Contacts of the helix formed by residues 52 - 67 (chain C) in PDB entry 2Y4T
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 GLN 52 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B HIS* 3.0 34.3 + - - -
43B LEU* 4.4 0.7 - - + -
59B GLN* 3.0 30.9 + - - +
62B ALA* 4.5 4.2 - - - +
47C LEU* 2.7 36.8 + - + +
48C LEU 4.1 0.4 + - - -
50C ALA* 3.6 22.7 + - + +
51C GLY* 1.3 72.9 + - - +
53C LEU* 1.3 63.8 + - - +
54C ALA 3.5 2.0 - - - -
55C ASP* 3.6 6.0 + - - +
56C ALA* 3.1 23.7 + - - +
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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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48C LEU* 4.7 14.8 - - + +
51C GLY* 3.2 28.4 + - - +
52C GLN* 1.3 72.0 - - - +
54C ALA* 1.3 66.0 + - - +
56C ALA* 3.3 3.9 + - - +
57C LEU* 3.0 19.8 + - - +
80C VAL* 3.3 18.0 - - + +
83C ALA* 3.8 35.2 - - + +
84C MET* 3.8 30.7 - - + -
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Residues in contact with ALA 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B SER* 5.9 0.2 - - - +
52C GLN 3.5 0.2 - - - -
53C LEU* 1.3 77.9 - - - +
55C ASP* 1.3 64.0 - - - +
57C LEU* 3.3 21.5 - - - +
58C SER* 3.3 9.2 + - - -
84C MET* 3.6 23.3 - - + +
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Residues in contact with ASP 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ASP* 3.8 20.8 - - + +
58B SER* 2.7 38.7 + - - -
59B GLN* 2.9 22.0 - - - +
47C LEU* 3.8 18.5 - - + +
52C GLN* 3.6 8.0 + - - +
53C LEU 3.2 0.2 - - - -
54C ALA* 1.3 80.4 - - - +
56C ALA* 1.3 65.8 + - - +
57C LEU 3.3 0.2 - - - -
58C SER* 3.4 9.1 + - - +
59C GLN* 3.2 24.9 + - - +
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Residues in contact with ALA 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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44C GLY* 3.5 28.0 - - - +
47C LEU* 4.0 5.2 - - - +
48C LEU* 3.7 18.2 - - + +
52C GLN 3.1 18.6 + - - +
53C LEU* 3.6 5.4 - - - +
55C ASP* 1.3 76.7 - - - +
57C LEU* 1.3 56.8 + - - +
59C GLN* 3.0 5.0 + - - +
60C PHE* 2.9 34.6 + - + -
80C VAL* 4.1 10.5 - - + -
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Residues in contact with LEU 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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53C LEU 3.0 13.2 + - - +
54C ALA 3.3 11.9 - - - +
56C ALA* 1.3 72.7 - - - +
58C SER* 1.3 65.3 + - - +
60C PHE* 3.5 4.2 + - - +
61C HIS* 2.9 42.4 + - + +
77C ARG* 4.3 4.0 - - + -
80C VAL* 3.7 23.0 - - + +
81C PHE* 3.5 52.5 - - + +
84C MET* 4.2 20.4 - - + -
86C LYS* 6.0 2.7 - - + -
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Residues in contact with SER 58 (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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54B ALA* 6.0 0.3 - - - +
55B ASP* 3.2 32.5 + - - -
54C ALA 3.3 9.8 + - - -
55C ASP* 3.5 5.8 - - - -
56C ALA 3.3 0.8 - - - -
57C LEU* 1.3 77.9 - - - +
59C GLN* 1.3 59.5 + - - +
61C HIS* 3.2 9.6 + - - +
62C ALA* 2.9 27.0 + - - +
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Residues in contact with GLN 59 (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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47B LEU* 3.8 17.2 - - + +
52B GLN* 3.1 25.9 + - - +
55B ASP* 3.2 18.9 + - - +
40C HIS* 3.3 44.8 - - - +
43C LEU* 3.4 26.7 - - - +
44C GLY* 3.7 17.7 - - - +
47C LEU* 4.3 2.9 - - + -
55C ASP 3.2 10.7 + - - +
56C ALA 3.0 9.4 + - - +
58C SER* 1.3 82.1 + - - +
60C PHE* 1.3 58.1 + - - +
62C ALA* 3.3 2.6 + - - +
63C ALA* 2.9 22.2 + - - +
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Residues in contact with PHE 60 (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 LEU* 3.8 25.4 - - + -
44C GLY* 3.2 39.5 - - - -
45C LYS* 3.4 9.4 - - - -
48C LEU* 3.7 10.3 - - + -
56C ALA* 2.9 18.1 + - + +
57C LEU* 4.2 1.3 - - - +
59C GLN* 1.3 75.3 - - - +
61C HIS* 1.3 59.8 + - - +
63C ALA* 3.1 5.7 + - - +
64C VAL* 2.8 32.6 + - - +
73C ALA* 4.2 3.3 - - - +
76C ARG* 3.4 45.5 - - + -
77C ARG* 3.7 23.8 - - + +
80C VAL* 3.4 29.2 - - + -
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Residues in contact with HIS 61 (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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57C LEU* 2.9 37.6 + - + +
58C SER* 3.2 13.2 - - - +
60C PHE* 1.3 77.0 - - - +
62C ALA* 1.3 59.9 + - - +
64C VAL* 3.4 2.8 + - - +
65C ASP* 3.1 35.3 + - - +
77C ARG* 3.0 41.2 + - - +
81C PHE* 3.4 23.8 - + - -
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Residues in contact with ALA 62 (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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52B GLN* 4.8 2.2 - - - +
40C HIS* 3.5 36.6 + - + +
58C SER 2.9 12.2 + - - +
59C GLN* 3.3 12.1 - - - +
61C HIS* 1.3 75.7 - - - +
63C ALA* 1.3 56.6 + - - +
65C ASP* 3.2 8.1 + - - +
66C GLY* 2.9 27.9 + - - -
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Residues in contact with ALA 63 (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* 3.3 20.5 - - + +
40C HIS* 4.1 7.6 - - + +
41C LEU* 3.8 25.1 - - + +
59C GLN 2.9 14.0 + - - +
60C PHE* 3.4 13.9 - - - +
62C ALA* 1.3 76.4 - - - +
64C VAL* 1.3 59.9 + - - +
67C ASP 3.3 18.0 + - - +
73C ALA* 3.7 20.9 - - + +
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Residues in contact with VAL 64 (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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60C PHE 2.8 15.4 + - - +
62C ALA 3.3 0.2 - - - -
63C ALA* 1.3 71.1 - - - +
65C ASP* 1.3 67.5 + - - +
67C ASP 4.3 2.7 - - - -
68C PRO* 3.0 30.4 - - + +
73C ALA* 3.8 19.3 - - + +
74C TYR* 3.5 49.4 - - + +
77C ARG* 3.3 40.4 - - - +
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Residues in contact with ASP 65 (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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61C HIS* 3.1 23.0 + - - +
62C ALA* 3.7 7.5 - - - +
64C VAL* 1.3 85.0 - - - +
66C GLY* 1.3 62.3 - - - +
68C PRO* 3.8 8.6 - - - +
77C ARG* 4.9 2.3 + - - -
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Residues in contact with GLY 66 (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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34C MET* 5.8 1.9 - - - +
36C ASP* 5.2 4.8 - - - +
37C VAL* 3.4 22.2 - - - +
40C HIS* 6.3 0.4 - - - -
62C ALA 2.9 13.9 + - - -
64C VAL 3.3 0.2 - - - -
65C ASP* 1.3 78.7 - - - +
67C ASP* 1.3 61.2 + - - +
68C PRO* 3.9 2.5 - - - +
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Residues in contact with ASP 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C MET* 3.4 26.9 - - - +
37C VAL* 3.7 13.4 - - + +
63C ALA 3.3 9.8 + - - +
64C VAL* 3.2 5.5 - - - +
66C GLY* 1.3 78.9 - - - +
68C PRO* 1.4 55.7 - - - +
69C ASP* 2.8 30.5 + - - +
70C ASN* 2.8 44.6 + - + +
74C TYR* 4.2 1.7 - - - -
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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