Contacts of the helix formed by residues 204 - 213 (chain T) in PDB entry 5L4K
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 ARG 204 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165T GLU* 5.4 6.9 + - - -
198T PHE* 4.6 8.5 - - - -
199T LEU* 3.2 45.0 + - + +
202T GLN* 3.3 44.2 + - - +
203T ASN* 1.3 76.6 - - - +
205T VAL* 1.3 51.3 + - - +
206T ALA* 2.8 8.0 + - + -
207T GLU* 2.7 48.6 + - + +
208T PHE 3.5 5.0 + - - -
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Residues in contact with VAL 205 (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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300S LEU* 3.7 21.5 - - + -
199T LEU 4.6 1.5 + - - -
200T LEU* 5.3 2.7 - - + -
203T ASN* 3.7 2.6 - - - +
204T ARG* 1.3 73.8 - - - +
206T ALA* 1.3 62.6 + - + +
207T GLU 3.2 0.7 - - - -
208T PHE* 3.5 14.3 + - + -
209T HIS* 3.0 35.6 + - + -
233T GLU* 3.1 40.4 - - + +
236T LEU* 4.6 15.3 - - + -
237T MET* 4.5 7.9 - - + -
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Residues in contact with ALA 206 (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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299S GLN* 3.8 32.5 - - + +
300S LEU* 4.6 9.2 - - + -
204T ARG* 2.8 4.4 + - + +
205T VAL* 1.3 84.3 - - + +
207T GLU* 1.3 73.2 + - - +
209T HIS* 3.9 2.3 + - - +
210T THR* 3.7 21.3 + - - +
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Residues in contact with GLU 207 (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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265S ASP* 5.6 5.5 - - - +
268S GLU* 5.7 1.2 - - - +
269S LYS* 5.7 2.8 + - - -
299S GLN* 5.8 1.4 - - - +
199T LEU* 4.4 16.6 - - + -
204T ARG* 2.7 43.0 + - + +
206T ALA* 1.3 86.8 - - - +
208T PHE* 1.3 63.5 + - - +
209T HIS 3.1 2.9 - - - -
210T THR* 2.6 29.4 + - - +
211T GLU* 2.9 15.8 + - + +
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Residues in contact with PHE 208 (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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196T LEU* 3.8 44.2 - - + +
199T LEU* 4.4 15.5 - - + +
200T LEU* 3.6 26.0 - - + -
204T ARG 3.5 3.2 + - - +
205T VAL* 3.5 19.8 + - + +
207T GLU* 1.3 78.7 - - - +
209T HIS* 1.3 65.3 + + - +
211T GLU* 3.6 3.0 + - - +
212T LEU* 2.9 43.3 + - + +
229T PRO 3.7 25.6 - - - -
230T VAL* 3.8 14.8 - - + -
233T GLU* 3.7 30.5 - - + -
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Residues in contact with HIS 209 (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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298S ILE* 3.9 9.9 - - - +
300S LEU* 3.8 23.5 - - + +
393S THR* 4.4 5.5 - - + +
396S ILE* 6.4 0.2 - - + -
397S ARG* 3.2 50.6 + - + +
400S HIS* 5.6 0.6 - - - -
205T VAL* 3.0 28.4 + - + +
206T ALA 4.3 2.9 - - - +
207T GLU 3.1 0.8 - - - -
208T PHE* 1.3 81.8 - + - +
210T THR* 1.3 66.6 + - - +
212T LEU* 3.0 23.8 + - + +
213T GLU* 3.0 14.8 + - - +
233T GLU* 3.1 41.7 + - + -
234T GLN* 5.3 0.4 + - - -
237T MET* 4.4 3.5 - - - -
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Residues in contact with THR 210 (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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264S TYR* 4.3 9.7 - - + -
265S ASP* 5.2 3.8 - - + +
268S GLU* 5.0 4.0 - - - +
298S ILE* 4.3 28.9 + - + +
299S GLN* 4.5 12.1 - - + -
206T ALA 3.8 12.3 + - - +
207T GLU* 2.6 36.1 + - - +
209T HIS* 1.3 74.2 - - - +
211T GLU* 1.3 64.2 + - - +
213T GLU* 3.0 16.0 + - - +
214T ARG* 2.8 40.3 + - - +
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Residues in contact with GLU 211 (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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1N MET* 4.3 8.5 - - - +
265S ASP* 6.0 0.2 - - - -
172T LYS* 2.7 46.3 + - - +
192T LEU* 4.7 6.8 - - + +
195T ASN* 3.4 3.6 - - - +
196T LEU* 3.8 16.2 - - + -
199T LEU* 3.8 18.8 - - + -
207T GLU* 2.9 20.6 + - + +
208T PHE 3.7 4.3 - - - +
210T THR* 1.3 78.2 + - - +
212T LEU* 1.3 64.3 + - - +
214T ARG* 2.9 46.1 + - - +
215T LEU* 4.0 3.1 + - - +
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Residues in contact with LEU 212 (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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393S THR* 4.6 13.0 + - + +
396S ILE* 4.1 26.0 - - + -
196T LEU* 4.3 16.5 - - + +
208T PHE* 2.9 36.1 + - + +
209T HIS* 3.0 16.1 + - + +
211T GLU* 1.3 76.6 - - - +
213T GLU* 1.3 58.8 + - - +
214T ARG 3.5 0.2 + - - -
215T LEU* 3.4 19.0 + - + +
220T ILE* 3.9 23.9 - - + +
226T ILE* 5.0 1.6 - - + -
230T VAL* 3.4 31.9 - - + -
233T GLU* 6.1 0.2 - - - +
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Residues in contact with GLU 213 (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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262S SER* 3.7 9.8 - - - -
264S TYR* 2.9 41.2 + - + +
294S ARG* 4.8 3.0 + - - -
298S ILE* 3.0 30.5 - - + +
390S GLY* 2.8 31.2 - - - +
393S THR* 3.2 24.6 + - + +
209T HIS 3.0 9.2 + - - +
210T THR 3.5 11.4 - - - +
211T GLU 3.0 1.6 - - - -
212T LEU* 1.3 77.2 - - - +
214T ARG* 1.3 63.6 + - - +
215T LEU 3.5 4.4 - - - +
216T PRO* 5.6 0.5 - - - +
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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