Contacts of the strand formed by residues 219 - 226 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A GLY* 4.0 3.3 - - - -
216A GLU* 2.8 35.6 + - - +
218A ASN* 1.3 82.0 - - - +
220A ILE* 1.3 60.1 - - - +
221A LYS* 2.6 42.7 + - - +
526A ASN* 3.6 26.1 + - - +
626A VAL* 3.5 17.9 - - + +
628A THR* 4.1 3.5 + - - -
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Residues in contact with ILE 220 (chain A).
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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213A PHE* 3.7 29.4 - - + -
214A TYR 3.5 5.2 - - - -
216A GLU 4.0 2.2 - - - +
217A VAL 3.0 29.8 - - - +
218A ASN* 3.9 4.3 - - - -
219A ASP* 1.3 76.7 - - - +
221A LYS* 1.3 65.2 + - - +
222A THR* 4.1 4.2 + - + +
338A TYR* 3.4 31.6 - - + +
463A LEU* 5.1 6.1 - - + -
465A VAL* 5.4 0.2 - - + -
474A MET* 4.5 19.7 - - - -
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Residues in contact with LYS 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A PHE* 3.4 3.1 - - - -
214A TYR* 2.7 66.7 + - + +
215A GLY* 4.1 11.7 - - - -
219A ASP* 2.6 46.1 + - - +
220A ILE* 1.3 75.8 - - - +
222A THR* 1.3 59.8 + - - +
626A VAL* 4.1 10.8 - - + -
627A LEU 5.3 0.9 - - - -
628A THR* 3.4 33.1 + - - +
629A ILE* 5.1 13.7 - - + -
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Residues in contact with THR 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A VAL* 4.9 8.1 - - + -
212A ILE 3.5 7.9 - - - -
213A PHE* 3.2 42.4 - - + -
214A TYR* 3.8 5.3 + - - -
220A ILE* 4.1 6.0 + - + +
221A LYS* 1.3 74.3 - - - +
223A ARG* 1.3 65.0 + - - +
472A ASP 5.1 4.7 - - - +
720A GLU* 4.7 6.4 + - - +
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Residues in contact with ARG 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A VAL* 3.4 3.9 - - - -
212A ILE* 2.8 49.3 + - + +
214A TYR* 4.0 13.2 - - + -
222A THR* 1.3 77.9 - - - +
224A SER* 1.3 75.8 + - - +
225A TRP* 3.5 25.0 - - - -
289A PRO 4.7 0.6 + - - -
290A SER 4.2 2.0 + - - -
292A TRP 2.8 29.3 + - - -
293A THR* 4.1 7.7 - - - +
315A TRP* 3.9 17.8 - - - +
706A ILE* 4.7 4.2 - - - +
718A TYR* 3.5 65.0 + - + +
720A GLU* 4.2 6.1 - - - -
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Residues in contact with SER 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ILE* 4.8 1.3 - - - -
210A GLY 3.2 9.3 + - - -
211A VAL* 4.3 7.7 - - - +
223A ARG* 1.3 94.0 + - - +
225A TRP* 1.3 59.5 + - - +
293A THR 3.9 0.2 - - - +
704A LYS* 3.5 28.0 + - - +
706A ILE* 3.6 28.9 - - - +
720A GLU* 3.2 31.1 + - - +
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Residues in contact with TRP 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ILE* 3.6 0.9 - - - -
210A GLY* 2.5 43.8 + - - +
212A ILE* 3.6 30.3 - - + -
223A ARG* 3.5 37.0 - - - -
224A SER* 1.3 76.2 - - - +
226A SER* 1.3 63.9 + - - +
227A TYR* 3.4 27.6 + + + -
292A TRP* 3.7 29.4 - - + -
293A THR 3.6 4.3 - - - -
294A GLY* 3.2 24.0 - - - -
295A SER* 3.0 25.9 + - - +
298A ILE* 4.3 3.1 - - + -
315A TRP* 4.4 9.9 - + - -
316A VAL* 4.1 23.3 - - + -
319A GLY* 3.5 19.6 - - - -
320A VAL 4.4 0.9 - - - -
706A ILE* 4.1 2.7 - - - -
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Residues in contact with SER 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A ASP 3.9 4.3 - - - -
209A ILE* 4.4 2.7 - - - -
225A TRP* 1.3 73.3 + - - +
227A TYR* 1.3 57.8 + - - +
228A GLY* 3.8 9.9 + - - -
293A THR 3.1 10.1 + - - -
294A GLY* 3.1 10.1 - - - -
295A SER 2.8 30.0 + - - -
296A VAL* 4.3 7.8 - - - +
668A ASP* 3.2 27.6 + - - -
670A PRO* 3.9 14.8 - - - +
706A ILE* 3.8 12.4 - - - +
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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