Contacts of the helix formed by residues 204 - 216 (chain B) in PDB entry 4GDF
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150B VAL 6.0 0.2 - - - +
152B SER 3.2 25.5 + - - +
153B ASN* 3.7 18.0 + - - +
154B ARG 2.9 22.7 - - - +
155B THR* 3.9 9.2 - - + -
159B PHE* 4.2 1.3 - - - -
203B HIS* 1.3 76.0 - - - +
205B VAL* 1.3 70.9 - - - +
206B SER* 3.5 23.2 + - - +
207B ALA* 2.7 14.6 + - - +
208B ILE* 3.1 8.3 + - - +
14C T 6.1 0.2 - - - +
15C A 3.0 46.8 + - + +
16C G 2.9 49.8 + - - +
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Residues in contact with VAL 205 (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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147B SER* 6.1 1.8 - - - -
150B VAL* 4.2 25.6 - - + +
152B SER* 6.1 0.9 - - - +
154B ARG* 4.3 1.8 + - + +
156B LEU* 4.4 10.5 - - + -
159B PHE* 3.9 18.1 - - + -
203B HIS 3.6 1.2 + - - -
204B ARG* 1.3 72.9 - - - +
206B SER* 1.3 64.3 + - - +
208B ILE* 3.0 6.6 + - + +
209B ASN* 2.9 21.3 + - + +
223B CYS* 3.5 36.6 - - + +
224B LYS* 3.8 7.6 - - - -
225B GLY* 3.6 26.5 - - - +
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Residues in contact with SER 206 (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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150B VAL* 4.0 16.0 + - - -
151B PHE* 5.7 6.3 - - - -
152B SER 5.4 2.0 - - - -
204B ARG* 2.9 29.4 + - - +
205B VAL* 1.3 77.6 - - - +
207B ALA* 1.3 55.9 + - - +
209B ASN* 3.3 7.0 + - - +
210B ASN* 2.7 49.2 + - - +
14C T 6.0 0.5 - - - +
15C A 4.4 4.9 + - - -
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Residues in contact with ALA 207 (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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179B TYR* 4.0 5.1 + - - +
203B HIS* 4.8 2.9 - - + -
204B ARG* 2.7 12.8 + - - +
206B SER* 1.3 77.0 + - - +
208B ILE* 1.3 61.1 + - - +
210B ASN* 3.3 2.0 + - - +
211B TYR* 3.0 23.6 + - - +
15C A 3.6 35.6 + - + +
16C G 3.2 30.1 - - - +
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Residues in contact with ILE 208 (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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159B PHE* 4.0 37.0 - - + -
161B ILE* 4.3 15.9 - - + -
175B ILE* 5.0 4.0 - - + -
179B TYR* 3.6 38.4 - - + +
197B PHE* 4.0 22.7 - - + -
199B THR* 5.3 0.2 - - + -
203B HIS* 3.9 19.7 - - + -
204B ARG 3.1 10.9 + - - +
205B VAL* 3.0 7.9 + - - +
207B ALA* 1.3 72.3 - - - +
209B ASN* 1.3 66.1 + - - +
211B TYR* 3.0 14.9 + - - +
212B ALA* 3.1 11.8 + - - +
223B CYS* 4.7 5.4 - - + -
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Residues in contact with ASN 209 (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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205B VAL* 2.9 12.5 + - + +
206B SER* 3.5 10.7 - - - +
208B ILE* 1.3 77.3 - - - +
210B ASN* 1.3 76.0 + - - +
212B ALA* 3.4 3.5 + - - +
213B GLN* 3.0 52.7 + - - +
221B LEU* 4.4 5.7 - - - +
223B CYS* 3.8 34.7 + - + +
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Residues in contact with ASN 210 (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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206B SER* 2.7 37.9 + - - +
207B ALA 3.7 4.5 - - - +
209B ASN* 1.3 85.8 - - - +
211B TYR* 1.3 64.2 + - - +
213B GLN* 3.4 17.9 - - - +
214B LYS* 3.4 19.1 + - - +
14C T 4.1 13.3 + - - +
15C A 2.9 31.6 + - - +
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Residues in contact with TYR 211 (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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174B LYS* 3.1 25.3 + - - +
175B ILE* 4.1 17.7 - - + -
178B LYS* 3.4 45.4 - - + +
179B TYR* 3.6 27.8 - + - +
207B ALA 3.0 7.9 + - - +
208B ILE 3.0 10.1 + - - +
210B ASN* 1.3 75.0 - - - +
212B ALA* 1.3 73.1 + - - +
213B GLN 3.1 0.7 + - - -
214B LYS* 3.2 35.3 + - + +
215B LEU* 3.4 38.3 + - + +
15C A 5.3 0.2 + - - -
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Residues in contact with ALA 212 (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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161B ILE* 4.6 11.9 - - + -
171B LEU* 4.2 24.0 - - + -
175B ILE* 5.0 1.8 - - + -
208B ILE 3.1 9.0 + - - +
209B ASN* 3.8 8.1 - - - +
211B TYR* 1.3 87.6 - - + +
213B GLN* 1.3 64.7 + - - +
215B LEU* 2.9 22.2 - - - +
218B PHE* 3.3 13.3 - - + -
221B LEU* 4.3 16.6 - - + -
223B CYS* 5.2 0.2 - - - -
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Residues in contact with GLN 213 (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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209B ASN* 3.0 44.5 + - - +
210B ASN* 3.4 11.0 - - - +
212B ALA* 1.3 75.1 - - - +
214B LYS* 1.3 58.8 + - - +
215B LEU 2.8 2.3 + - - -
216B CYS 2.7 26.7 - - - +
218B PHE* 4.3 9.5 - - - +
221B LEU* 3.0 35.1 - - - +
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Residues in contact with LYS 214 (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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210B ASN* 3.4 19.0 + - - +
211B TYR* 3.2 26.0 - - + +
213B GLN* 1.3 77.9 - - - +
215B LEU* 1.3 61.9 + - + +
216B CYS 4.8 0.2 - - - -
15C A 4.8 10.3 + - - -
22D C 5.7 2.6 + - - -
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Residues in contact with LEU 215 (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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170B LEU* 4.7 10.8 - - + -
171B LEU* 3.2 33.2 - - + -
174B LYS* 3.7 31.9 - - + -
211B TYR* 3.4 38.6 + - + +
212B ALA 2.9 14.6 + - - +
213B GLN 2.8 2.8 + - - -
214B LYS* 1.3 81.9 - - + +
216B CYS* 1.3 61.7 + - + +
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Residues in contact with CYS 216 (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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167B LYS* 3.0 34.5 - - + -
170B LEU* 3.7 29.6 - - + -
212B ALA 3.7 1.2 + - - -
213B GLN 2.7 18.7 + - - +
215B LEU* 1.3 82.8 - - + +
217B THR* 1.3 73.1 + - - +
218B PHE* 3.5 16.8 - - + -
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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