Contacts of the strand formed by residues 207 - 213 (chain B) in PDB entry 3GZN
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 LYS 207 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A ASP* 4.1 19.1 + - - +
203B THR* 3.7 3.5 + - - -
204B GLU* 2.8 42.3 + - - +
205B GLY* 6.2 0.2 - - - -
206B PHE* 1.3 81.2 - - - +
208B GLY* 1.3 54.7 + - - +
316B THR* 3.8 3.6 - - - +
344B VAL* 5.9 0.4 - - + -
345B PHE 3.2 6.3 - - - +
346B ASN* 3.0 29.6 - - + +
348B VAL* 5.6 1.9 - - + +
8I LEU* 3.9 27.6 - - + -
71I LEU* 4.2 19.7 - - + -
73I LEU* 3.6 21.3 - - + -
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Residues in contact with GLY 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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202B GLY 3.5 9.4 - - - -
203B THR* 4.2 2.0 - - - -
207B LYS* 1.3 75.9 - - - +
209B ASN* 1.3 60.0 + - - +
316B THR* 4.4 1.9 - - - +
320B ILE* 3.5 20.4 - - - -
344B VAL* 3.4 5.0 - - - +
345B PHE* 2.6 40.4 + - - +
73I LEU* 3.5 8.4 - - - +
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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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200B ASP* 4.7 2.9 - - - +
201B GLY* 3.4 0.2 - - - -
202B GLY* 2.9 42.6 + - - +
208B GLY* 1.3 74.1 - - - +
210B ALA* 1.3 63.8 + - - +
211B ARG* 4.2 14.6 + - - -
320B ILE* 3.3 12.5 - - - +
342B TYR* 3.3 36.0 + - + +
343B LEU 3.1 14.6 - - - +
344B VAL* 4.4 1.1 - - - -
71I LEU 4.2 1.3 - - - +
72I ALA* 4.4 0.7 - - - -
73I LEU* 2.8 46.1 + - + +
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Residues in contact with ALA 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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199B ILE* 5.6 0.2 - - + -
200B ASP 3.3 5.6 - - - -
209B ASN* 1.3 76.5 - - - +
211B ARG* 1.3 62.7 + - - +
320B ILE* 4.3 4.5 - - + +
323B VAL* 4.0 27.4 - - + -
324B CYS* 3.9 23.3 - - - +
339B LEU* 4.1 5.4 - - + +
341B ASN 3.6 0.5 - - - +
342B TYR* 3.5 4.5 - - - -
343B LEU* 3.0 37.2 + - + +
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Residues in contact with ARG 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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198B LEU 3.8 0.2 - - - +
199B ILE* 3.2 12.6 - - - +
200B ASP* 2.7 57.7 + - + +
209B ASN* 4.2 9.6 + - - +
210B ALA* 1.3 75.4 - - - +
212B VAL* 1.3 63.0 + - - +
213B ILE* 4.0 20.9 - - + -
220B CYS 5.6 0.9 - - - -
221B ILE* 3.7 31.3 + - - +
224B THR* 2.8 35.7 + - - -
227B LEU* 5.6 0.2 - - - +
228B TYR* 2.7 37.6 + - - -
339B LEU* 4.8 0.4 - - - -
341B ASN* 3.2 6.3 - - - +
342B TYR* 3.5 37.6 - - + -
72I ALA* 4.8 3.5 - - - +
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Residues in contact with VAL 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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197B PRO* 5.8 0.2 - - + -
198B LEU 3.8 2.2 - - - +
199B ILE* 3.9 10.3 - - + -
211B ARG* 1.3 75.2 - - - +
213B ILE* 1.3 69.1 + - - +
214B LEU* 4.7 12.7 - - + +
218B THR* 4.0 6.2 + - - +
327B GLU* 3.9 34.3 - - + -
331B ILE* 4.1 20.6 - - + -
338B PRO* 4.9 6.7 - - + -
339B LEU* 3.7 30.5 - - + +
341B ASN* 3.0 29.5 + - - +
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Residues in contact with ILE 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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176B ASN* 4.5 2.5 - - - +
197B PRO* 3.6 4.2 - - - +
198B LEU* 2.8 60.2 + - + +
200B ASP* 4.9 2.2 - - + -
211B ARG* 4.2 20.4 - - + -
212B VAL* 1.3 77.1 - - - +
214B LEU* 1.3 68.5 + - - +
215B PRO* 3.6 17.4 - - + +
218B THR* 4.0 2.5 - - - +
219B ALA 3.5 22.9 - - - +
220B CYS* 3.7 16.6 - - + -
221B ILE* 3.6 45.8 - - + +
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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