Contacts of the strand formed by residues 44 - 50 (chain A) in PDB entry 2CR9
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 SER 44 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ALA* 4.1 9.9 - - - +
35A VAL* 4.4 1.6 - - - -
42A VAL* 3.1 26.7 + - - +
43A PHE* 1.3 77.2 - - - +
45A ALA* 1.3 59.8 + - - +
46A THR* 4.4 0.9 + - - -
61A LYS* 3.1 19.9 + - - -
62A LEU 3.6 4.5 - - - -
63A GLN* 4.0 15.3 + - - -
116A TRP* 4.4 1.4 - - - -
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Residues in contact with ALA 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A PHE 4.0 0.4 - - - -
44A SER* 1.3 73.6 - - - +
46A THR* 1.3 64.4 + - - +
47A LEU* 4.0 2.2 + - + +
61A LYS* 3.2 5.2 - - - +
62A LEU* 3.1 34.6 + - + +
104A PHE* 5.0 0.2 - - - -
108A TYR* 3.1 42.4 - - + +
116A TRP* 3.9 14.8 - - + -
130A PRO* 6.5 0.2 - - + -
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Residues in contact with THR 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A SER* 4.9 0.9 + - - -
45A ALA* 1.3 75.1 - - - +
47A LEU* 1.3 64.5 + - - +
59A TYR* 6.4 1.3 - - + -
60A TYR 4.0 1.8 - - - -
61A LYS* 3.2 36.4 + - + -
130A PRO* 3.6 4.8 - - - +
131A LEU* 2.9 45.6 + - + +
132A GLU* 4.3 11.7 + - + +
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Residues in contact with LEU 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ALA* 4.0 1.5 - - + +
46A THR* 1.3 79.8 - - - +
48A GLY* 1.3 59.1 + - - +
59A TYR* 3.8 3.1 - - - +
60A TYR* 2.8 46.2 + - + +
62A LEU* 6.3 0.2 - - + -
108A TYR* 3.4 45.5 - - + +
111A LYS* 4.0 18.8 - - + -
112A THR* 3.2 29.8 - - + -
128A PHE* 3.8 11.4 - - + -
129A TYR 3.0 27.1 - - - +
130A PRO* 3.6 7.2 - - + -
131A LEU* 3.5 12.3 - - - +
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Residues in contact with GLY 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LEU* 1.3 76.3 - - - +
49A LEU* 1.3 61.6 + - - +
50A VAL* 5.6 0.2 - - - -
58A SER 3.7 9.2 - - - -
59A TYR* 4.2 2.2 - - - -
60A TYR 4.5 0.2 - - - -
128A PHE* 4.1 2.4 - - - +
129A TYR* 2.8 45.0 + - - -
131A LEU* 3.3 20.7 - - - +
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A GLY* 1.3 71.2 - - - -
50A VAL* 1.3 64.6 + - - +
51A ASP* 5.5 2.5 - - + +
56A THR 4.3 0.2 - - - +
58A SER* 2.4 52.5 + - - +
123A LYS* 4.7 6.1 - - - +
126A LYS* 2.6 46.9 - - + +
127A LYS 2.8 19.3 - - - +
128A PHE* 3.1 34.0 - - + -
129A TYR* 4.2 12.1 - - + -
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Residues in contact with VAL 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A GLY 5.6 0.2 - - - -
49A LEU* 1.3 84.6 - - - +
51A ASP* 1.3 71.9 + - - +
52A ILE* 3.8 1.4 + - - +
55A GLY 5.0 2.0 - - - +
56A THR 3.1 15.5 - - - +
57A ASN* 3.5 29.2 - - + +
129A TYR* 3.7 19.2 + - + +
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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