Contacts of the helix formed by residues 21 - 33 (chain T) 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 ASN 21 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21T THR* 1.3 83.2 + - - -
216T SER 3.0 2.8 - - - +
217T LEU* 3.4 22.8 + - + +
218T SER 4.4 3.6 + - - +
219T GLY* 1.3 59.0 + - - +
220T LEU* 3.2 15.8 + - + +
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Residues in contact with GLY 219 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21T ASN* 1.3 77.9 + - - +
73T HIS* 3.5 18.2 - - - +
141T VAL* 4.3 16.9 - - - +
215T CYS* 3.3 21.2 - - - -
216T SER 3.0 18.0 + - - -
217T LEU* 3.8 6.0 - - - +
220T LEU* 1.3 61.7 + - - +
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Residues in contact with LEU 220 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21T ASN* 2.8 58.6 + - + +
72T ARG* 3.5 29.2 - - + +
73T HIS* 5.1 1.8 - - + -
214T TRP 3.8 0.5 - - - +
215T CYS* 3.8 2.0 - - - -
219T GLY* 1.3 87.5 - - - +
221T HIS* 1.3 66.0 + - - +
222T LYS* 3.4 10.3 + - + +
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Residues in contact with HIS 221 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48T PHE* 4.4 7.2 - + - -
67T ILE* 3.7 9.6 - - + +
68T GLN 4.5 1.1 - - - -
69T VAL* 3.8 27.0 - - + +
72T ARG 3.3 8.7 + - - +
73T HIS* 4.1 2.4 - - - +
74T ILE 3.9 23.3 - - - +
75T GLY* 3.3 29.0 - - - -
213T SER* 3.0 33.3 + - - -
214T TRP 3.5 9.9 - - - -
215T CYS* 3.8 10.1 - - + -
220T LEU* 1.3 72.2 - - - +
222T LYS* 1.3 66.2 + - - +
223T PHE* 3.7 30.4 - + - -
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Residues in contact with LYS 222 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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711 ASP* 5.4 5.1 + - - -
21T THR* 3.7 36.6 - - - +
213T SER* 3.2 4.3 - - - -
214T TRP* 2.8 39.9 + - + +
220T LEU* 3.4 19.1 - - + +
221T HIS* 1.3 83.9 + - - +
223T PHE* 1.3 67.6 + - - +
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Residues in contact with PHE 223 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65T VAL* 3.5 26.7 - - + -
67T ILE* 3.4 42.2 - - + -
68T GLN* 5.0 0.7 - - - -
69T VAL* 5.5 7.0 - - + -
211T GLU* 3.8 11.2 - - + -
212T ILE 3.8 13.7 - - - +
213T SER* 4.0 2.5 - - - -
214T TRP* 4.8 2.6 + - - -
221T HIS* 3.7 18.4 - + - -
222T LYS* 1.3 81.2 - - - +
224T VAL* 1.3 64.3 + - - +
225T LYS* 3.3 28.8 + - + +
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Residues in contact with VAL 224 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190T VAL* 4.2 13.9 - - + -
212T ILE* 3.0 48.2 + - + +
213T SER* 3.8 6.5 - - - +
214T TRP* 4.0 22.2 - - + +
223T PHE* 1.3 72.8 - - - +
225T LYS* 1.3 60.9 + - - +
228T LEU* 3.8 22.4 - - + -
229T LEU* 3.7 46.5 - - + +
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Residues in contact with LYS 225 (chain T).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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691 PRO* 4.7 13.5 + - - +
711 ASP* 6.1 2.5 - - - -
223T PHE* 3.3 28.5 + - + +
224T VAL* 1.3 78.9 - - - +
226T GLY* 1.3 69.8 + - - +
227T ASP 3.4 1.6 + - - -
228T LEU* 3.6 7.8 + - - +
229T LEU* 3.6 13.2 + - - -
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Residues in contact with GLY 226 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225T LYS* 1.3 75.0 - - - +
227T ASP* 1.3 64.2 + - - -
229T LEU* 3.0 12.3 + - - +
230T GLN* 2.9 23.5 + - - +
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Residues in contact with ASP 227 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225T LYS 3.4 1.2 + - - -
226T GLY* 1.3 70.4 - - - -
228T LEU* 1.3 66.9 + - - +
229T LEU 3.0 0.2 + - - -
230T GLN* 3.1 7.2 + - - +
231T GLU* 2.8 28.7 + - - +
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Residues in contact with LEU 228 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187T ARG* 3.1 32.5 - - + +
190T VAL* 4.7 11.8 - - + +
191T LYS* 6.4 1.1 - - + -
214T TRP* 3.5 40.4 - - + +
224T VAL* 3.8 23.8 - - + +
225T LYS 3.6 6.5 + - - +
226T GLY 3.5 0.6 - - - -
227T ASP* 1.3 77.3 - - - +
229T LEU* 1.3 61.6 + - - +
231T GLU* 3.7 20.2 - - + +
232T ALA* 3.3 21.7 + - - +
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Residues in contact with LEU 229 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62T GLN* 4.4 19.3 - - - +
210T LEU* 4.7 17.3 - - + +
211T GLU* 5.5 0.2 - - - -
212T ILE* 4.4 28.0 - - + +
224T VAL* 3.7 28.6 - - + +
225T LYS* 3.6 14.8 + - - -
226T GLY* 3.0 12.1 + - - +
227T ASP 3.0 0.6 - - - -
228T LEU* 1.3 77.1 - - - +
230T GLN* 1.3 61.2 + - - +
232T ALA* 3.0 6.6 + - - +
233T ILE* 2.8 52.1 + - + +
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Residues in contact with GLN 230 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226T GLY 2.9 12.9 + - - +
227T ASP* 3.7 9.6 - - - +
229T LEU* 1.3 75.7 - - - +
231T GLU* 1.3 63.1 + - - +
233T ILE* 3.1 27.1 + - - +
234T ASP* 2.9 59.7 + - - +
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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