Contacts of the strand formed by residues 219 - 226 (chain B) in PDB entry 1GGT
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 ASP 219 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215B GLY* 4.0 0.3 - - - -
216B GLU* 2.7 35.5 + - - +
218B ASN* 1.3 82.9 - - - +
220B ILE* 1.3 63.4 + - - +
221B LYS* 2.6 47.6 + - - +
526B ASN* 4.4 23.9 - - + +
626B VAL* 3.4 22.0 - - + +
628B THR* 4.5 3.3 + - - -
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Residues in contact with ILE 220 (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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213B PHE* 3.8 10.5 - - + -
214B TYR 3.6 4.7 - - - -
216B GLU 3.6 5.6 - - - +
217B VAL 3.5 18.4 - - - +
218B ASN 3.7 0.8 + - - -
219B ASP* 1.3 75.8 - - - +
221B LYS* 1.3 69.4 + - - +
222B THR* 4.8 3.0 - - + +
338B TYR* 3.7 24.0 - - + +
463B LEU* 3.5 28.9 - - + -
474B MET* 3.4 39.3 - - + -
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Residues in contact with LYS 221 (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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213B PHE* 3.4 3.1 - - - -
214B TYR* 2.8 55.9 + - + +
215B GLY* 4.0 12.3 - - - -
219B ASP* 2.6 53.6 + - - +
220B ILE* 1.3 74.7 + - - +
222B THR* 1.3 70.4 + - - +
626B VAL* 4.0 12.3 - - + +
627B LEU 5.6 1.6 - - - +
628B THR* 4.3 25.9 + - - +
629B ILE* 5.6 5.6 - - + +
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Residues in contact with THR 222 (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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211B VAL* 5.0 7.6 - - - -
212B ILE 3.4 9.2 - - - -
213B PHE* 3.2 37.5 - - + -
214B TYR* 3.6 8.7 + - - -
220B ILE* 4.8 4.9 - - + +
221B LYS* 1.3 79.7 - - - +
223B ARG* 1.3 65.9 + - - +
472B ASP 5.2 5.4 + - - +
718B TYR* 5.5 0.3 - - - -
720B GLU* 5.3 2.8 + - - +
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Residues in contact with ARG 223 (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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211B VAL* 3.4 4.6 - - - -
212B ILE* 2.9 46.3 + - - +
214B TYR* 3.8 15.8 - - + -
222B THR* 1.3 80.1 + - - +
224B SER* 1.3 78.5 + - - +
225B TRP* 3.6 16.2 - - - -
289B PRO 4.5 1.6 + - - -
290B SER 3.8 2.6 + - - -
292B TRP 2.8 29.5 + - - -
293B THR* 4.0 7.3 - - - +
315B TRP* 3.4 29.3 - - - +
706B ILE* 5.1 1.6 - - - +
718B TYR* 3.4 59.2 + - + -
720B GLU* 4.1 6.5 - - - -
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Residues in contact with SER 224 (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 ILE* 4.3 1.5 - - - +
210B GLY 3.4 10.6 + - - -
211B VAL* 4.0 6.2 - - - +
223B ARG* 1.3 95.3 + - - +
225B TRP* 1.3 61.2 + - - +
704B LYS* 3.0 40.5 - - - +
706B ILE* 3.7 28.8 - - - +
718B TYR* 6.0 0.2 - - - +
720B GLU* 3.3 22.0 + - - -
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Residues in contact with TRP 225 (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 ILE* 3.6 2.1 - - - +
210B GLY 2.8 37.7 + - - +
212B ILE* 3.4 34.3 - - + -
223B ARG* 3.6 33.4 - - - -
224B SER* 1.3 74.6 - - - +
226B SER* 1.3 68.9 + - - +
227B TYR* 3.4 21.4 + + + -
292B TRP* 3.7 25.4 - - + -
293B THR 3.5 5.6 - - - -
294B GLY* 3.5 22.0 - - - -
295B SER* 3.3 27.2 + - - +
298B ILE* 4.4 4.9 - - + -
315B TRP* 3.6 15.0 - + - -
316B VAL* 3.9 24.5 - - + -
319B GLY* 3.9 17.1 - - - -
706B ILE* 4.0 3.1 - - - -
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Residues in contact with SER 226 (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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208B ASP 3.8 3.8 - - - -
209B ILE* 4.7 0.9 - - - +
225B TRP* 1.3 73.0 - - - +
227B TYR* 1.3 59.7 + - - +
228B GLY* 3.7 10.2 + - - -
293B THR 3.1 8.4 + - - -
294B GLY* 3.9 10.1 - - - -
295B SER 2.8 26.5 + - - -
296B VAL* 4.1 9.1 + - - +
668B ASP* 3.9 16.6 + - - -
670B PRO* 3.4 33.7 - - - +
706B ILE* 3.7 7.6 - - - +
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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