Contacts of the helix formed by residues 3 - 12 (chain M) in PDB entry 1YIT
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 3 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2420 A 3.3 17.9 + - - -
2430 A 3.1 24.5 - - - -
3770 C 5.6 0.2 - - - -
34F ASN* 3.7 2.2 - - - -
37F THR* 4.6 0.9 - - - -
38F LYS* 3.3 7.4 - - - +
1M ALA 3.6 0.6 + - - -
2M ARG* 1.3 75.0 - - - +
4M ALA* 1.3 63.1 + - - +
5M TYR* 3.4 13.5 + - - +
6M SER* 2.6 46.2 + - - -
7M TYR* 3.2 9.1 - - - -
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Residues in contact with ALA 4 (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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33F THR* 4.0 11.4 - - + -
34F ASN* 2.7 44.1 + - + +
37F THR* 3.6 24.2 - - - +
59F ILE 5.3 0.9 - - - +
62F HIS* 4.2 5.1 + - + +
3M SER* 1.3 71.1 - - - +
5M TYR* 1.3 69.0 + - + +
7M TYR* 2.9 24.1 + - - +
8M ILE* 3.8 6.6 + - + +
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Residues in contact with TYR 5 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2420 A 3.5 33.2 + - - -
2430 A 5.1 1.1 - - - -
2460 G 5.9 0.2 + - - -
2630 U 5.5 0.4 - - - -
2640 G 2.8 48.1 + + - +
34F ASN* 4.2 21.9 + - + -
3M SER* 3.4 16.4 - - - +
4M ALA* 1.3 78.8 - - + +
6M SER* 1.3 53.3 + - - +
7M TYR 2.6 1.4 + - - -
8M ILE* 2.6 37.6 + - + +
9M ARG 3.1 8.5 + - - -
46M LEU* 3.9 16.4 - - + -
47M ASP* 3.8 26.7 - - + +
50M ARG* 3.4 31.1 + - - -
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Residues in contact with SER 6 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3780 A 4.8 3.4 - - - -
2M ARG* 3.3 27.6 + - - -
3M SER* 2.6 41.3 + - - -
5M TYR* 1.3 73.6 - - - +
7M TYR* 1.3 57.2 + - - +
9M ARG* 3.7 34.8 + - - +
10M ASP* 3.0 28.1 + - - +
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Residues in contact with TYR 7 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F THR* 3.8 9.4 - - + -
41F GLU* 2.9 27.2 + - - -
58F GLU 5.8 1.3 - - - +
61F MET* 5.6 0.8 - - - +
62F HIS* 3.5 46.0 - + + +
66F LEU* 3.6 26.4 - - + +
2M ARG* 3.3 43.3 + - + +
3M SER 3.2 26.9 - - - -
4M ALA* 2.9 11.3 + - - +
5M TYR 2.6 5.5 + - - -
6M SER* 1.3 76.8 + - - +
8M ILE* 1.3 64.1 + - - +
10M ASP* 3.8 2.4 - - + +
11M ALA* 2.9 25.1 + - - +
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Residues in contact with ILE 8 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F GLU* 3.9 40.6 - - + +
59F ILE* 4.4 18.6 - - + +
61F MET* 5.6 0.9 - - - -
62F HIS* 6.3 0.7 - - + +
4M ALA 4.3 3.4 - - - +
5M TYR* 2.6 27.5 + - + +
7M TYR* 1.3 72.4 - - + +
9M ARG* 1.3 62.2 + - - +
11M ALA* 3.1 13.4 + - - +
12M TRP* 3.2 20.0 + - + -
45M ARG* 4.2 14.1 - - - -
46M LEU* 3.5 34.5 - - + +
47M ASP* 3.2 20.4 - - - +
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Residues in contact with ARG 9 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2420 A 6.4 0.2 - - - -
3780 A 2.5 37.8 + - - -
3790 G 3.9 24.7 + - - -
3800 A 3.0 31.5 + - + +
5M TYR 3.1 4.2 + - - +
6M SER* 3.7 29.4 + - - +
8M ILE* 1.3 80.6 - - - +
10M ASP* 1.3 64.9 + - - +
12M TRP* 3.1 15.9 + - - +
13M GLU* 3.3 22.5 + - + +
45M ARG* 5.7 2.1 + - - +
47M ASP* 2.9 29.6 + - + +
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Residues in contact with ASP 10 (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 ARG* 4.0 18.0 + - - +
6M SER 3.0 19.4 + - - +
7M TYR* 3.8 4.5 - - + +
9M ARG* 1.3 78.9 - - - +
11M ALA* 1.3 62.3 + - - +
13M GLU* 3.4 34.7 + - - +
14M ASN* 4.5 4.0 + - - +
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Residues in contact with ALA 11 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F MET* 4.1 24.9 - - + -
7M TYR 2.9 17.9 + - - +
8M ILE 3.1 5.4 + - - +
10M ASP* 1.3 80.2 - - - +
12M TRP* 1.3 60.4 + - + +
13M GLU 3.2 1.8 + - - -
14M ASN* 3.4 16.1 + - - +
17M ASP 5.3 0.2 - - - +
20M LEU* 3.3 23.3 - - + +
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Residues in contact with TRP 12 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3800 A 3.8 9.0 + - - +
3810 G 5.2 6.3 - - - +
58F GLU* 3.5 28.2 + - + +
8M ILE* 3.2 24.0 + - + +
9M ARG* 3.1 10.5 + - - +
11M ALA* 1.3 74.9 - - + +
13M GLU* 1.3 58.9 + - - +
14M ASN 3.0 5.6 - - - -
15M PRO* 3.3 32.6 - - + +
20M LEU* 3.4 28.5 - - + +
24M GLN* 3.7 20.6 - - - -
27M ARG* 3.8 8.7 - - - -
44M THR* 4.1 3.4 - - + -
45M ARG* 3.6 53.8 + - + +
119M SER 4.3 1.1 - - - -
120M VAL* 3.6 43.3 - - + -
121M GLY* 4.1 3.8 - - - -
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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