Contacts of the strand formed by residues 41 - 47 (chain 2) 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 ILE 41 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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372 VAL* 2.9 42.8 + - + +
382 HIS* 3.0 27.6 + - + +
402 LYS* 1.3 83.5 - - - +
422 TRP* 1.3 63.3 + - - +
632 LEU* 4.6 0.7 - - + -
732 THR* 5.9 0.2 - - + -
742 PRO* 3.7 27.6 - - + +
752 SER 3.6 28.0 - - - +
762 THR* 4.0 12.1 - - + +
792 ALA* 3.5 22.2 - - + -
1012 VAL* 4.2 11.7 - - + -
1022 ALA 3.6 9.2 - - - +
1032 GLY* 4.9 0.4 - - - -
1042 TYR 5.8 0.9 - - - +
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Residues in contact with TRP 42 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142 LEU* 3.6 18.6 - - + -
342 LEU* 3.7 15.9 - - + -
352 THR 3.3 19.1 - - - -
362 ARG* 3.3 29.0 - - + +
372 VAL* 4.4 2.5 - - - +
382 HIS 3.9 0.7 - - - -
392 ASP 3.3 13.9 + - - -
412 ILE* 1.3 91.3 - - - +
432 CYS* 1.3 64.1 + - - +
1012 VAL* 3.7 5.9 - - - +
1022 ALA 2.8 30.1 + - - +
1762 VAL* 3.7 28.5 - - + -
1782 LEU* 3.9 19.6 - - + +
1842 VAL* 4.0 11.8 - - + +
1862 ARG* 3.6 31.2 - - + -
209M GLN* 3.8 4.3 - - - -
211M ILE* 3.7 34.5 - - + -
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Residues in contact with CYS 43 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142 LEU* 4.0 6.9 - - - +
332 LYS 3.5 0.7 - - - +
342 LEU* 3.4 6.2 - - - -
352 THR* 2.8 55.9 + - - -
372 VAL* 4.4 4.3 - - + -
422 TRP* 1.3 78.4 - - - +
442 CYS* 1.3 60.4 + - - +
452 ARG* 4.1 13.7 - - - -
562 ALA* 4.6 4.0 - - - -
832 PHE* 3.9 29.8 - - + -
992 ILE* 3.9 15.9 - - + -
1002 ILE 3.1 12.1 - - - +
1012 VAL* 4.5 0.7 - - - -
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Residues in contact with CYS 44 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32 ILE* 3.5 26.1 - - + +
42 MET 3.7 25.8 - - - -
52 ALA* 4.7 1.1 - - - -
142 LEU* 3.9 15.7 - - - -
152 GLY 4.0 4.9 - - - -
332 LYS 3.6 4.3 - - - -
342 LEU* 3.6 23.1 - - - -
432 CYS* 1.3 72.4 - - - +
452 ARG* 1.3 62.7 + - - +
992 ILE* 3.4 10.2 - - - +
1002 ILE* 2.7 39.9 + - + -
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Residues in contact with ARG 45 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12 THR* 3.3 18.9 + - - +
32 ILE* 3.7 6.4 - - - +
312 THR* 4.7 8.7 - - - +
322 ASP 3.0 26.7 + - - -
332 LYS* 3.1 27.6 + - + +
352 THR* 2.9 24.5 + - - +
432 CYS* 4.1 12.3 - - - -
442 CYS* 1.3 75.7 - - - +
462 SER* 1.3 59.1 + - - +
492 ALA* 4.2 8.9 + - - +
522 THR* 3.1 51.3 + - - +
532 GLN* 3.9 16.7 - - - +
562 ALA* 4.6 3.8 - - + -
982 GLY 4.1 1.1 - - - -
992 ILE* 4.9 4.5 - - + -
206M TYR* 3.4 27.4 - - - +
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Residues in contact with SER 46 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12 THR* 3.9 16.8 - - - -
32 ILE* 3.7 14.3 - - - +
452 ARG* 1.3 76.4 - - - +
472 GLY* 1.3 60.9 + - - +
522 THR* 3.3 13.1 - - - +
972 ALA* 3.5 0.2 - - - -
982 GLY* 2.5 54.5 + - - +
1272 ALA* 4.6 2.4 - - - +
1282 GLY* 4.2 17.8 + - - -
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Residues in contact with GLY 47 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12 THR* 4.5 7.2 + - - -
462 SER* 1.3 74.9 - - - +
482 SER* 1.3 64.8 + - - -
492 ALA* 3.5 2.3 + - - -
962 THR* 3.5 17.7 - - - -
972 ALA* 4.6 0.2 - - - -
982 GLY 4.7 0.4 - - - -
1152 LEU* 6.2 1.6 - - - -
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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