Contacts of the strand formed by residues 323 - 334 (chain A) 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 ILE 323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A LEU* 5.9 4.0 - - + -
41A VAL* 4.0 26.5 - - + -
105A LEU* 4.8 4.5 - - + -
172A MET* 3.5 22.4 - - + +
174A LEU* 4.6 14.4 - - + +
305A VAL* 3.0 38.4 + - + +
306A PHE* 3.6 38.8 - - + +
312A LEU* 4.6 0.7 - - + -
322A LYS* 1.3 73.3 - - - +
324A SER* 1.3 55.4 + - - +
325A GLN 3.3 26.2 - - - +
326A ALA* 4.1 4.9 - - + -
2E NAG 3.1 15.6 + - - -
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Residues in contact with SER 324 (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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169A GLN 4.6 0.7 + - - -
170A THR* 3.9 17.0 - - - -
171A ALA* 2.9 36.0 + - - +
172A MET 2.8 14.7 + - - -
322A LYS* 3.4 11.9 + - - +
323A ILE* 1.3 71.6 - - - +
325A GLN* 1.3 71.9 + - - +
2E NAG 3.0 39.5 + - - +
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Residues in contact with GLN 325 (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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161A LEU* 4.9 7.9 - - + -
165A SER* 2.9 37.1 - - - +
166A VAL* 5.2 1.1 - - + -
170A THR* 5.6 0.7 - - + -
172A MET 3.7 2.0 + - - -
173A VAL* 3.5 21.0 - - + -
174A LEU 3.0 22.6 + - - -
292A ASN* 4.9 1.6 + - - -
294A THR* 4.1 5.5 + - - -
323A ILE* 3.3 10.9 + - - +
324A SER* 1.3 92.8 + - - +
326A ALA* 1.3 62.4 + - - +
327A VAL* 6.3 0.2 - - + -
1E NAG 3.1 53.1 + - - +
2E NAG 5.0 5.7 - - - -
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Residues in contact with ALA 326 (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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174A LEU* 3.3 24.2 - - + -
292A ASN* 3.7 7.1 - - - +
293A LEU* 2.8 40.8 + - + -
294A THR* 3.5 16.0 + - - +
297A LEU* 5.6 1.1 - - + -
306A PHE* 4.3 7.2 - - + -
323A ILE* 4.1 13.2 - - + -
325A GLN* 1.3 78.3 + - - +
327A VAL* 1.3 61.2 + - - +
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Residues in contact with VAL 327 (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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160A VAL* 4.0 22.9 - - + +
161A LEU* 4.0 16.6 - - + -
174A LEU 3.0 17.1 + - - +
175A VAL* 3.8 20.5 - - + -
176A ASN* 3.0 24.9 + - - +
290A LYS* 3.5 35.9 - - + -
291A TYR 3.5 8.7 - - - +
292A ASN* 5.3 1.1 - - - -
293A LEU* 3.9 4.7 - - - +
325A GLN* 6.3 0.2 - - + -
326A ALA* 1.3 76.3 - - - +
328A HIS* 1.3 63.7 + - - +
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Residues in contact with HIS 328 (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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29A TYR* 3.5 20.7 - - + +
30A CYS* 3.0 41.0 + - + +
33A ALA* 4.5 1.8 - - + -
34A ILE* 3.5 22.1 - - + +
176A ASN* 2.9 34.0 + - - -
178A ILE* 4.6 1.8 - - + -
290A LYS* 3.0 6.1 - - - +
291A TYR* 2.7 50.6 + + + +
293A LEU* 3.7 24.0 - - + +
327A VAL* 1.3 74.7 - - - +
329A ALA* 1.3 70.0 + - - +
330A ALA* 4.1 3.6 - - + +
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Residues in contact with ALA 329 (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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157A ILE* 4.0 28.3 - - + -
160A VAL* 4.2 9.4 - - + +
176A ASN 3.1 7.6 + - - +
177A ALA* 3.2 5.7 - - + +
178A ILE* 2.9 26.2 + - - +
288A GLU* 6.0 2.7 - - + -
289A GLU 3.3 9.4 - - - +
290A LYS* 4.0 16.4 - - + -
327A VAL 4.3 0.2 - - - -
328A HIS* 1.3 79.1 - - - +
330A ALA* 1.3 62.0 + - - +
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Residues in contact with ALA 330 (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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28A PHE* 3.5 24.7 - - + +
29A TYR* 4.0 21.5 - - - -
30A CYS 4.2 2.0 - - - +
157A ILE* 5.0 0.2 - - - -
178A ILE* 3.4 23.3 - - + -
288A GLU* 3.2 7.1 - - - +
289A GLU 3.1 28.8 + - - -
328A HIS* 4.1 4.5 - - - +
329A ALA* 1.3 75.2 - - - +
331A HIS* 1.3 60.2 + - - +
378A PHE* 4.5 1.3 - - + -
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Residues in contact with HIS 331 (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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28A PHE* 3.8 2.5 - - - -
156A ILE* 3.5 30.2 - - + +
157A ILE* 4.5 3.8 - - + -
178A ILE* 2.9 11.5 + - - +
179A VAL* 3.3 16.9 - - + -
180A PHE* 3.0 24.7 + - - +
286A LYS* 4.3 16.8 - - + -
287A MET 3.1 9.4 + - - -
288A GLU* 2.6 36.3 + - + +
330A ALA* 1.3 75.7 - - - +
332A ALA* 1.3 68.0 + - - +
333A GLU* 3.0 31.4 + - - +
378A PHE* 5.0 1.4 - - - -
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Residues in contact with ALA 332 (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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28A PHE* 3.4 24.6 - - + -
180A PHE* 3.4 30.5 - - + +
285A MET 4.0 0.5 - - - +
286A LYS 3.7 0.2 - - - -
287A MET* 2.7 43.6 + - + +
331A HIS* 1.3 80.6 - - - +
333A GLU* 1.3 63.0 + - - +
334A ILE* 4.1 7.2 + - + +
368A ILE* 5.5 2.9 - - + -
378A PHE* 5.2 0.2 - - + -
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Residues in contact with GLU 333 (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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156A ILE* 5.5 2.8 - - - +
180A PHE* 3.7 7.7 + - - +
181A LYS* 3.1 37.6 + - + +
182A GLY 5.0 1.6 + - - +
285A MET 3.4 4.3 - - - +
286A LYS* 3.6 40.9 + - + +
331A HIS* 3.0 26.6 + - + +
332A ALA* 1.3 73.7 - - - +
334A ILE* 1.3 68.9 + - - +
335A ASN* 4.8 8.2 + - - +
402A SO4 4.3 9.9 + - - -
154B ASN 5.7 0.6 - - - +
155B GLY* 6.1 0.7 - - - -
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Residues in contact with ILE 334 (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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180A PHE* 5.3 3.8 - - + -
182A GLY 6.3 0.2 - - - +
184A TRP* 3.6 28.0 - - + -
211A MET* 4.3 5.6 - - + -
234A PHE* 4.5 13.2 - - + -
241A MET* 3.5 32.8 - - + -
282A LEU* 4.2 16.4 - - + -
283A PRO 4.4 0.9 - - - +
284A ARG* 3.4 4.2 - - - +
285A MET* 2.8 62.0 + - + +
287A MET* 5.6 2.7 - - + -
332A ALA* 4.1 8.5 + - + +
333A GLU* 1.3 81.2 - - - +
335A ASN* 1.3 65.5 + - - +
366A PHE* 5.7 0.7 - - + -
368A ILE* 4.7 5.4 - - + -
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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