Contacts of the strand formed by residues 45 - 51 (chain D) in PDB entry 3TDD
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 GLY 45 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42D THR* 2.8 35.5 + - - +
43D LYS 3.5 1.0 - - - -
44D GLU* 1.3 82.0 - - - +
46D VAL* 1.3 64.6 + - - -
47D VAL 4.4 0.2 + - - -
146D TYR* 3.4 13.4 - - - -
186D LEU* 4.1 7.5 - - - +
215D ILE 3.4 15.0 - - - -
216D THR* 4.2 3.1 - - - -
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Residues in contact with VAL 46 (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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40D ILE 3.3 17.3 - - - +
41D ALA* 3.8 15.9 - - + -
45D GLY* 1.3 78.8 - - - +
47D VAL* 1.3 69.8 + - - +
48D LEU* 5.6 0.2 - - - +
139D ALA* 3.5 28.7 - - + -
140D GLY 4.3 2.9 - - - +
146D TYR* 3.5 27.6 - - + -
147D GLN 3.9 14.1 - - - +
148D LEU* 4.2 9.4 - - + -
214D CYS* 3.0 25.3 - - - +
215D ILE* 3.1 17.0 + - + +
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Residues in contact with VAL 47 (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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38D ILE 3.8 0.6 - - - +
39D GLY* 3.1 5.9 - - - -
40D ILE 2.8 35.7 + - - +
45D GLY 5.5 0.2 - - - +
46D VAL* 1.3 73.6 - - - +
48D LEU* 1.3 69.1 + - - +
186D LEU* 3.5 29.2 - - + -
189D ALA* 4.0 15.5 - - + -
190D GLU* 3.9 23.3 - - + -
193D VAL* 3.8 25.1 - - + +
212D LEU* 3.9 20.2 - - + -
213D SER 3.4 9.4 - - - +
214D CYS* 4.3 4.7 - - + -
224D TYR* 5.6 0.7 - - - +
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Residues in contact with LEU 48 (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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38D ILE 3.4 2.2 - - - +
39D GLY* 3.8 7.2 - - - -
46D VAL* 4.3 0.9 + - + +
47D VAL* 1.3 86.6 - - - +
49D GLY* 1.3 58.3 + - - +
67D ILE* 3.7 5.8 - - + +
75D GLY* 4.0 2.2 - - - +
76D CYS* 3.8 35.2 - - - +
77D ALA* 3.8 21.1 - - + +
137D LEU* 4.0 8.7 - - + +
139D ALA* 3.8 29.4 - - + -
148D LEU* 3.8 16.6 - - + -
212D LEU* 3.5 1.7 - - - -
213D SER* 2.8 51.3 + - - +
214D CYS* 5.6 0.9 - - - -
215D ILE* 5.9 2.0 - - + -
221D PHE* 4.7 6.1 - - + -
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Residues in contact with GLY 49 (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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37D ALA* 3.4 0.2 - - - -
38D ILE* 2.7 37.9 + - - +
48D LEU* 1.3 75.2 - - - +
50D VAL* 1.3 65.5 + - - +
67D ILE* 4.3 0.4 - - - -
77D ALA* 5.1 0.3 - - - +
193D VAL* 3.9 18.4 - - - +
197D LEU* 4.1 8.1 - - - +
211D GLN 3.1 11.0 - - - -
212D LEU* 4.0 2.9 - - - -
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Residues in contact with VAL 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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35D SER* 6.3 0.2 - - - -
36D THR 3.5 7.2 - - - +
37D ALA* 4.0 10.1 - - + -
49D GLY* 1.3 79.4 - - - +
51D GLU* 1.3 63.8 + - - +
52D LYS* 4.8 4.7 - - + +
64D ILE* 6.5 0.2 - - + -
66D LYS* 3.9 25.6 - - + +
67D ILE* 3.5 36.3 - - + -
77D ALA* 3.8 18.4 - - + -
78D MET 4.7 1.6 - - - +
197D LEU* 3.9 10.8 - - - +
210D ALA* 3.4 4.5 - - - -
211D GLN* 2.9 44.6 + - + +
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Residues in contact with GLU 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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20D ASN 3.8 3.6 - - - -
35D SER* 3.2 15.0 - - - -
36D THR* 2.9 43.8 + - - +
50D VAL* 1.3 70.7 - - - +
52D LYS* 1.3 68.3 + - - +
53D ARG* 3.0 51.1 + - + +
66D LYS* 3.6 5.7 + - - +
167D SER* 4.3 0.3 + - - -
197D LEU* 4.2 4.5 - - + +
200D VAL 5.5 0.5 - - - +
201D MET* 3.8 43.5 - - + +
202D GLU* 4.8 10.2 + - - +
205D GLU* 5.7 2.6 + - - +
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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