Contacts of the helix formed by residues 16 - 25 (chain C) in PDB entry 2YIN
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 LYS 16 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1539A VAL* 5.7 1.8 - - - -
8C VAL* 3.3 45.4 + - + +
9C VAL* 4.3 9.8 - - - +
10C GLY* 3.9 20.7 + - - +
11C ASP 4.5 13.5 - - - +
12C GLY* 5.5 3.4 - - - +
14C VAL* 3.6 12.8 - - + -
15C GLY* 1.3 72.1 - - - +
17C THR* 1.3 69.1 + - - +
18C CYS 3.1 2.0 - - - -
19C LEU* 2.8 29.7 + - + +
20C LEU* 3.2 10.0 + - - +
57C ASP* 3.5 15.5 + - - +
58C THR* 2.6 33.1 + - - -
60C GLY* 4.7 3.0 - - - +
81C CYS* 5.0 6.7 - - + -
115C THR* 5.5 0.2 - - - -
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Residues in contact with THR 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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1539A VAL* 3.4 14.4 - - - +
1540A MET* 3.9 17.3 - - - -
15C GLY* 3.4 1.3 - - - -
16C LYS* 1.3 79.9 - - - +
18C CYS* 1.3 66.6 + - - +
20C LEU* 3.1 6.2 + - - +
21C ILE* 3.0 38.4 + - + +
40C TYR* 3.7 23.3 - - + +
57C ASP* 2.8 28.8 + - - +
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Residues in contact with CYS 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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15C GLY* 3.9 17.0 - - - +
16C LYS 3.1 0.8 - - - -
17C THR* 1.3 77.9 - - - +
19C LEU* 1.3 61.0 + - - +
21C ILE* 4.4 4.0 - - - +
22C SER* 2.5 33.1 + - - -
32C TYR* 2.8 36.3 - - + +
159C ALA* 3.8 20.2 - - + -
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Residues in contact with LEU 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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15C GLY 4.2 9.0 - - - +
16C LYS* 2.8 16.2 + - + +
18C CYS* 1.3 77.4 - - - +
20C LEU* 1.3 67.9 + - + +
22C SER* 3.8 2.4 - - - -
23C TYR* 3.1 24.6 + - - +
79C LEU* 6.4 1.1 - - + -
81C CYS* 4.6 10.5 - - - -
113C VAL* 4.3 13.5 - - + -
115C THR* 4.6 14.6 - - + +
157C CYS* 3.6 31.6 - - - -
159C ALA* 3.5 33.7 - - + +
165C LEU* 4.0 17.9 - - + +
168C VAL* 5.4 2.9 - - + -
169C PHE* 4.5 11.4 - - + -
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Residues in contact with LEU 20 (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 VAL* 3.8 34.8 - - + -
16C LYS 3.6 12.8 - - - +
17C THR* 3.1 4.8 + - - +
19C LEU* 1.3 79.3 - - + +
21C ILE* 1.3 57.9 + - - +
23C TYR* 3.9 0.3 - - - -
24C THR* 3.0 36.3 + - - +
40C TYR* 3.5 25.1 - - + -
55C LEU* 4.1 18.4 - - + -
57C ASP* 3.8 43.5 - - + +
79C LEU* 5.3 0.4 - - + -
169C PHE* 3.9 24.2 - - + -
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Residues in contact with ILE 21 (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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1540A MET* 5.3 2.2 - - + -
17C THR* 3.0 28.2 + - + +
18C CYS* 4.4 3.8 - - - +
20C LEU* 1.3 73.7 - - - +
22C SER* 1.3 60.0 + - - +
24C THR* 3.9 4.3 - - - -
25C THR* 2.5 51.2 + - + +
32C TYR* 4.8 18.8 - - + -
33C ILE 3.6 19.7 - - - +
34C PRO* 4.3 21.8 - - + -
35C THR* 4.7 3.8 - - + +
40C TYR* 3.4 37.5 - - + +
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Residues in contact with SER 22 (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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18C CYS 2.5 24.8 + - - -
19C LEU 3.8 2.7 - - - -
21C ILE* 1.3 77.3 - - - +
23C TYR* 1.3 64.3 + - - +
25C THR* 4.2 2.9 - - - -
26C ASN* 3.2 2.6 + - - -
27C ALA* 3.1 33.3 + - - +
28C PHE 5.9 0.2 - - - -
29C PRO 5.5 0.6 + - - -
32C TYR* 3.5 20.3 - - - -
159C ALA* 4.2 10.3 + - - +
162C GLN* 4.3 15.8 + - - +
165C LEU* 3.9 17.5 - - - -
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Residues in contact with TYR 23 (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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1370A ARG* 2.5 65.2 + - - +
1372A GLU* 5.5 0.4 - - - -
19C LEU 3.1 16.2 + - - +
20C LEU 3.9 1.8 - - - +
22C SER* 1.3 80.9 - - - +
24C THR* 1.3 67.2 + - + +
26C ASN 3.2 5.9 + - - -
42C ALA* 4.4 8.7 - - + -
44C VAL* 3.5 24.0 - - + +
53C LEU* 4.3 13.7 - - + -
55C LEU* 4.5 1.8 - - + -
162C GLN* 6.4 0.2 - - - -
165C LEU* 4.4 11.0 - - + -
166C LYS* 4.3 25.0 - - + +
169C PHE* 3.4 55.4 - + + +
170C ASP* 4.3 10.0 + - - -
173C ILE* 5.3 0.3 - - - +
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Residues in contact with THR 24 (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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1370A ARG* 4.3 4.7 + - - +
20C LEU 3.0 20.0 + - - +
21C ILE* 3.8 6.4 + - - -
23C TYR* 1.3 84.7 - - + +
25C THR* 1.3 63.3 + - - +
26C ASN* 3.3 1.6 + - - +
40C TYR* 3.5 31.7 - - + +
41C SER 3.9 18.9 - - - +
42C ALA* 4.2 14.8 - - + +
55C LEU* 3.7 21.5 - - + -
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Residues in contact with THR 25 (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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1410A THR* 5.4 3.1 - - - +
21C ILE* 2.5 37.7 + - + +
24C THR* 1.3 82.9 - - - +
26C ASN* 1.3 71.1 + - - +
27C ALA* 3.0 18.3 + - - +
32C TYR* 4.9 1.6 - - - +
33C ILE 5.4 3.0 + - - +
40C TYR* 6.0 1.3 - - + -
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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