Contacts of the strand formed by residues 42 - 46 (chain H) in PDB entry 5A0Q
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 PHE 42 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14H LEU* 5.2 2.3 - - + +
34H LEU 3.4 12.8 - - - +
35H THR 3.9 3.4 - - - +
36H PRO* 3.4 24.9 - - + -
37H ILE* 4.0 1.1 - - - +
38H HIS 3.0 28.3 - - - -
39H ASP* 3.3 21.3 - - - -
40H ARG 3.6 3.0 + - - -
41H ILE* 1.3 73.7 - - - +
43H CYS* 1.3 62.6 + - - +
44H CYS* 4.1 5.1 + - - -
101H ALA* 3.6 26.4 + - - +
177H ALA* 5.4 2.0 - - + -
179H ILE* 3.7 21.4 - - + +
184H VAL* 4.3 20.6 - - + -
186H ARG* 2.9 44.6 - - - -
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Residues in contact with CYS 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H LYS 4.2 0.9 - - - -
34H LEU* 3.0 29.5 - - - +
35H THR* 3.2 11.4 + - - +
37H ILE* 3.6 30.0 - - + +
42H PHE* 1.3 72.6 - - - +
44H CYS* 1.4 61.9 + - - +
45H ARG* 5.2 0.4 - - - -
52H THR* 4.9 2.2 - - - -
56H ALA* 4.1 10.1 - - + -
83H PHE* 3.6 19.3 - - - -
98H ILE* 3.1 39.7 - - - -
99H ILE 4.5 2.5 - - - -
100H ILE* 4.6 4.5 - - - +
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Residues in contact with CYS 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H ILE* 3.7 28.5 - - + -
14H LEU* 3.5 37.9 - - - -
33H LYS 3.4 9.4 - - - +
34H LEU* 3.6 12.3 - - + -
42H PHE* 4.4 3.1 - - - -
43H CYS* 1.4 78.2 - - - +
45H ARG* 1.4 61.3 + - - +
98H ILE* 3.3 10.6 - - - +
99H ILE* 3.1 42.1 + - - +
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Residues in contact with ARG 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1H THR* 4.3 1.0 - - - +
3H ILE* 3.3 22.2 - - - +
20H THR* 4.5 1.6 - - - +
31H THR* 3.3 31.7 - - - +
32H ASP 3.8 8.5 + - - -
33H LYS* 3.7 29.7 + - + +
35H THR* 3.9 15.0 + - - +
43H CYS* 5.2 0.9 - - - -
44H CYS* 1.4 76.9 - - - +
46H SER* 1.3 60.8 + - - +
49H ALA* 3.9 10.9 - - - +
52H THR* 3.5 45.1 - - + +
53H GLN* 4.0 21.1 + - - +
97H GLY 3.3 6.1 - - - +
98H ILE* 4.3 1.8 - - + +
300H KNM 2.5 38.6 - - + +
120I ASP* 5.6 0.2 + - - -
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Residues in contact with SER 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1H THR* 4.4 0.2 - - - -
3H ILE* 4.4 8.5 - - - -
45H ARG* 1.3 75.5 - - - +
47H GLY* 1.3 71.7 + - - +
48H SER 4.8 0.9 - - - -
52H THR* 4.0 6.6 + - - -
96H ALA* 3.3 4.7 - - - -
97H GLY* 2.4 45.6 + - - +
116H MET* 5.9 1.0 - - - -
128H GLY* 4.4 1.8 - - - -
129H GLY* 3.5 35.1 + - - -
300H KNM 3.8 17.9 - - - +
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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
------------------------------------------------------------
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