Contacts of the strand formed by residues 323 - 334 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C LEU* 5.8 3.4 - - + -
41C VAL* 4.0 26.9 - - + -
105C LEU* 4.7 3.6 - - + -
172C MET* 3.7 23.8 - - + +
174C LEU* 4.5 15.5 - - + +
305C VAL* 3.0 37.1 + - + +
306C PHE* 3.5 51.5 - - + +
322C LYS* 1.3 76.4 - - - +
324C SER* 1.3 56.6 + - - +
325C GLN 3.4 26.5 - - - +
326C ALA* 4.1 4.9 - - + -
2G NAG 5.4 1.7 + - - -
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Residues in contact with SER 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C GLN 4.4 1.9 + - - -
170C THR* 3.7 17.3 - - - -
171C ALA* 2.9 34.9 + - - +
172C MET 2.8 15.1 + - - -
294C THR* 4.8 2.6 + - - -
306C PHE* 5.7 0.2 - - - -
322C LYS* 3.4 11.8 + - - +
323C ILE* 1.3 73.6 - - - +
325C GLN* 1.3 75.0 + - - +
2G NAG 4.1 17.3 + - - -
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Residues in contact with GLN 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C LEU* 4.7 10.1 - - + -
164C DSN 5.2 0.2 + - - -
165C SER* 2.9 42.6 + - - +
166C VAL* 5.4 0.2 - - + -
170C THR* 5.7 0.4 - - + -
172C MET 3.6 2.0 + - - -
173C VAL* 3.4 22.5 - - + -
174C LEU 3.0 23.3 + - - -
292C ASN* 5.0 1.0 - - - +
294C THR* 4.2 4.8 + - - -
323C ILE* 3.4 9.1 - - - +
324C SER* 1.3 95.0 + - - +
326C ALA* 1.3 61.1 + - - +
327C VAL* 6.4 0.2 - - + -
1G NAG 3.1 47.9 + - - +
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Residues in contact with ALA 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C LEU* 3.2 26.9 - - + -
292C ASN* 3.7 6.1 + - - +
293C LEU* 2.8 41.1 + - + -
294C THR* 3.6 15.7 + - - +
297C LEU* 5.6 1.1 - - + -
306C PHE* 4.2 7.4 - - + -
323C ILE* 4.1 9.6 - - + -
325C GLN* 1.3 78.0 + - - +
327C VAL* 1.3 61.9 + - - +
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Residues in contact with VAL 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C VAL* 3.9 26.7 - - + +
161C LEU* 4.1 15.7 - - + -
174C LEU 3.0 12.3 + - - +
175C VAL* 3.8 16.7 - - + -
176C ASN* 3.0 29.2 + - - +
290C LYS* 3.4 38.1 - - + -
291C TYR 3.5 9.0 - - - +
292C ASN* 5.4 1.3 - - - -
293C LEU* 4.1 5.3 - - - +
326C ALA* 1.3 76.9 - - - +
328C HIS* 1.3 63.5 + - - +
329C ALA 4.3 0.2 - - - -
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Residues in contact with HIS 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C TYR* 3.7 20.7 - - + +
30C CYS* 3.0 41.4 + - + +
33C ALA* 4.3 3.1 - - + -
34C ILE* 3.6 20.3 - - + +
176C ASN* 2.7 34.8 + - - -
178C ILE* 4.5 2.5 - - + -
289C GLU 4.2 0.2 - - - +
290C LYS* 3.2 3.8 - - - +
291C TYR* 2.8 45.8 + + + +
293C LEU* 3.7 24.1 - - + +
327C VAL* 1.3 76.3 - - - +
329C ALA* 1.3 69.6 + - - +
330C ALA* 4.0 4.7 - - + +
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Residues in contact with ALA 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C ILE* 3.7 34.5 - - + -
160C VAL* 4.2 14.1 - - + -
176C ASN 2.9 8.0 + - - +
177C ALA* 3.1 5.0 - - + -
178C ILE* 2.9 26.5 + - - +
288C GLU* 6.4 0.9 - - + -
289C GLU 3.5 9.6 - - - +
290C LYS* 4.3 8.7 - - + -
328C HIS* 1.3 76.6 - - - +
330C ALA* 1.3 61.9 + - - +
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Residues in contact with ALA 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C PHE* 3.7 26.0 - - + +
29C TYR* 4.1 11.2 - - - -
30C CYS 4.4 1.6 - - - +
157C ILE* 4.7 1.1 - - - -
178C ILE* 3.4 21.1 - - + -
288C GLU* 3.3 6.2 - - - +
289C GLU 3.1 31.4 + - - +
328C HIS* 4.0 14.1 + - + +
329C ALA* 1.3 76.1 - - - +
331C HIS* 1.3 60.1 + - - +
378C PHE* 4.7 0.7 - - + -
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Residues in contact with HIS 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C PHE* 3.9 2.3 - - - -
156C ILE* 3.3 34.7 - - + +
157C ILE* 4.5 3.6 - - + -
178C ILE* 3.0 10.5 + - - +
179C VAL* 3.3 16.2 - - + -
180C PHE* 3.0 25.1 + - - +
286C LYS* 4.5 29.5 + - + +
287C MET 3.2 8.5 - - - -
288C GLU* 2.5 39.3 + - + +
330C ALA* 1.3 74.9 - - - +
332C ALA* 1.3 77.4 + - - +
333C GLU* 4.4 6.1 + - + +
378C PHE* 5.3 0.9 - - - -
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Residues in contact with ALA 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C PHE* 3.5 27.2 - - + -
180C PHE* 3.3 30.7 - - + +
285C MET 4.0 0.3 - - - +
286C LYS 3.6 0.7 - - - -
287C MET* 2.8 34.9 + - + +
331C HIS* 1.3 82.2 - - - +
333C GLU* 1.3 60.6 + - - +
334C ILE* 4.3 13.3 + - + +
368C ILE* 5.7 1.6 - - + -
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Residues in contact with GLU 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C PHE* 3.6 9.2 + - - +
181C LYS* 3.6 29.1 + - + +
182C GLY 5.0 1.6 + - - +
284C ARG* 4.1 2.4 + - - -
285C MET 3.2 11.7 - - - +
286C LYS* 3.9 30.9 + - + -
331C HIS* 4.4 7.0 + - - +
332C ALA* 1.3 74.7 - - - +
334C ILE* 1.3 69.8 + - - +
335C ASN* 3.1 33.3 + - - +
2401C SO4 3.1 23.5 + - - -
150D GLU* 5.6 0.6 - - - +
155D GLY* 5.8 3.6 - - - -
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Residues in contact with ILE 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C PHE* 6.1 0.4 - - + -
180C PHE* 6.1 1.8 - - + -
181C LYS* 4.8 0.2 - - - +
184C TRP* 3.5 27.6 - - + -
211C MET* 3.9 15.5 - - + -
234C PHE* 5.5 4.5 - - + -
241C MET* 3.7 28.7 - - + -
282C LEU* 4.2 2.9 - - + -
283C PRO 4.2 0.9 - - - +
284C ARG* 3.4 3.1 - - - +
285C MET* 2.7 71.0 + - + +
287C MET* 5.2 5.4 - - + -
332C ALA* 4.3 14.8 - - + +
333C GLU* 1.3 86.5 - - - +
335C ASN* 1.3 64.6 + - - +
366C PHE* 5.3 5.6 - - + -
368C ILE* 5.5 3.8 - - + -
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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