Contacts of the strand formed by residues 30 - 35 (chain B) in PDB entry 1TAD
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 VAL 30 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ARG* 4.2 12.8 - - - +
29B THR* 1.3 81.2 - - - +
31B LYS* 1.3 66.4 + - - +
32B LEU* 3.6 3.3 + - + +
190B LEU* 4.0 28.5 - - + -
191B ASN 2.9 10.8 + - - +
192B PHE* 3.6 16.6 - - + -
193B ARG* 2.8 30.0 + - - +
215B THR* 3.7 22.0 - - + -
216B CYS 5.1 0.2 - - - +
339B ILE* 3.9 37.7 - - + -
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Residues in contact with LYS 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LEU* 4.0 17.4 - - - +
60A GLU* 2.8 28.9 + - - +
29B THR* 4.2 3.0 + - + +
30B VAL* 1.3 70.8 - - - +
32B LEU* 1.3 61.7 + - - +
33B LEU* 4.4 4.0 - - - -
193B ARG* 3.4 9.0 - - + -
195B PHE* 3.9 20.4 - - + -
210B CYS* 2.9 28.2 + - - +
212B GLU 2.8 28.7 + - - +
213B GLY 3.7 19.1 - - - +
214B VAL* 3.7 8.2 - - + +
215B THR* 2.8 35.6 + - - +
216B CYS 3.3 6.8 + - - +
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Residues in contact with LEU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B VAL* 3.6 3.5 + - + -
31B LYS* 1.3 74.9 - - - +
33B LEU* 1.3 75.5 + - - +
34B LEU* 4.3 2.5 - - + +
192B PHE* 4.1 20.2 - - + -
193B ARG 2.9 10.5 + - - +
194B MET* 3.3 32.3 - - + -
195B PHE* 2.8 29.6 + - - -
216B CYS* 3.4 14.8 - - - +
218B ILE* 3.8 24.5 - - + -
332B PHE* 3.9 31.0 - - + -
335B VAL* 4.9 0.7 - - + -
339B ILE* 4.4 12.6 - - + -
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Residues in contact with LEU 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LYS* 4.2 5.4 + - - -
32B LEU* 1.3 78.0 - - - +
34B LEU* 1.3 61.6 + - - +
35B LEU* 3.8 19.9 + - + -
195B PHE* 3.6 30.7 - - + +
210B CYS* 3.7 27.6 - - + +
211B PHE* 3.8 24.7 - - + -
214B VAL* 3.8 25.1 - - + -
216B CYS 3.0 8.0 + - - +
217B ILE* 3.4 7.5 - - + +
218B ILE 2.9 26.9 + - - +
255B PHE* 4.7 2.9 - - + -
354B CAC 4.1 14.1 - - + +
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Residues in contact with LEU 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B LEU* 4.2 2.9 + - + +
33B LEU* 1.3 70.5 - - - +
35B LEU* 1.3 69.7 + - - +
42B LYS* 3.4 38.5 - - + +
45B ILE* 4.2 13.5 - - + -
46B VAL* 3.5 20.6 - - + -
194B MET* 4.0 22.2 - - + -
195B PHE 2.8 15.3 + - - +
196B ASP* 3.8 19.9 - - + -
197B VAL* 4.1 2.4 + - - +
218B ILE* 3.6 26.0 - - + +
220B ILE* 3.6 28.9 - - + -
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Residues in contact with LEU 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B LEU* 3.8 14.6 + - + -
34B LEU* 1.3 85.6 - - - +
36B GLY* 1.3 60.2 + - - +
42B LYS* 3.7 5.8 - - - -
197B VAL* 4.3 6.7 - - + -
207B TRP* 4.1 22.0 - - + -
211B PHE* 4.3 10.8 - - + -
217B ILE* 4.1 20.0 - - + -
218B ILE 3.0 9.0 + - - +
219B PHE* 3.4 15.1 - - + -
220B ILE* 2.8 30.0 + - - +
249B ILE* 3.9 39.0 - - + -
354B CAC 4.0 20.9 - - - +
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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