Contacts of the helix formed by residues 315 - 324 (chain C) in PDB entry 6UWZ
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 PRO 315 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313C THR 3.2 8.7 - - - +
314C MET* 1.3 103.9 - - + +
316C ASN* 1.3 64.7 + - - +
317C TRP* 3.6 31.6 - - + +
318C ILE* 3.7 24.9 - - + -
319C ARG* 3.6 10.9 + - - +
428C TRP* 4.3 1.1 - - + -
328D THR* 3.6 18.4 - - + +
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Residues in contact with ASN 316 (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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315C PRO* 1.3 78.0 - - - +
317C TRP* 1.3 61.7 + - - +
318C ILE 3.4 0.4 - - - -
319C ARG* 3.7 15.7 + - - +
320C GLN* 2.9 31.1 + - - +
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Residues in contact with TRP 317 (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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315C PRO* 3.6 22.9 - - + +
316C ASN* 1.3 76.8 - - - +
318C ILE* 1.3 100.0 + - + +
320C GLN* 4.4 12.1 - - - +
321C ILE* 2.9 58.1 + - + +
322C PHE* 4.9 9.4 - + - -
328D THR* 5.7 0.7 - - - -
512D POV 4.2 28.5 - - - -
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Residues in contact with ILE 318 (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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304C LEU* 5.1 1.8 - - + -
307C ARG* 4.7 0.2 - - - +
314C MET* 4.6 6.3 - - + -
315C PRO* 3.7 28.4 + - + -
316C ASN 3.4 0.2 - - - -
317C TRP* 1.3 111.3 - - + +
319C ARG* 1.3 67.6 + - - +
322C PHE* 2.9 37.0 + - + +
428C TRP* 4.3 20.2 - - + -
431C VAL* 4.0 32.1 - - + -
512D POV 4.1 24.7 - - - -
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Residues in contact with ARG 319 (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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314C MET* 2.8 36.0 + - - +
315C PRO 3.6 16.2 + - - +
316C ASN* 3.5 17.8 + - - +
317C TRP 3.4 0.2 - - - -
318C ILE* 1.3 79.4 - - - +
320C GLN* 1.3 66.0 + - - +
323C ILE* 2.9 56.5 + - + +
324C GLU* 3.7 14.9 + - + +
334C ARG* 5.8 0.6 - - - +
424C LEU* 5.8 4.6 - - - +
427C ASP* 3.6 23.2 + - - +
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Residues in contact with GLN 320 (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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316C ASN 2.9 20.1 + - - +
317C TRP* 3.7 13.9 + - - +
319C ARG* 1.3 71.9 - - - +
321C ILE* 1.3 72.0 + - + +
324C GLU* 2.9 52.2 + - - +
325C THR* 3.2 12.6 + - - +
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Residues in contact with ILE 321 (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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317C TRP* 2.9 48.5 + - + +
318C ILE 4.1 1.3 - - - +
320C GLN* 1.3 82.7 - - + +
322C PHE* 1.3 73.3 + - + +
325C THR* 3.5 10.9 + - + +
326C LEU* 3.1 50.5 + - + +
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Residues in contact with PHE 322 (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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304C LEU* 6.2 2.0 - - + -
317C TRP* 4.9 13.9 - + - -
318C ILE* 2.9 33.0 + - + +
321C ILE* 1.3 91.8 - - + +
323C ILE* 1.3 64.7 + - - +
326C LEU* 3.7 21.5 - - + -
327C PRO* 3.7 5.4 - - - +
430C TYR* 4.3 0.3 - - - -
431C VAL* 4.0 26.4 - - + -
434C VAL* 3.5 37.0 - - + +
435C ALA* 3.8 31.9 - - + -
438C LEU* 4.6 9.6 - - + -
439C PHE* 5.9 3.1 - + - -
512D POV 6.5 0.9 - - - -
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Residues in contact with ILE 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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314C MET* 3.9 17.3 - - + -
319C ARG* 2.9 38.5 + - + +
322C PHE* 1.3 84.8 - - - +
324C GLU* 1.3 67.3 + - + +
327C PRO* 3.8 15.4 - - - +
328C PRO* 5.6 0.2 - - - +
334C ARG* 4.0 21.5 - - - +
427C ASP* 4.3 10.1 - - + +
430C TYR* 4.0 16.2 - - + -
431C VAL* 3.7 25.8 - - + -
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Residues in contact with GLU 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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319C ARG* 3.9 17.7 - - + +
320C GLN* 2.9 40.5 + - - +
323C ILE* 1.3 88.6 - - + +
325C THR* 1.3 62.5 + - - +
327C PRO* 4.2 2.2 - - - -
328C PRO* 3.9 14.8 - - - +
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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