Contacts of the strand formed by residues 43 - 53 (chain C) in PDB entry 2H5X
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 GLU 43 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C ARG* 4.0 26.9 + - + +
7C GLY* 3.3 27.7 - - - -
8C GLU* 3.5 5.5 + - - +
42C THR* 1.3 88.1 - - + +
44C ALA* 1.3 63.2 + - - +
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Residues in contact with ALA 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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5C VAL 3.6 1.7 - - - +
6C ARG* 3.1 6.0 - - - -
7C GLY 2.9 31.6 + - - +
9C VAL* 3.6 24.9 - - + -
19C ILE* 3.9 8.9 - - + +
38C LEU* 4.4 22.0 - - + -
42C THR* 5.9 0.2 - - - -
43C GLU* 1.3 79.3 - - - +
45C ARG* 1.3 61.8 + - - +
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Residues in contact with ARG 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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8B GLU* 5.5 1.2 + - - -
10B LEU* 3.8 24.7 - - - +
20B GLU* 3.0 33.5 + - - -
4C SER* 4.3 15.7 - - - -
5C VAL 3.3 7.6 - - - +
6C ARG* 3.7 32.3 - - + +
19C ILE* 6.3 0.2 - - - -
38C LEU* 5.4 2.9 - - - +
44C ALA* 1.3 77.9 - - - +
46C LEU* 1.3 82.4 + - - +
47C ILE* 4.7 10.4 - - + +
63C PRO* 5.8 0.7 - - - +
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Residues in contact with LEU 46 (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 SER* 3.2 4.6 - - - -
5C VAL* 3.0 32.0 + - + +
17C VAL* 4.0 20.6 - - + -
19C ILE* 5.1 7.2 - - + -
28C VAL* 3.7 26.7 - - + -
30C ALA* 4.8 2.9 - - + -
34C THR* 3.8 22.4 - - + -
38C LEU* 4.8 13.9 - - + -
45C ARG* 1.3 84.2 - - - +
47C ILE* 1.3 67.5 + - - +
48C THR* 3.3 5.7 + - + +
61C GLY* 3.6 5.6 - - - -
62C PHE 3.3 31.9 - - - +
63C PRO* 4.3 3.8 - - + -
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Residues in contact with ILE 47 (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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3C ALA 3.6 6.5 - - - +
4C SER* 4.2 5.4 - - - -
45C ARG* 4.7 13.2 - - + +
46C LEU* 1.3 74.9 - - - +
48C THR* 1.3 57.9 + - - +
60C TYR 3.5 0.5 - - - +
61C GLY* 3.2 1.6 - - - -
62C PHE* 2.7 42.2 + - - +
63C PRO 3.8 18.6 - - - +
64C ASP* 3.9 6.1 - - - +
65C GLY* 3.8 19.7 - - - +
68C ARG* 3.1 50.9 - - + +
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Residues in contact with THR 48 (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 ILE* 2.9 35.7 + - - +
3C ALA* 2.8 21.6 + - - +
4C SER 3.3 2.1 + - - -
5C VAL* 4.3 16.4 - - + +
28C VAL* 4.1 13.9 - - + -
46C LEU* 3.4 17.9 - - + +
47C ILE* 1.3 76.1 - - - +
49C ALA* 1.3 59.8 + - - +
59C LEU* 4.0 12.8 - - + -
60C TYR 2.9 11.7 - - - +
61C GLY* 3.9 9.2 - - - -
68C ARG* 3.0 24.6 + - - -
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Residues in contact with ALA 49 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48C THR* 1.3 73.2 - - - +
50C MET* 1.3 61.0 + - - +
51C ILE* 4.8 1.1 - - + -
59C LEU* 4.5 1.3 - - - -
60C TYR* 2.8 40.2 + - - +
62C PHE* 4.4 0.2 - - + -
68C ARG* 3.9 13.5 - - + +
71C PHE* 3.8 31.6 - - + -
72C LEU* 3.8 19.5 - - + -
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Residues in contact with MET 50 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B MET* 5.4 3.1 - - - +
1C MET* 4.0 33.3 + - + +
2C ILE* 3.3 55.2 + - + +
49C ALA* 1.3 70.9 - - - +
51C ILE* 1.3 64.9 + - - +
52C VAL* 3.7 22.3 + - + +
57C MET* 4.6 15.0 - - + +
58C THR 3.5 7.4 - - - +
59C LEU* 3.7 12.1 - - + -
1D MET* 3.2 35.0 - - + +
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Residues in contact with ILE 51 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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49C ALA 4.2 1.6 - - - +
50C MET* 1.3 76.8 - - - +
52C VAL* 1.3 62.4 + - - +
53C ARG* 3.7 40.3 + - + +
56C SER* 4.0 1.9 + - - +
57C MET* 3.5 2.9 - - - -
58C THR* 2.8 37.2 + - - +
60C TYR* 3.4 31.6 - - + -
71C PHE* 4.4 6.3 - - + -
72C LEU* 4.6 10.8 - - + -
75C LEU* 3.9 24.5 - - + -
82C PRO* 4.3 16.6 - - + -
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Residues in contact with VAL 52 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53B ARG 4.8 2.5 - - - +
54B GLU 3.9 9.6 - - - +
55B ASP* 3.0 14.5 + - - +
56B SER* 3.9 25.8 - - - +
57B MET* 4.1 28.5 - - + +
1C MET 6.0 0.7 - - - +
50C MET* 3.7 23.1 + - + +
51C ILE* 1.3 75.7 - - - +
53C ARG* 1.3 88.1 + - - +
56C SER 3.9 2.2 - - - -
57C MET* 4.3 24.7 - - + +
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Residues in contact with ARG 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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54B GLU 3.6 8.4 - - - +
55B ASP* 3.6 32.3 + - - +
51C ILE* 3.7 34.3 + - + +
52C VAL* 1.3 95.3 + - - +
54C GLU* 1.3 67.5 + - - +
55C ASP 3.4 1.6 - - - +
56C SER* 2.9 38.9 + - - +
75C LEU* 5.7 5.7 - - - +
82C PRO* 5.2 8.9 - - - +
52D VAL* 4.4 4.2 - - - +
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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