Contacts of the strand formed by residues 49 - 57 (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 49 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45C MET* 3.2 3.6 - - - +
46C VAL 2.9 32.6 + - - +
47C ASP* 3.0 30.6 + - - +
48C GLY* 1.3 80.7 - - - +
50C PRO* 1.3 67.2 - - + +
51C VAL* 3.7 7.1 - - + +
177C LEU* 4.2 32.5 - - + +
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Residues in contact with PRO 50 (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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1368A TYR* 3.5 38.8 - - + +
-1C GLY* 6.1 2.0 - - - -
0C THR 4.3 17.2 - - - +
1C MET* 4.0 9.1 - - + -
2C GLN* 3.8 13.7 + - - +
44C VAL 3.3 5.8 - - - +
45C MET* 3.8 9.2 - - + -
48C GLY 3.9 5.6 - - - +
49C LYS* 1.3 89.2 - - + +
51C VAL* 1.3 64.2 + - - +
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Residues in contact with VAL 51 (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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1C MET* 4.2 6.4 - - - +
2C GLN* 3.0 36.1 - - + +
4C ILE* 3.7 24.5 - - + -
42C ALA 3.5 1.7 - - - +
43C ASN* 3.3 2.6 - - - -
44C VAL* 2.6 50.1 + - - +
46C VAL* 4.0 7.0 - - + -
49C LYS* 3.7 12.6 - - + +
50C PRO* 1.3 79.7 - - - +
52C ASN* 1.3 62.0 + - - +
53C LEU 3.5 1.4 + - - +
173C ILE* 3.9 29.6 - - + -
177C LEU* 5.1 4.7 - - + -
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Residues in contact with ASN 52 (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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1526A PRO* 3.6 31.4 - - - +
1C MET* 4.0 20.2 - - + +
2C GLN 3.0 12.4 + - - +
3C ALA* 3.5 6.9 - - + +
4C ILE 3.0 24.4 + - - -
41C SER* 4.3 11.5 - - - -
42C ALA 3.7 7.3 - - - +
43C ASN* 3.7 16.4 - - - +
51C VAL* 1.3 70.1 - - - +
53C LEU* 1.3 69.4 + - - +
54C GLY* 3.7 2.1 + - - -
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Residues in contact with LEU 53 (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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4C ILE* 3.7 22.2 - - + +
6C CYS* 4.0 26.0 - - + -
23C TYR* 4.3 19.7 - - + -
40C TYR 3.9 0.3 - - - +
41C SER* 3.2 4.7 - - - -
42C ALA* 2.7 45.0 + - + +
44C VAL* 4.6 5.8 - - + -
51C VAL* 3.5 2.3 + - + +
52C ASN* 1.3 73.5 - - - +
54C GLY* 1.3 59.0 + - - +
55C LEU* 3.9 30.1 - - + +
77C VAL* 5.8 0.7 - - + -
169C PHE* 4.5 8.7 - - + +
172C ALA* 5.8 2.7 - - + -
173C ILE* 4.2 31.9 - - + -
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Residues in contact with GLY 54 (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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1529A MET* 3.5 22.0 - - - -
4C ILE 2.9 14.5 + - - -
5C LYS* 4.9 1.3 - - - -
6C CYS* 2.9 34.3 + - - +
40C TYR 3.8 1.3 - - - -
41C SER* 4.5 2.2 - - - -
52C ASN* 3.7 3.6 + - - -
53C LEU* 1.3 72.7 - - - +
55C LEU* 1.3 61.1 + - - +
56C TRP* 4.0 3.4 - - - -
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Residues in contact with LEU 55 (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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1529A MET* 3.5 1.9 - - - -
6C CYS* 3.6 27.1 - - + +
8C VAL* 4.8 2.2 - - + -
20C LEU* 4.1 24.5 - - + -
23C TYR* 4.5 2.7 - - + -
24C THR* 3.7 28.0 - - + -
39C ASN* 3.4 5.0 + - - +
40C TYR* 2.7 41.0 + - + +
53C LEU* 3.9 26.7 - - + +
54C GLY* 1.3 78.6 - - - +
56C TRP* 1.3 64.0 + - - +
57C ASP 3.6 1.2 + - - -
169C PHE* 3.8 31.2 - - + -
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Residues in contact with TRP 56 (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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1525A ASN* 4.1 7.3 + - - +
1528A SER* 3.9 14.1 - - - -
1529A MET* 3.2 57.8 - - + +
1532A ASN* 4.5 10.8 - - + -
1598A PHE* 4.2 15.3 - + - -
5C LYS* 3.3 48.6 - - + +
6C CYS 2.9 21.3 + - - +
7C VAL* 3.9 17.3 - - + -
8C VAL* 2.9 33.4 + - - +
20C LEU* 4.5 0.2 - - - -
39C ASN* 3.0 12.1 - - - +
54C GLY* 4.0 5.3 - - - -
55C LEU* 1.3 71.4 - - - +
57C ASP* 1.3 61.4 + - - +
58C THR* 3.5 8.5 + - + +
71C SER* 3.7 30.1 - - - -
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Residues in contact with ASP 57 (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 23.6 - - - +
8C VAL* 4.5 1.6 - - - -
16C LYS* 3.5 21.7 + - - +
17C THR* 2.8 34.5 + - - +
20C LEU* 3.8 21.7 - - + +
38C ASP* 3.3 37.0 - - + +
39C ASN* 3.1 8.8 + - - +
40C TYR* 4.0 1.3 + - + -
55C LEU 3.6 1.4 + - - -
56C TRP* 1.3 68.1 - - - +
58C THR* 1.3 64.2 + - - +
59C ALA 4.0 0.2 + - - -
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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