Contacts of the strand formed by residues 207 - 213 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184C ASP* 4.2 19.5 + - - +
203D THR* 3.5 1.9 - - - -
204D GLU* 2.7 40.6 + - - +
206D PHE* 1.3 81.7 - - - +
208D GLY* 1.3 55.7 + - - +
316D THR* 3.8 6.2 - - - +
344D VAL* 6.2 0.4 - - + -
345D PHE 3.2 7.9 - - - +
346D ASN* 3.3 35.0 - - + +
348D VAL* 5.1 2.0 - - + -
8J LEU* 4.3 15.5 - - + +
71J LEU* 3.6 30.5 - - - +
73J LEU* 3.8 17.9 - - + +
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Residues in contact with GLY 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202D GLY 3.2 12.3 - - - -
203D THR* 4.1 1.1 - - - -
207D LYS* 1.3 75.3 - - - +
209D ASN* 1.3 60.1 + - - +
316D THR* 4.5 1.1 - - - +
320D ILE* 3.5 19.5 - - - -
344D VAL* 3.4 3.8 - - - +
345D PHE* 2.6 42.3 + - - +
73J LEU* 3.8 8.2 - - - +
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Residues in contact with ASN 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200D ASP* 4.5 5.7 - - - +
201D GLY* 3.4 2.3 - - - -
202D GLY* 2.8 43.5 + - - +
208D GLY* 1.3 74.3 - - - +
210D ALA* 1.3 62.8 + - - +
211D ARG* 4.0 19.4 + - - -
228D TYR* 5.4 0.5 + - - -
320D ILE* 3.4 8.4 - - - +
342D TYR* 3.4 32.7 + - + +
343D LEU 3.1 14.8 - - - +
344D VAL* 4.4 1.1 - - - -
71J LEU 4.2 4.5 - - - +
73J LEU* 2.7 42.8 + - + +
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Residues in contact with ALA 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199D ILE* 5.6 0.2 - - + -
200D ASP 3.4 6.1 - - - -
209D ASN* 1.3 76.6 - - - +
211D ARG* 1.3 63.6 + - - +
320D ILE* 4.2 7.7 - - + +
323D VAL* 3.8 28.0 - - + -
324D CYS* 3.8 24.9 - - - +
339D LEU* 4.2 3.6 - - + +
342D TYR* 3.6 1.4 - - - -
343D LEU* 2.8 35.2 + - + +
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Residues in contact with ARG 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D LEU 3.8 0.5 - - - +
199D ILE* 3.3 9.2 - - - +
200D ASP* 2.9 58.5 + - + +
209D ASN* 4.0 9.9 + - - +
210D ALA* 1.3 76.3 - - - +
212D VAL* 1.3 64.2 + - - +
213D ILE* 4.1 18.2 - - + -
220D CYS 4.4 0.6 + - - -
221D ILE* 3.7 25.3 + - - +
224D THR* 2.7 33.1 + - - -
227D LEU* 5.5 0.2 - - - +
228D TYR* 3.0 39.4 + - - -
339D LEU* 4.5 1.8 - - - -
341D ASN* 2.9 17.0 - - - +
342D TYR* 3.9 27.2 - - + -
72J ALA* 4.3 5.9 - - - +
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Residues in contact with VAL 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D LEU 3.8 2.5 - - - +
199D ILE* 4.0 11.2 - - + -
211D ARG* 1.3 73.4 - - - +
213D ILE* 1.3 65.3 + - - +
214D LEU* 4.3 18.1 + - + -
218D THR* 4.4 4.7 + - - -
219D ALA 4.8 0.2 - - - +
327D GLU* 3.8 35.7 - - + +
331D ILE* 3.9 22.9 - - + -
338D PRO* 4.9 5.8 - - + -
339D LEU* 3.7 30.1 - - + +
341D ASN* 3.0 26.8 + - - +
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Residues in contact with ILE 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D ASN* 4.6 3.8 - - - +
197D PRO* 3.5 4.7 - - - +
198D LEU* 2.8 59.9 + - + +
200D ASP* 5.0 1.3 - - + -
211D ARG* 4.1 20.0 - - + -
212D VAL* 1.3 77.7 - - - +
214D LEU* 1.3 67.2 + - - +
215D PRO* 3.6 17.9 - - + +
218D THR* 4.2 2.0 - - - +
219D ALA 3.6 20.2 - - - +
220D CYS* 3.8 15.7 - - + -
221D ILE* 3.5 47.6 - - + +
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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