VAL 29 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5M ARG* 3.8 33.7 - - + +
8M LEU* 4.7 2.2 - - + -
9M ALA* 3.6 35.0 - - + +
12M MET* 4.0 13.7 - - - -
25M LEU* 3.1 16.2 + - + +
26M GLY 3.9 5.8 - - - +
28M TRP* 1.3 75.3 - - - +
30M CYS* 1.3 65.5 + - - +
32M ALA* 3.3 3.6 + - - +
33M LYS* 3.0 18.7 + - - +
38M PHE* 3.5 15.7 - - + -
123M TRP* 3.8 18.2 - - + +
124M ILE* 4.4 3.6 - - + -
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Residues in contact with CYS 30 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26M GLY 2.9 18.9 + - - +
27M ASN* 3.8 2.2 - - - +
29M VAL* 1.3 73.6 - - - +
31M ALA* 1.3 65.6 + - - +
33M LYS* 3.1 10.0 + - - +
34M PHE* 3.1 27.1 + - - -
114M ARG 4.3 2.5 - - - -
115M CYS* 2.0 53.4 - - + -
120M VAL* 4.9 1.6 - - + -
123M TRP* 3.4 46.2 - - + +
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Residues in contact with ALA 31 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27M ASN 2.9 19.6 + - - +
28M TRP 3.6 5.6 - - - +
29M VAL 3.3 0.2 - - - -
30M CYS* 1.3 77.8 - - - +
32M ALA* 1.3 57.9 + - - +
34M PHE* 3.7 0.7 - - - +
35M GLU* 2.8 40.5 + - + +
56M LEU* 4.2 12.8 - - + -
105M MET* 3.8 18.8 - - + -
108M TRP* 4.9 3.1 - - + -
111M TRP* 4.0 15.7 - - + +
115M CYS* 3.7 7.6 - - - -
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Residues in contact with ALA 32 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8M LEU* 3.5 32.1 - - + -
12M MET* 4.2 5.6 - - + -
28M TRP 3.1 12.9 + - - +
29M VAL 3.3 4.2 + - - +
31M ALA* 1.3 74.4 - - - +
33M LYS* 1.3 67.5 + - - +
36M SER* 3.0 26.7 + - - -
37M ASN 3.2 1.7 + - - -
38M PHE* 3.5 3.8 + - + -
55M ILE* 3.6 27.4 - - + +
56M LEU* 4.2 3.3 - - + +
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Residues in contact with LYS 33 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29M VAL 3.0 9.4 + - - +
30M CYS 3.1 8.7 + - - +
32M ALA* 1.3 74.7 - - - +
34M PHE* 1.3 77.8 + - + +
37M ASN* 2.8 54.4 + - - +
38M PHE* 3.6 38.7 - - + -
123M TRP* 3.7 28.3 - - + -
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Residues in contact with PHE 34 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30M CYS* 3.1 29.6 + - - +
31M ALA 4.3 0.7 - - - +
33M LYS* 1.3 96.4 - - + +
35M GLU* 1.3 63.8 + - - +
37M ASN 4.7 0.2 - - - -
110M ALA* 3.5 29.5 - - + +
114M ARG* 3.3 68.0 - - + -
115M CYS* 4.0 0.7 - - - -
123M TRP* 3.6 32.3 - + - -
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Residues in contact with GLU 35 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31M ALA* 2.8 30.9 + - - +
32M ALA* 4.5 0.2 - - - -
34M PHE* 1.3 76.3 - - - +
36M SER* 1.3 58.1 + - - +
44M ASN* 4.4 6.1 + - - -
52M ASP* 5.5 1.0 - - - +
55M ILE 4.2 8.5 - - - +
56M LEU* 4.7 1.3 - - - -
57M GLN* 3.3 44.3 - - + +
108M TRP* 3.4 32.4 - - + +
109M VAL* 3.3 12.4 + - - +
110M ALA* 2.9 34.2 + - + +
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Residues in contact with SER 36 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32M ALA 3.0 9.4 + - - -
35M GLU* 1.3 77.6 - - - +
37M ASN* 1.3 70.6 + - - +
38M PHE 3.2 8.0 + - - -
39M ASN* 3.1 31.2 + - - +
42M ALA* 3.8 12.8 - - - +
54M GLY 3.5 17.7 - - - -
55M ILE* 2.9 31.8 + - - +
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Residues in contact with ASN 37 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2M VAL* 4.3 9.2 - - - +
33M LYS* 2.8 53.0 + - - +
34M PHE 4.7 0.2 - - - -
35M GLU 3.8 0.2 - - - -
36M SER* 1.3 80.0 - - - +
38M PHE* 1.3 71.5 + - - +
39M ASN* 3.3 4.8 + - + +
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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