Contacts of the strand formed by residues 376 - 382 (chain B) 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 VAL 376 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B SER* 3.1 11.3 + - - +
8B MET* 3.2 40.6 - - + -
11B CYS* 4.1 15.5 - - + -
12B PHE* 5.6 2.2 - - + -
31B PRO* 3.8 22.2 - - + +
32B ILE* 3.7 19.6 + - - +
264B LEU* 5.3 0.9 - - + -
367B CYS* 3.6 23.1 - - - -
368B ILE 3.9 2.2 - - - -
369B LYS* 4.5 2.2 - - + +
374B ASN 4.5 1.3 - - - +
375B ALA* 1.3 73.6 - - - +
377B LEU* 1.3 60.7 + - - +
378B PHE 3.4 28.3 - - - +
379B PHE* 4.4 0.2 - - + -
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Residues in contact with LEU 377 (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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30B CYS* 3.1 34.7 - - - -
31B PRO* 3.5 3.6 - - - +
32B ILE* 4.1 17.4 - - + +
86B ILE* 4.3 9.2 - - + -
90B ILE* 4.1 27.1 - - + -
99B PHE* 5.3 2.5 - - + -
239B MET* 3.7 37.5 - - + -
368B ILE* 2.8 19.0 + - + +
369B LYS 4.0 2.5 - - - -
370B HIS* 3.9 32.1 - - + +
375B ALA* 4.6 2.2 - - + +
376B VAL* 1.3 78.1 - - - +
378B PHE* 1.3 73.2 + - + +
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Residues in contact with PHE 378 (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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28B PHE* 3.4 41.1 - + + -
29B TYR 3.4 7.2 - - - -
30B CYS* 3.6 23.1 - - + -
31B PRO* 4.1 1.1 - - - -
99B PHE* 3.6 29.8 - + - -
178B ILE* 3.8 13.9 - - + -
180B PHE* 3.5 38.8 - + + -
330B ALA* 4.7 0.7 - - + -
331B HIS 5.4 1.8 - - - -
366B PHE* 5.7 1.3 - - + -
367B CYS* 3.3 3.5 - - - -
368B ILE* 2.9 51.9 + - + -
376B VAL* 3.4 9.6 - - - +
377B LEU* 1.3 91.0 - - + +
379B PHE* 1.3 61.8 + - - +
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Residues in contact with PHE 379 (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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11B CYS* 3.5 27.8 - - - -
12B PHE* 3.7 31.0 - + - -
15B PHE* 3.5 38.4 - + + -
28B PHE* 3.4 7.3 - - - -
29B TYR* 3.0 55.7 + + + +
31B PRO* 4.7 0.2 - - + -
244B LEU* 5.7 2.0 - - + -
259B ILE* 4.6 5.2 - - + -
264B LEU* 5.8 1.1 - - + -
365B LEU* 4.2 23.8 - - + -
366B PHE* 3.5 16.8 - - - -
367B CYS* 3.9 19.3 - - + -
376B VAL* 4.4 0.7 - - + -
378B PHE* 1.3 76.1 - - - +
380B GLY* 1.3 78.5 + - - +
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Residues in contact with GLY 380 (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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15B PHE* 5.3 0.2 - - - -
27B ILE* 3.0 15.5 - - - -
28B PHE* 4.2 0.2 - - - -
365B LEU* 3.4 7.8 - - - +
366B PHE* 2.9 49.5 + - - +
379B PHE* 1.3 86.5 - - - +
381B ARG* 1.3 60.9 + - - +
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Residues in contact with ARG 381 (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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15B PHE* 4.5 4.5 - - + -
19B LYS* 4.0 15.4 + - - +
22B HIS 2.9 23.4 + - - -
23B ALA* 5.1 3.0 - - - +
24B ASN 3.9 6.3 - - - +
25B GLU 2.9 33.9 + - - +
26B ASN* 3.3 8.1 - - - +
27B ILE* 2.8 54.5 + - + +
252B LEU* 3.9 9.5 - - + +
256B GLU* 2.8 41.0 + - - +
364B PHE 3.6 5.2 - - - +
365B LEU* 3.8 11.7 - - + -
366B PHE* 4.1 2.8 - - - -
380B GLY* 1.3 74.9 - - - -
382B CYS* 1.3 62.3 + - - +
383B VAL* 3.3 21.8 - - + -
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Residues in contact with CYS 382 (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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26B ASN* 3.5 5.2 - - - -
198B PHE* 4.3 1.9 - - - -
285B MET* 3.5 36.1 - - + -
363B PRO* 3.2 6.4 - - - +
364B PHE* 2.9 51.5 + - + +
366B PHE* 4.1 2.8 - - + -
381B ARG* 1.3 73.6 - - - +
383B VAL* 1.3 60.5 + - - +
384B SER 4.2 0.9 - - - -
385B PRO* 3.5 42.2 - - - -
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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