Contacts of the strand formed by residues 30 - 35 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28C ARG* 4.1 9.2 - - - +
29C THR* 1.3 80.5 - - - +
31C LYS* 1.3 60.1 + - - +
32C LEU* 3.2 30.8 + - + +
190C LEU* 3.8 41.3 - - + -
191C ASN 2.7 11.5 + - - +
192C PHE* 3.5 12.7 - - + +
193C ARG* 2.8 29.6 + - - +
215C THR* 3.6 19.3 - - + -
339C ILE* 4.1 12.8 - - + -
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Residues in contact with LYS 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C THR* 4.2 3.8 + - + +
30C VAL* 1.3 70.4 - - - +
32C LEU* 1.3 61.3 + - - +
33C LEU* 3.8 15.5 - - + -
193C ARG* 3.5 8.5 - - + -
195C PHE* 4.0 25.6 - - + -
209C HIS 5.4 0.4 + - - -
210C CYS* 2.8 33.3 + - - +
212C GLU* 2.7 31.2 + - - +
213C GLY 3.7 19.5 - - - +
214C VAL* 3.7 5.3 - - - +
215C THR* 2.8 34.2 + - - +
216C CYS 3.2 7.4 + - - +
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Residues in contact with LEU 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C VAL* 3.2 35.9 + - + -
31C LYS* 1.3 72.1 - - - +
33C LEU* 1.3 67.1 + - - +
34C LEU* 6.3 0.4 - - + -
192C PHE* 3.6 17.0 - - + -
193C ARG 2.9 8.1 + - - +
194C MET* 3.3 31.0 - - + +
195C PHE* 2.8 27.7 + - - -
216C CYS* 3.3 21.3 - - + +
218C ILE* 3.7 32.3 - - + -
332C PHE* 4.0 12.1 - - + -
335C VAL* 5.0 0.7 - - + -
339C ILE* 3.7 11.0 - - + -
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Residues in contact with LEU 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C LYS* 3.8 19.1 - - - -
32C LEU* 1.3 79.2 - - - +
34C LEU* 1.3 59.7 + - - +
35C LEU* 3.8 12.9 + - + -
195C PHE* 3.5 17.9 - - + +
210C CYS* 3.6 32.8 - - + +
211C PHE* 3.7 28.3 - - + -
214C VAL* 3.9 19.5 - - + +
216C CYS 3.0 7.2 + - - +
217C ILE* 3.5 5.6 - - + +
218C ILE* 2.8 33.7 + - - +
255C PHE* 4.4 6.7 - - + -
354C CAC 4.2 11.4 - - + +
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Residues in contact with LEU 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LEU* 6.3 0.2 - - + -
33C LEU* 1.3 71.4 - - - +
35C LEU* 1.3 66.9 + - - +
42C LYS* 3.5 29.3 - - + +
45C ILE* 4.1 14.6 - - + -
46C VAL* 3.5 32.5 - - + -
194C MET* 3.8 24.9 - - + -
195C PHE 2.9 14.0 + - - +
196C ASP* 4.0 19.4 - - + -
197C VAL* 4.1 2.6 + - - +
218C ILE* 3.5 28.7 - - + -
220C ILE* 3.6 26.5 - - + -
354C CAC 5.9 0.2 - - - +
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Residues in contact with LEU 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C LEU* 4.4 15.9 - - + -
34C LEU* 1.3 82.5 - - - +
36C GLY* 1.3 53.2 + - - +
42C LYS* 3.8 7.0 - - - -
197C VAL* 4.1 7.6 - - + -
207C TRP* 3.9 22.4 - - + -
211C PHE* 4.2 13.5 - - + -
217C ILE* 4.1 17.3 - - + -
218C ILE 2.9 9.5 + - - +
219C PHE* 3.2 14.3 - - + -
220C ILE* 2.7 35.2 + - - +
249C ILE* 4.0 36.8 - - + -
255C PHE* 4.8 0.2 - - + -
354C CAC 3.8 23.3 - - + +
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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