Contacts of the strand formed by residues 49 - 58 (chain A) in PDB entry 4JDA
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 THR 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A ARG* 4.5 2.9 + - - +
46A SER* 2.7 51.9 + - - +
47A PRO 3.9 3.1 - - - +
48A ASN* 1.3 84.2 - - - +
50A CYS* 1.3 59.8 + - - +
51A THR* 4.3 0.7 + - - -
173A ILE* 3.8 23.6 - - + +
174A VAL 3.3 7.6 - - - +
175A ASP* 4.0 17.9 - - - +
176A ILE* 3.6 10.2 - - - +
182A GLU* 3.6 12.3 - - - +
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Residues in contact with CYS 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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49A THR* 1.3 75.1 - - - +
51A THR* 1.3 63.9 + - - +
172A TYR* 4.1 9.3 - - - -
173A ILE* 3.3 5.2 - - - +
174A VAL* 2.8 47.3 + - + +
176A ILE* 4.0 12.8 - - + -
182A GLU* 3.8 18.2 - - + -
185A THR* 4.1 5.6 - - - -
186A ARG* 3.5 47.3 - - - -
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Residues in contact with THR 51 (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* 3.7 31.0 + - - +
45A ARG* 5.9 7.4 - - + -
49A THR 4.2 1.2 + - - -
50A CYS* 1.3 75.8 - - - +
52A SER* 1.3 65.8 + - - +
172A TYR* 2.8 20.4 + - - -
173A ILE* 4.6 9.6 - - - -
182A GLU* 5.3 2.4 + - - +
186A ARG* 3.7 14.4 + - - -
45C ARG* 4.1 17.8 + - - +
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Residues in contact with SER 52 (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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51A THR* 1.3 82.0 + - - +
53A LEU* 1.3 74.8 + - - +
171A SER* 3.2 5.8 - - - -
172A TYR* 3.0 59.0 + - - +
186A ARG* 3.9 11.2 - - - +
190A ASP* 3.0 20.2 + - - -
45C ARG* 5.2 7.8 - - - +
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Residues in contact with LEU 53 (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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23A TYR* 5.6 11.9 - - + +
25A LEU* 6.3 1.1 - - + -
37A ILE* 3.6 42.8 - - + -
41A HIS* 4.5 11.4 - - + -
52A SER* 1.3 82.1 + - - +
54A ILE* 1.3 85.1 + - - +
55A ALA* 4.0 10.5 - - + +
169A LEU* 4.5 11.9 - - + -
170A GLU 3.6 5.8 - - - +
171A SER* 4.0 11.4 - - - +
45C ARG* 5.9 0.6 - - - +
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Residues in contact with ILE 54 (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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53A LEU* 1.3 85.2 - - - +
55A ALA* 1.3 66.8 + - - +
56A HIS* 5.2 0.7 - - + -
168A VAL 3.9 0.5 - - - +
169A LEU* 3.6 0.7 - - - -
170A GLU* 2.8 38.2 + - - +
172A TYR* 5.4 2.7 - - + -
190A ASP* 3.9 39.0 - - + +
193A VAL* 4.7 8.1 - - + -
194A LYS* 4.1 26.2 - - + +
197A LEU* 3.8 22.5 - - + +
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Residues in contact with ALA 55 (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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23A TYR 3.4 26.3 + - - +
24A GLY* 6.0 0.5 - - - -
25A LEU* 3.6 22.0 - - + -
53A LEU* 4.0 5.1 - - + +
54A ILE* 1.3 79.5 - - - +
56A HIS* 1.3 63.5 + - - +
57A ARG* 4.4 2.3 + - - +
167A VAL* 4.6 2.0 - - + -
168A VAL 3.4 4.5 - - - -
169A LEU* 3.8 15.3 - - + -
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Residues in contact with HIS 56 (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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54A ILE* 4.3 1.1 - - + -
55A ALA* 1.3 75.6 - - - +
57A ARG* 1.3 89.3 + - - +
58A VAL* 3.8 4.8 + - + +
167A VAL* 4.5 2.0 - - - +
168A VAL* 2.8 44.2 + - + +
194A LYS* 5.2 12.1 - - + -
197A LEU* 3.7 49.5 + - + -
198A GLN* 3.3 38.9 + - - -
201A ALA* 4.1 10.3 - - + -
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Residues in contact with ARG 57 (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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24A GLY 3.0 26.6 + - - -
25A LEU* 3.9 5.9 - - + +
26A THR* 4.0 11.6 - - - +
29A GLU* 2.9 37.8 + - - -
55A ALA 5.8 2.0 + - - +
56A HIS* 1.3 94.3 + - - +
58A VAL* 1.3 61.5 + - - +
59A ASP* 5.7 3.4 - - - +
165A TYR* 3.9 18.4 - - + -
166A SER 3.3 7.4 - - - +
167A VAL* 4.2 15.7 - - + +
201A ALA* 4.8 1.0 - - - +
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Residues in contact with VAL 58 (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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56A HIS* 4.3 5.4 - - - +
57A ARG* 1.3 78.8 - - - +
59A ASP* 1.3 65.0 + - - +
60A ALA* 2.9 14.2 + - + -
65A ILE* 3.4 29.2 - - + -
165A TYR* 3.5 2.5 - - - +
166A SER 2.9 32.5 + - - +
168A VAL* 4.1 15.5 - - + -
197A LEU 4.9 2.0 - - - +
200A LEU* 5.2 1.6 - - + -
201A ALA* 3.8 36.8 - - + +
204A SER* 3.6 21.5 - - - +
205A THR* 4.9 0.9 - - - -
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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
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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