Contacts of the strand formed by residues 37 - 45 (chain C) in PDB entry 2Y05
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 VAL 37 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32C LEU* 3.5 8.0 - - - +
35C GLY 5.0 0.2 - - - +
36C GLU* 1.3 79.5 - - - +
38C LEU* 1.3 59.4 + - - +
39C LEU* 3.6 27.4 - - + -
71C VAL* 3.9 10.5 - - + -
73C GLU 3.4 7.9 - - - +
74C SER* 3.7 20.6 - - - +
76C ASN* 4.0 6.5 - - + -
79C LEU* 3.7 29.6 - - + +
95C SER 3.8 0.2 - - - +
96C ILE* 3.4 5.9 - - - -
97C SER* 2.8 44.9 + - - +
102C LEU* 4.2 10.1 - - + -
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Residues in contact with LEU 38 (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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2C SER* 4.2 18.4 - - - +
29C LEU* 3.8 24.7 - - + -
32C LEU* 3.7 9.0 - - + +
37C VAL* 1.3 71.5 - - - +
39C LEU* 1.3 63.1 + - - +
71C VAL* 3.6 4.5 - - - -
72C VAL* 3.0 44.5 + - + +
73C GLU* 2.9 34.1 + - + +
94C HIS* 4.6 12.3 - - + -
95C SER 3.3 20.0 - - - +
96C ILE* 4.0 9.6 - - + -
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Residues in contact with LEU 39 (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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37C VAL* 3.6 25.4 - - + -
38C LEU* 1.3 75.4 - - - +
40C GLU* 1.3 59.8 + - - +
41C ALA 4.2 0.4 - - - -
67C GLN* 4.9 1.6 - - - +
69C ALA* 4.1 8.3 - - + -
70C LYS 3.6 3.1 - - - +
71C VAL* 3.8 23.8 - - + -
72C VAL* 4.8 0.2 - - - -
85C VAL* 3.9 16.8 - - + -
87C ALA* 3.9 17.0 - - + -
93C THR 3.9 0.2 - - - +
94C HIS* 3.1 11.3 - - - +
95C SER* 2.7 53.2 + - - +
97C SER* 3.9 12.3 - - - -
102C LEU* 3.8 28.0 - - + -
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Residues in contact with GLU 40 (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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39C LEU* 1.3 73.8 - - - +
41C ALA* 1.3 75.3 + - - +
42C LEU* 3.3 12.8 + - + +
69C ALA* 4.0 2.5 - - - -
70C LYS* 3.0 37.4 + - + +
72C VAL* 3.9 25.5 - - + +
93C THR 3.5 5.2 - - - +
94C HIS* 3.0 33.8 + - + +
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Residues in contact with ALA 41 (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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39C LEU 4.2 0.2 - - - -
40C GLU* 1.3 81.4 - - - +
42C LEU* 1.3 60.4 + - - +
44C LEU* 4.1 22.2 - - + -
67C GLN* 3.3 29.2 + - + +
68C VAL 3.9 2.9 - - - -
69C ALA* 4.3 0.2 - - - +
92C THR 3.7 18.8 - - - +
93C THR* 2.9 15.7 + - - +
329C ALA* 3.6 15.7 - - + +
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Residues in contact with LEU 42 (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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40C GLU* 3.9 19.5 - - - +
41C ALA* 1.3 77.1 - - - +
43C PHE* 1.3 84.5 + - + +
68C VAL* 2.8 17.7 + - + +
70C LYS* 4.0 22.2 - - + +
84C ILE* 4.0 27.8 - - + -
115C LEU* 4.3 17.5 - - + -
328C LYS* 3.7 4.5 - - - +
329C ALA* 3.1 24.6 + - - +
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Residues in contact with PHE 43 (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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41C ALA 3.8 0.2 - - - -
42C LEU* 1.3 97.7 - - + +
44C LEU* 1.3 62.1 + - - +
67C GLN* 3.2 5.2 - - - +
68C VAL* 2.8 42.7 + - + -
114C PRO* 5.7 2.9 - - + -
115C LEU* 4.3 22.2 - - + -
116C SER* 3.8 26.5 - - - -
119C LEU* 3.5 15.0 - - + +
302C ILE* 5.4 5.6 - - + -
326C ILE* 3.7 23.6 - - + -
327C VAL 3.2 6.3 - - - +
328C LYS* 4.0 37.7 - - + -
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Residues in contact with LEU 44 (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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41C ALA* 4.1 17.7 - - + -
43C PHE* 1.3 79.1 - - - +
45C THR* 1.3 59.9 + - - +
66C GLN 3.9 7.2 - - - +
67C GLN* 4.1 11.7 - - + +
90C GLY 4.2 4.5 - - - +
92C THR 3.8 32.1 - - - +
119C LEU* 3.9 3.1 - - - -
306C PHE* 4.1 19.7 - - + -
309C MET* 3.7 30.7 - - + -
326C ILE* 3.7 4.2 - - - +
327C VAL* 2.8 51.9 + - + +
329C ALA* 4.1 14.4 - - + -
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Residues in contact with THR 45 (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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44C LEU* 1.3 75.3 - - - +
46C VAL* 1.3 58.1 + - - +
47C ASP* 2.6 27.2 + - - +
49C TYR* 5.7 0.4 - - - +
50C MET* 3.4 9.9 - - + +
65C GLY* 5.0 0.3 - - - -
66C GLN* 3.3 38.7 + - + +
91C TRP* 4.5 0.2 + - - -
119C LEU* 3.8 22.0 - - + +
309C MET* 3.4 15.8 - - - +
324C LYS* 2.7 32.0 + - - -
325C THR 4.1 5.4 - - - -
326C ILE* 4.6 0.4 - - - -
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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