Contacts of the strand formed by residues 49 - 58 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45D ARG* 5.1 0.2 - - - -
46D SER* 2.8 53.7 + - - +
47D PRO 3.4 9.2 - - - +
48D ASN* 1.3 80.4 - - - +
50D CYS* 1.3 63.1 + - - +
173D ILE* 4.1 15.6 - - + +
174D VAL 3.4 9.4 - - - +
175D ASP* 4.1 18.4 - - - +
176D ILE* 3.0 15.7 - - - +
182D GLU* 4.7 6.4 - - - +
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Residues in contact with CYS 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D THR* 1.3 78.3 - - - +
51D THR* 1.3 62.6 + - - +
172D TYR* 4.2 8.8 - - - -
173D ILE* 3.3 4.7 - - - +
174D VAL* 2.9 43.4 + - + +
176D ILE* 3.7 18.8 - - + -
182D GLU* 4.0 12.6 - - + +
185D THR* 4.1 5.2 - - - -
186D ARG* 3.7 47.3 - - - +
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Residues in contact with THR 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D PHE* 3.6 30.1 + - + +
50D CYS* 1.3 77.7 - - - +
52D SER* 1.3 67.1 + - - +
172D TYR* 2.5 25.0 + - - -
173D ILE* 3.9 10.0 - - - +
182D GLU* 5.7 0.2 + - - -
186D ARG* 3.9 15.6 + - - +
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Residues in contact with SER 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D THR* 1.3 81.3 + - - +
53D LEU* 1.3 63.2 + - - +
54D ILE* 4.2 2.0 - - - +
171D SER* 3.4 3.6 - - - -
172D TYR* 2.8 47.1 + - - +
186D ARG* 3.7 17.0 - - - +
190D ASP* 2.8 30.2 + - - -
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Residues in contact with LEU 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D TYR 4.6 22.8 + - - +
37D ILE* 3.7 39.0 - - + -
41D HIS* 4.8 4.9 - - + -
52D SER* 1.3 76.3 - - - +
54D ILE* 1.3 103.0 + - - +
55D ALA* 4.2 4.8 + - + +
169D LEU* 3.9 22.4 - - + -
170D GLU 3.4 10.8 - - - +
171D SER* 4.1 13.5 - - - +
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Residues in contact with ILE 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D SER* 4.2 5.6 - - - +
53D LEU* 1.3 87.3 - - - +
55D ALA* 1.3 66.6 + - - +
56D HIS* 4.9 2.5 - - + -
168D VAL 3.8 0.5 - - - +
169D LEU* 3.4 0.7 - - - -
170D GLU 2.8 35.8 + - - +
172D TYR* 4.9 4.0 - - + -
190D ASP* 3.4 40.2 - - + +
193D VAL* 3.8 20.9 - - + -
194D LYS* 4.1 29.4 - - + -
197D LEU* 3.4 25.6 - - + +
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Residues in contact with ALA 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D TYR 5.6 2.4 - - - +
24D GLY* 4.7 25.6 - - - +
25D LEU* 5.2 8.1 - - + +
53D LEU* 4.6 4.0 - - + -
54D ILE* 1.3 77.4 - - - +
56D HIS* 1.3 62.5 + - - +
57D ARG 4.3 0.6 + - - -
167D VAL* 4.3 13.2 - - + -
168D VAL 3.3 8.5 - - - +
169D LEU* 4.5 9.9 - - + -
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Residues in contact with HIS 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C THR* 5.8 0.7 - - + -
54D ILE* 4.9 2.0 - - + -
55D ALA* 1.3 75.6 - - - +
57D ARG* 1.3 77.5 + - - +
58D VAL* 3.5 9.7 - - - +
167D VAL* 4.4 2.8 - - - +
168D VAL* 3.1 29.3 + - + +
194D LYS* 5.4 5.8 - - + -
197D LEU* 3.7 39.0 + - + +
198D GLN* 3.3 44.4 + - + -
201D ALA* 3.9 22.1 - - + +
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Residues in contact with ARG 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D GLY 3.8 8.9 + - - -
25D LEU* 3.8 19.2 - - - +
26D THR* 4.0 13.7 + - - +
29D GLU* 3.0 36.9 + - - -
55D ALA 4.3 0.4 - - - -
56D HIS* 1.3 90.3 + - - +
58D VAL* 1.3 58.8 + - - +
59D ASP* 4.3 6.4 + - - +
165D TYR* 3.9 25.8 - - + -
166D SER 3.7 3.6 - - - -
167D VAL* 4.1 11.1 - - + +
201D ALA* 5.0 0.3 - - - +
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Residues in contact with VAL 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D HIS* 3.5 20.6 - - - +
57D ARG* 1.3 77.4 - - - +
59D ASP* 1.3 63.3 + - - +
60D ALA* 2.8 17.5 + - + +
65D ILE* 3.7 25.1 - - + -
165D TYR* 3.3 2.6 - - - +
166D SER 2.9 33.7 + - - +
168D VAL* 3.7 22.2 - - + -
197D LEU* 5.3 1.3 - - + +
200D LEU* 5.7 1.3 - - + -
201D ALA* 3.9 35.0 - - + +
204D SER* 4.0 8.5 - - - +
205D THR* 4.6 0.2 - - - +
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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