Contacts of the helix formed by residues 373 - 381 (chain B) in PDB entry 1U7V
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 THR 373 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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371B HIS 3.5 14.1 - - - +
372B ARG* 1.3 78.0 - - - +
374B GLU* 1.3 71.8 + - - +
375B ALA* 3.3 7.9 + - - +
376B ILE* 3.3 30.3 + - + +
377B GLU* 3.2 26.9 + - - +
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Residues in contact with GLU 374 (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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373B THR* 1.3 79.1 - - - +
375B ALA* 1.3 98.2 + - - +
377B GLU* 3.8 9.5 + - - +
378B ARG* 3.4 31.9 + - - +
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Residues in contact with ALA 375 (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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467A SEP 5.7 0.9 - - - +
373B THR* 3.3 7.1 + - - +
374B GLU* 1.3 98.9 + - - +
376B ILE* 1.3 61.6 + - + +
378B ARG* 3.3 24.6 + - - +
379B ALA* 3.2 23.4 + - - +
507B LYS* 5.4 1.9 + - - -
522B PRO* 4.5 4.4 - - + +
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Residues in contact with ILE 376 (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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330B GLU* 3.4 29.4 - - + +
331B MET* 4.2 24.2 - - + -
369B ASN* 5.3 0.4 - - - +
372B ARG* 4.2 6.3 - - + -
373B THR* 3.3 29.5 + - + +
374B GLU 3.4 0.2 - - - -
375B ALA* 1.3 78.0 - - + +
377B GLU* 1.3 66.7 + - - +
378B ARG 2.9 2.0 - - - -
379B ALA 3.1 0.2 + - - -
380B ARG* 2.8 44.4 + - + +
522B PRO* 3.1 42.2 - - + +
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Residues in contact with GLU 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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406A TYR* 4.8 8.1 + - + -
410A ARG* 5.3 9.2 + - - -
372B ARG* 4.4 16.7 + - - +
373B THR 3.2 18.9 + - - +
374B GLU* 4.1 8.3 - - - +
376B ILE* 1.3 79.5 - - - +
378B ARG* 1.3 62.2 + - - +
380B ARG* 3.9 12.0 - - - +
381B LEU* 3.3 35.5 + - + +
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Residues in contact with ARG 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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463A CYS* 5.0 2.4 - - - -
467A SEP 2.9 60.4 + - - +
374B GLU* 3.4 18.9 + - - +
375B ALA* 3.3 28.1 + - - +
376B ILE 2.9 0.6 - - - -
377B GLU* 1.3 77.2 - - - +
379B ALA* 1.3 65.8 + - - +
381B LEU* 3.0 30.4 - - + +
382B HIS* 3.3 17.3 + - - +
507B LYS* 5.1 1.8 - - - +
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Residues in contact with ALA 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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463A CYS* 4.2 12.9 - - - -
375B ALA 3.2 6.3 + - - +
376B ILE 3.1 1.7 + - - +
378B ARG* 1.3 77.6 - - - +
380B ARG* 1.3 54.1 + - - +
382B HIS* 2.7 31.8 + - - +
383B ILE* 3.6 3.5 + - - +
506B VAL* 3.7 12.7 - - + +
507B LYS* 4.3 12.1 - - - +
522B PRO* 3.5 37.9 - - + -
523B CYS* 4.4 6.3 - - - -
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Residues in contact with ARG 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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406A TYR* 3.4 22.7 + - - +
328B TYR* 2.9 28.4 + - - +
330B GLU* 3.5 4.1 + - - -
352B GLY* 4.7 4.5 - - - +
364B LEU* 3.0 33.1 + - - +
365B GLY* 3.2 24.2 + - - -
367B LEU 3.5 3.0 + - - -
372B ARG* 3.2 42.5 - - - +
376B ILE* 2.8 44.7 + - + +
377B GLU* 3.9 6.0 - - - +
379B ALA* 1.3 73.2 - - - +
381B LEU* 1.3 62.1 + - - +
382B HIS 3.0 1.4 + - - -
383B ILE* 3.2 30.3 + - + +
384B GLY 4.7 0.5 + - - -
523B CYS* 4.5 6.7 - - + -
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Residues in contact with LEU 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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402A PHE* 3.9 13.6 - - + -
403A GLU* 5.7 13.2 - - + -
406A TYR* 3.7 43.2 - - + -
407A GLN* 6.2 1.8 - - + -
459A PRO* 3.4 35.3 - - + +
377B GLU* 3.3 22.6 + - + +
378B ARG* 3.0 22.8 + - + +
379B ALA 3.0 0.4 + - - -
380B ARG* 1.3 78.7 - - - +
382B HIS* 1.3 66.0 + - + +
383B ILE 3.6 0.4 + - - -
384B GLY* 4.6 4.4 + - - -
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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