Contacts of the strand formed by residues 24 - 30 (chain H) in PDB entry 2R92
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 CYS 24 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15H VAL* 3.7 23.1 - - + -
16H ASP 3.1 11.0 - - - +
17H PRO* 3.3 36.1 - - - -
20H TYR 5.0 2.0 - - - -
23H VAL* 1.3 80.8 - - - +
25H ARG* 1.3 56.1 + - - +
26H ILE* 4.0 2.8 + - + +
41H ASP* 3.5 1.1 - - - -
42H ILE* 2.7 40.0 + - - +
44H VAL* 3.4 24.5 - - + +
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Residues in contact with ARG 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A ARG* 3.2 21.4 - - - +
598A LEU* 2.9 48.9 + - - +
600A PRO* 3.2 33.8 + - - +
14H GLU 4.2 0.7 - - - +
15H VAL* 3.9 0.2 - - - -
16H ASP* 3.0 39.4 + - + +
24H CYS* 1.3 74.7 - - - +
26H ILE* 1.3 65.1 + - - +
27H GLU* 5.4 4.0 - - + -
39H THR* 3.7 25.7 - - + +
40H LEU 4.1 4.3 - - - -
41H ASP* 2.8 30.6 + - - +
122H LEU* 4.2 0.6 - - - +
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Residues in contact with ILE 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H VAL* 3.4 27.8 - - + -
14H GLU 3.7 2.9 - - - +
15H VAL* 3.3 28.7 - - + -
24H CYS* 4.6 6.3 - - + +
25H ARG* 1.3 80.9 - - - +
27H GLU* 1.3 82.4 + - - +
28H ALA* 4.6 2.2 - - + +
38H LEU* 3.9 0.7 - - - +
39H THR* 3.2 4.3 - - - +
40H LEU* 2.7 46.8 + - + +
42H ILE* 5.3 13.0 - - + -
44H VAL* 5.5 1.3 - - + -
49H VAL* 3.3 38.8 - - + -
55H LEU* 5.8 2.5 - - + -
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Residues in contact with GLU 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H VAL* 3.6 1.9 - - - -
13H SER* 2.7 45.1 + - - +
14H GLU* 3.5 15.6 + - - +
25H ARG* 5.4 3.4 - - + -
26H ILE* 1.3 85.5 - - - +
28H ALA* 1.3 54.2 + - - +
38H LEU* 3.0 8.1 - - - +
39H THR* 3.5 31.3 + - + +
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Residues in contact with ALA 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H PHE* 3.6 12.3 - - + -
11H GLN 2.8 39.0 - - - +
12H VAL* 3.5 6.7 - - + +
13H SER* 4.0 4.3 - - - +
26H ILE* 4.6 2.9 - - + +
27H GLU* 1.3 75.0 - - - +
29H ALA* 1.3 59.2 + - - +
37H LYS* 4.0 1.6 - - - +
38H LEU* 3.0 37.9 + - + +
55H LEU* 6.4 0.9 - - + -
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Residues in contact with ALA 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H PHE* 2.8 34.1 - - - +
11H GLN* 3.2 12.0 + - + +
13H SER* 5.5 1.0 - - - -
28H ALA* 1.3 75.2 - - - +
30H SER* 1.3 64.7 + - - +
31H THR* 5.2 0.2 + - - -
36H CYS 4.1 3.8 - - - +
37H LYS* 4.9 4.3 - - + +
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Residues in contact with SER 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H ASP* 2.7 28.5 + - - -
9H ILE 3.7 4.9 - - - -
10H PHE* 4.1 2.0 - - - -
29H ALA* 1.3 79.7 - - - +
31H THR* 1.3 59.2 + - - +
32H THR* 3.2 16.0 + - - -
33H GLN* 3.7 16.3 + - - +
34H ASP* 5.4 2.6 - - - +
36H CYS* 3.2 38.5 + - - +
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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