Contacts of the helix formed by residues 322 - 330 (chain C) 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 ASN 322 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282C LEU* 4.2 15.2 - - - +
320C ASN 3.6 4.7 + - - +
321C ARG* 1.3 76.6 - - - +
323C ALA* 1.3 65.3 + - - +
324C THR* 2.4 33.1 + - - +
325C VAL* 2.9 29.3 + - - +
326C GLU* 3.1 25.4 + - - +
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Residues in contact with ALA 323 (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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322C ASN* 1.3 73.0 - - - +
324C THR* 1.3 56.0 + - - +
326C GLU* 3.1 8.3 + - - +
327C MET* 2.7 38.0 + - - +
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Residues in contact with THR 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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322C ASN* 2.4 32.1 + - - -
323C ALA* 1.3 76.1 - - - +
325C VAL* 1.3 51.1 + - - +
327C MET* 3.0 27.2 + - + +
328C THR* 2.7 42.5 + - - -
428C ARG* 5.9 4.3 - - - +
435C PRO* 4.6 9.0 - - + -
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Residues in contact with VAL 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C GLU* 3.1 45.1 - - + +
282C LEU* 4.5 12.8 - - + -
321C ARG* 3.8 7.2 - - + -
322C ASN* 2.9 35.4 - - - +
323C ALA 3.3 0.2 - - - -
324C THR* 1.3 75.0 + - - +
326C GLU* 1.3 64.6 + - - +
328C THR* 3.1 2.8 + - - -
329C ARG* 2.9 32.9 + - + +
435C PRO* 3.8 31.8 - - + +
436C CYS* 4.0 0.6 - - - -
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Residues in contact with GLU 326 (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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492B VAL* 5.6 0.3 - - - +
493B ASP* 3.2 44.9 - - + +
494B ASP* 4.0 15.2 - - - +
497B ARG* 3.7 18.0 + - - -
321C ARG* 3.8 20.4 - - - +
322C ASN 3.1 16.2 + - - +
323C ALA* 3.4 7.6 - - - +
325C VAL* 1.3 79.3 - - - +
327C MET* 1.3 63.0 + - - +
329C ARG* 3.4 13.8 + - - +
330C ARG* 3.5 10.0 + - - +
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Residues in contact with MET 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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323C ALA 2.7 21.0 + - - +
324C THR* 3.3 30.5 - - + +
326C GLU* 1.3 73.2 - - - +
328C THR* 1.3 72.1 + - - +
330C ARG* 3.2 32.7 - - - +
331C HIS* 3.1 29.7 + - + -
419C VAL* 6.2 2.5 - - - -
420C LYS* 5.5 11.7 - - - +
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Residues in contact with THR 328 (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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324C THR* 2.7 22.8 + - - -
325C VAL 3.7 3.1 - - - -
327C MET* 1.3 81.2 - - - +
329C ARG* 1.3 66.3 + - - +
330C ARG 3.0 2.0 - - - -
331C HIS* 3.0 16.8 + - - -
332C ILE* 3.5 9.0 + - - +
418C PHE 3.6 10.1 - - - +
419C VAL* 3.4 35.1 - - + +
420C LYS* 4.6 7.4 - - + +
435C PRO* 3.5 27.9 - - + +
436C CYS* 3.9 11.7 - - + -
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Residues in contact with ARG 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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492B VAL* 3.9 15.2 - - + +
493B ASP* 3.0 33.4 + - - +
279C TYR* 3.6 8.2 + - - +
281C GLU* 3.1 8.3 + - - -
301C GLY* 4.8 6.2 + - - +
313C LEU* 2.4 33.1 + - - +
314C GLY* 3.8 18.8 + - - +
316C LEU* 3.2 19.6 + - - +
321C ARG* 3.0 32.5 - - - +
325C VAL* 2.9 26.4 + - - +
326C GLU 3.6 4.7 - - - +
327C MET 3.3 0.2 - - - -
328C THR* 1.3 77.1 - - - +
330C ARG* 1.3 62.9 + - - +
331C HIS 3.2 0.9 + - - -
332C ILE* 3.2 29.7 + - + +
333C GLY 4.5 1.2 + - - -
436C CYS* 3.7 15.3 - - - -
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Residues in contact with ARG 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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490B ILE 4.5 7.1 - - - +
491B GLY* 4.1 26.2 - - - -
492B VAL* 4.7 10.3 - - + +
547B ASP* 4.0 34.4 - - - +
548B PRO 5.6 0.6 - - - -
549B GLN 4.9 4.0 + - - -
326C GLU 3.5 7.2 + - - +
327C MET* 3.2 30.4 + - - +
328C THR 3.0 0.4 - - - -
329C ARG* 1.3 80.0 - - - +
331C HIS* 1.3 85.0 + - + +
332C ILE 3.8 0.2 + - - -
333C GLY* 4.3 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