Contacts of the helix formed by residues 9 - 19 (chain C) in PDB entry 5TIN
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 9 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8C MET* 1.3 76.9 - - - +
10C PRO* 1.3 74.8 - - - +
11C SER* 3.7 8.6 + - - -
12C ASP* 3.2 31.2 + - - +
13C PHE* 3.0 18.7 + - - +
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Residues in contact with PRO 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ILE* 3.7 29.8 - - + -
32B PHE* 3.5 40.4 - - + -
8C MET 3.6 3.3 - - - +
9C SER* 1.3 85.4 - - - +
11C SER* 1.3 56.6 + - - +
13C PHE* 3.1 4.4 + - + +
14C LEU* 2.9 43.0 + - + +
78C TYR* 3.9 12.6 - - + +
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Residues in contact with SER 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLY 5.3 2.1 + - - -
25B ASP* 2.9 36.3 + - - +
27B ARG* 4.2 9.5 + - - +
28B ILE* 4.0 6.1 - - - +
9C SER* 3.2 7.8 + - - -
10C PRO* 1.3 79.3 - - - +
12C ASP* 1.3 66.2 + - - +
14C LEU* 3.5 2.1 + - - +
15C ASP* 3.0 22.7 + - - +
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Residues in contact with ASP 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C MET* 3.8 21.9 - - + +
9C SER* 3.2 23.6 + - - +
11C SER* 1.3 81.6 - - - +
13C PHE* 1.3 57.0 - - - +
15C ASP* 3.2 9.6 + - - +
16C LYS* 2.9 30.0 + - - +
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Residues in contact with PHE 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C MET* 3.9 16.3 - - - +
9C SER 3.0 6.5 + - - +
10C PRO* 3.1 8.0 + - + +
12C ASP* 1.3 76.7 - - - +
14C LEU* 1.3 72.0 + - + +
16C LYS* 3.1 3.9 + - + +
17C LEU* 2.9 59.8 + - + +
75C TYR* 3.6 32.5 - + + -
77C GLU* 3.8 23.1 - - + -
78C TYR* 3.4 39.0 - + - +
83C LEU* 3.6 26.7 - - + -
85C LEU* 5.6 0.7 - - + -
120C ILE* 4.8 1.1 - - + -
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Residues in contact with LEU 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B ASP* 5.3 0.9 - - - +
27B ARG* 3.8 48.0 - - + +
28B ILE* 6.2 1.6 - - + -
10C PRO* 2.9 29.1 + - + +
11C SER 4.0 2.9 - - - +
13C PHE* 1.3 85.6 - - + +
15C ASP* 1.3 62.8 + - - +
17C LEU* 4.4 2.7 - - + +
18C MET* 3.1 27.3 + - + +
19C GLY* 3.0 18.8 + - - -
85C LEU* 4.2 35.4 - - + -
86C ASP* 6.3 1.1 - - + +
89C MET* 4.5 11.2 - - + -
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Residues in contact with ASP 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ARG* 5.7 0.2 - - - +
11C SER 3.0 14.6 + - - +
12C ASP* 3.3 14.8 - - - +
14C LEU* 1.3 76.3 - - - +
16C LYS* 1.3 58.7 + - - +
19C GLY* 3.2 29.2 + - - -
20C ARG* 3.4 26.0 + - - +
21C THR* 2.8 38.6 + - - +
22C SER 3.4 2.6 + - - -
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Residues in contact with LYS 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C MET* 4.3 15.5 - - + -
12C ASP 2.9 16.4 + - - +
13C PHE* 3.1 4.2 + - + +
15C ASP* 1.3 76.5 - - - +
17C LEU* 1.3 58.2 + - - +
21C THR* 3.6 13.9 - - - +
22C SER* 3.1 19.2 - - - +
77C GLU* 6.0 2.0 - - - +
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Residues in contact with LEU 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C PHE* 2.9 44.6 + - + +
14C LEU* 4.2 3.1 - - - +
15C ASP 3.3 0.2 - - - -
16C LYS* 1.3 79.1 - - - +
18C MET* 1.3 77.1 + - + +
22C SER* 3.4 9.0 - - - -
24C TYR* 3.9 14.4 - - - +
72C ARG 3.6 23.0 - - - +
73C LEU* 4.0 14.6 - - + +
74C ALA 3.9 17.5 - - - +
75C TYR* 5.0 0.4 - - + -
120C ILE* 3.7 30.5 - - + -
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Residues in contact with MET 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C LEU* 3.1 18.5 + - + +
17C LEU* 1.3 104.0 - - + +
19C GLY* 1.3 60.2 + - - +
22C SER* 3.2 11.6 + - - -
24C TYR* 4.0 14.2 - - + +
73C LEU* 4.0 14.6 - - + -
85C LEU* 4.0 20.0 - - + -
89C MET* 4.0 37.0 - - - +
92C SER* 4.0 26.0 + - - +
93C ILE* 3.9 26.9 - - + -
118C LEU* 5.7 0.7 - - + -
120C ILE* 4.8 2.2 - - + -
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Residues in contact with GLY 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C LEU 3.0 12.3 + - - -
15C ASP* 3.2 10.7 + - - -
18C MET* 1.3 78.4 - - - +
20C ARG* 1.3 66.4 + - - +
21C THR 3.3 2.5 - - - -
22C SER* 2.6 23.4 + - - -
23C GLY 4.3 1.0 + - - -
24C TYR 5.5 0.3 - - - +
92C SER* 5.9 0.7 - - - -
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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