Contacts of the strand formed by residues 325 - 334 (chain D) in PDB entry 1UHG
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 GLN 325 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161D LEU* 4.6 8.3 - - + -
165D SER* 2.7 37.2 + - - +
166D VAL* 4.7 2.2 - - + -
170D THR* 5.4 0.7 - - + -
172D MET 3.6 2.4 + - - -
173D VAL* 3.4 25.2 - - + -
174D LEU 2.8 23.9 + - - -
292D ASN* 5.1 0.5 - - - +
294D THR* 4.1 4.3 + - - -
323D ILE* 3.3 9.8 - - - +
324D SER* 1.3 87.7 + - - +
326D ALA* 1.3 61.1 + - - +
327D VAL* 4.3 0.4 - - + -
386D NAG 2.8 53.9 + - - +
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Residues in contact with ALA 326 (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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174D LEU* 3.3 28.5 - - + -
292D ASN* 3.7 6.3 + - - +
293D LEU* 2.8 40.9 + - + -
294D THR* 3.5 15.7 + - - +
297D LEU* 5.7 0.7 - - + -
306D PHE* 4.2 7.2 - - + -
323D ILE* 4.2 9.2 - - + -
325D GLN* 1.3 77.2 + - - +
327D VAL* 1.3 61.2 + - - +
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Residues in contact with VAL 327 (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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160D VAL* 3.7 36.1 - - + +
161D LEU* 4.3 11.9 - - + -
162D GLN* 4.8 4.7 - - - +
174D LEU 3.0 11.9 + - - +
175D VAL* 3.9 16.6 - - + -
176D ASN* 3.0 29.3 + - - +
290D LYS* 3.5 33.4 - - + -
291D TYR 3.5 9.2 - - - +
292D ASN* 5.4 1.1 - - - -
293D LEU* 4.3 4.1 - - - +
325D GLN* 6.3 0.2 - - + -
326D ALA* 1.3 74.6 - - - +
328D HIS* 1.3 63.7 + - - +
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Residues in contact with HIS 328 (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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29D TYR* 3.7 21.2 - - + +
30D CYS* 2.9 39.5 + - + +
33D ALA* 4.4 1.3 - - + -
34D ILE* 3.4 21.0 - - + +
176D ASN* 2.7 36.8 + - - -
178D ILE* 4.4 10.8 - - + -
289D GLU 4.0 0.3 - - - +
290D LYS* 3.2 2.6 - - - +
291D TYR* 2.7 49.3 + + + +
293D LEU* 3.7 24.4 - - + +
327D VAL* 1.3 74.3 - - - +
329D ALA* 1.3 64.9 + - - +
330D ALA* 4.1 3.8 - - + +
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Residues in contact with ALA 329 (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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157D ILE* 3.8 31.3 - - + +
160D VAL* 4.3 10.1 - - + +
176D ASN 3.0 7.6 + - - +
177D ALA* 3.2 4.5 - - + -
178D ILE* 3.0 26.3 + - - +
288D GLU* 6.0 2.5 - - + -
289D GLU 3.4 8.7 - - - +
290D LYS* 4.3 15.5 - - + -
328D HIS* 1.3 77.6 - - - +
330D ALA* 1.3 61.1 + - - +
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Residues in contact with ALA 330 (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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28D PHE* 3.7 23.3 - - + +
29D TYR* 3.9 22.0 - - - -
157D ILE* 5.0 0.7 - - - -
178D ILE* 3.1 26.7 - - + -
288D GLU* 3.1 26.7 - - - +
289D GLU 3.0 12.3 + - - -
328D HIS* 4.1 3.8 - - - +
329D ALA* 1.3 75.1 - - - +
331D HIS* 1.3 58.9 + - - +
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Residues in contact with HIS 331 (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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28D PHE* 3.9 1.9 - - - -
156D ILE* 3.4 32.8 - - + +
157D ILE* 4.7 3.4 - - + -
178D ILE* 3.0 13.7 + - - +
179D VAL* 3.2 16.4 - - + -
180D PHE* 2.9 25.5 + - - +
286D LYS* 5.6 10.9 - - + +
287D MET 3.1 9.4 - - - -
288D GLU* 2.6 36.8 + - + +
330D ALA* 1.3 76.4 - - - +
332D ALA* 1.3 76.3 + - - +
333D GLU* 4.6 10.0 + - - +
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Residues in contact with ALA 332 (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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28D PHE* 3.5 25.5 - - + -
180D PHE* 3.3 31.4 - - + +
285D MET 4.2 0.3 - - - +
286D LYS* 3.8 0.3 - - - -
287D MET* 2.8 37.8 + - + +
331D HIS* 1.3 83.1 - - - +
333D GLU* 1.3 61.8 + - - +
334D ILE* 4.2 5.0 + - + +
368D ILE* 5.6 2.9 - - + -
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Residues in contact with GLU 333 (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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150C GLU* 4.9 1.2 - - - +
154C ASN 6.1 0.3 - - - -
155C GLY* 5.7 4.3 - - - -
158C ARG* 4.6 4.5 + - - -
180D PHE* 3.6 8.0 + - - +
181D LYS* 3.5 34.1 + - + +
182D GLY 5.1 1.9 + - - +
284D ARG* 4.1 3.6 + - - -
285D MET 3.4 11.4 - - - +
286D LYS* 3.5 27.3 - - + +
331D HIS* 4.6 11.6 + - + +
332D ALA* 1.3 76.3 - - - +
334D ILE* 1.3 74.8 + - - +
335D ASN* 3.4 21.3 - - - +
3402D SO4 3.0 25.9 + - - -
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Residues in contact with ILE 334 (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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180D PHE* 5.3 4.5 - - + -
181D LYS* 5.5 0.2 - - - +
182D GLY 6.1 0.7 - - - +
184D TRP* 3.8 26.7 - - + -
211D MET* 4.2 13.7 - - + -
234D PHE* 4.6 11.9 - - + -
241D MET* 3.4 30.7 - - + -
282D LEU* 4.2 9.9 - - + -
283D PRO 4.4 0.7 - - - +
284D ARG* 3.3 4.5 - - - +
285D MET* 2.7 67.7 + - + +
287D MET* 5.8 2.5 - - + -
332D ALA* 5.3 6.5 - - + +
333D GLU* 1.3 82.5 - - - +
335D ASN* 1.3 63.9 + - - +
366D PHE* 5.6 3.1 - - + -
368D ILE* 4.9 5.6 - - + -
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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