Contacts of the helix formed by residues 15 - 25 (chain D) 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 GLY 15 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D ASP 4.4 0.2 + - - -
12D GLY 3.6 9.6 + - - -
13D ALA 3.1 5.8 - - - -
14D VAL* 1.3 78.8 - - - +
16D LYS* 1.3 63.0 + - - +
17D THR* 3.2 5.1 + - - -
18D CYS* 3.4 28.8 + - - +
19D LEU* 3.8 9.0 + - - +
115D THR* 4.4 3.9 - - - +
116D LYS* 4.9 8.0 - - - -
159D ALA* 5.2 0.5 - - - +
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Residues in contact with LYS 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1539B VAL* 5.3 2.7 - - - -
8D VAL* 3.1 21.3 + - + +
9D VAL* 3.9 18.6 - - - +
10D GLY* 4.0 16.2 + - - +
11D ASP 4.6 10.5 - - - +
12D GLY* 5.8 2.9 - - - +
14D VAL* 3.3 9.0 - - + -
15D GLY* 1.3 76.1 - - - +
17D THR* 1.3 70.3 + - - +
19D LEU* 3.2 27.0 + - + +
20D LEU* 3.4 12.7 + - - +
57D ASP* 3.5 13.7 - - - +
58D THR* 2.5 50.5 + - - +
59D ALA 4.7 0.2 - - - -
60D GLY 4.6 3.6 - - - +
81D CYS* 4.3 18.6 - - - -
115D THR* 5.5 0.2 - - - -
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Residues in contact with THR 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1539B VAL* 3.3 13.0 - - - +
1540B MET* 4.1 17.0 - - - -
15D GLY* 3.2 1.7 - - - -
16D LYS* 1.3 81.9 - - - +
18D CYS* 1.3 67.5 + - - +
20D LEU* 3.1 7.5 + - - +
21D ILE* 3.1 31.3 + - + +
40D TYR* 3.7 20.0 - - + +
57D ASP* 2.6 33.6 + - - +
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Residues in contact with CYS 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D GLY* 3.8 21.1 - - - +
16D LYS 3.2 0.8 - - - -
17D THR* 1.3 81.0 - - - +
19D LEU* 1.3 57.4 + - - +
21D ILE* 4.2 3.2 - - - +
22D SER* 2.4 35.0 + - - -
32D TYR* 3.1 35.4 - - + +
159D ALA* 3.9 17.5 - - + -
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Residues in contact with LEU 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D GLY 3.8 8.7 + - - +
16D LYS* 3.2 17.6 + - + +
17D THR 3.1 0.2 - - - -
18D CYS* 1.3 80.3 - - - +
20D LEU* 1.3 65.4 + - + +
22D SER* 3.3 2.2 + - - -
23D TYR* 3.1 24.3 + - - +
79D LEU* 6.4 1.1 - - + -
81D CYS* 5.1 7.6 - - - -
113D VAL* 4.3 12.8 - - + -
115D THR* 4.7 13.7 - - + +
157D CYS* 3.8 24.9 - - - -
159D ALA* 3.5 33.2 - - + +
165D LEU* 3.8 24.2 - - + +
168D VAL* 5.5 3.4 - - + -
169D PHE* 4.3 12.5 - - + -
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Residues in contact with LEU 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D VAL* 3.8 32.8 - - + -
16D LYS 3.4 15.0 - - - +
17D THR* 3.1 3.9 + - - +
19D LEU* 1.3 77.3 - - + +
21D ILE* 1.3 59.2 + - - +
24D THR* 2.7 37.2 + - - +
40D TYR* 3.7 22.9 - - + -
55D LEU* 4.1 15.9 - - + -
57D ASP* 3.8 43.3 - - + +
79D LEU* 5.2 0.4 - - + -
169D PHE* 4.0 26.7 - - + -
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Residues in contact with ILE 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1540B MET* 5.7 2.2 - - + -
17D THR* 3.1 27.5 + - + +
18D CYS* 4.3 3.4 - - - +
20D LEU* 1.3 75.5 - - - +
22D SER* 1.3 58.1 + - - +
24D THR* 3.4 4.7 + - - -
25D THR* 2.4 50.6 + - + +
32D TYR* 4.4 23.8 - - + -
33D ILE 3.8 17.9 - - - +
34D PRO* 4.2 21.8 - - + -
35D THR* 4.8 2.2 - - + +
40D TYR* 3.6 37.7 - - + +
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Residues in contact with SER 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1370B ARG* 5.1 0.2 + - - -
18D CYS 2.4 23.7 + - - -
19D LEU 3.8 2.9 - - - -
21D ILE* 1.3 79.0 - - - +
23D TYR* 1.3 61.7 + - - +
25D THR* 4.2 2.2 - - - -
26D ASN* 3.1 3.5 + - - -
27D ALA* 3.0 34.3 + - - +
28D PHE 5.7 0.4 - - - -
29D PRO 5.7 0.6 + - - -
32D TYR* 3.6 19.8 - - - -
159D ALA* 4.2 9.8 + - - +
162D GLN* 3.7 23.0 - - - +
165D LEU* 4.0 11.4 - - - -
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Residues in contact with TYR 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1370B ARG* 2.3 69.4 + - - +
1372B GLU* 4.9 1.6 - - - -
19D LEU 3.1 8.5 + - - +
20D LEU 4.1 2.5 - - - +
22D SER* 1.3 77.4 - - - +
24D THR* 1.3 66.2 + - + +
26D ASN 3.2 3.1 + - - -
42D ALA* 4.5 3.6 - - + -
44D VAL* 3.5 28.9 - - + +
53D LEU* 4.3 13.4 - - + +
55D LEU* 4.6 3.6 - - + -
165D LEU* 4.3 9.3 - - + +
166D LYS* 4.0 27.4 - - + +
169D PHE* 3.4 62.6 - + + +
170D ASP* 4.2 12.1 + - - -
173D ILE* 5.3 0.3 - - - +
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Residues in contact with THR 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1370B ARG* 4.3 5.2 + - - +
20D LEU 2.7 26.1 + - - +
21D ILE* 3.4 8.1 + - - -
23D TYR* 1.3 80.6 - - + +
25D THR* 1.3 69.5 + - - +
26D ASN* 3.2 1.1 + - - +
40D TYR* 3.4 33.5 - - + +
41D SER 3.9 21.0 - - - +
42D ALA* 4.4 9.0 - - + +
55D LEU* 3.8 20.2 - - + -
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Residues in contact with THR 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1410B THR* 5.2 4.5 - - - +
21D ILE* 2.4 37.5 + - + +
24D THR* 1.3 87.0 + - - +
26D ASN* 1.3 72.3 + - - +
27D ALA* 3.3 15.8 + - - +
32D TYR* 5.0 0.7 - - - +
33D ILE 5.8 2.1 + - - +
40D TYR* 6.2 0.9 - - + -
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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