Contacts of the helix formed by residues 321 - 333 (chain C) in PDB entry 1P7L
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 321 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318C GLU* 4.3 4.7 - - + +
319C LYS 4.7 1.3 - - - +
320C VAL* 1.3 79.9 - - - +
322C SER* 1.3 70.1 + - - +
323C GLU* 2.6 23.5 + - + +
324C GLN* 2.9 30.2 + - - +
325C LEU 3.3 4.5 + - - -
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Residues in contact with SER 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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312C VAL* 5.1 10.8 - - - -
314C THR* 5.1 3.1 - - - -
318C GLU* 2.9 21.0 + - - -
320C VAL 2.9 5.3 + - - -
321C PRO* 1.3 68.9 - - - +
323C GLU* 1.3 50.0 + - - +
325C LEU* 2.6 18.9 + - - +
326C THR* 2.6 45.5 + - - -
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Residues in contact with GLU 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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321C PRO* 2.6 26.6 + - + +
322C SER* 1.3 78.7 + - - +
324C GLN* 1.3 73.9 + - - +
326C THR* 3.0 6.2 + - - -
327C LEU* 3.0 37.9 + - + +
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Residues in contact with GLN 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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320C VAL* 3.1 24.8 - - + +
321C PRO* 2.9 42.6 + - - +
323C GLU* 1.3 90.1 + - - +
325C LEU* 1.3 61.2 + - - +
326C THR 3.2 0.2 - - - -
327C LEU* 3.8 8.0 - - - -
328C LEU* 2.9 39.1 + - + +
379C ALA 4.4 4.0 - - - +
380C ALA* 3.9 20.1 - - + +
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Residues in contact with LEU 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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285C ILE* 4.3 18.8 - - + -
290C LEU* 3.8 39.3 - - + +
294C CYS* 5.8 0.2 - - + -
312C VAL* 3.9 16.3 - - + +
314C THR* 3.5 32.1 - - + +
318C GLU* 4.4 9.2 - - + -
320C VAL* 3.7 15.0 - - + +
321C PRO 3.3 0.2 + - - -
322C SER* 2.6 28.3 + - - +
324C GLN* 1.3 80.3 - - - +
326C THR* 1.3 55.8 + - - +
328C LEU* 3.8 7.0 - - + +
329C VAL* 3.1 26.5 + - - +
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Residues in contact with THR 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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310C ILE* 5.3 7.6 - - + +
311C MET* 5.1 5.6 - - - -
312C VAL* 3.5 35.0 - - + +
322C SER* 2.6 30.2 + - - -
323C GLU* 3.6 5.3 + - - -
325C LEU* 1.3 71.2 - - - +
327C LEU* 1.3 64.9 + - - +
328C LEU 3.1 1.9 + - - -
329C VAL* 3.4 8.6 + - + +
330C ARG* 3.0 24.3 - - + +
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Residues in contact with LEU 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 GLU* 3.0 28.8 + - + +
324C GLN* 4.1 7.0 - - - +
326C THR* 1.3 79.3 - - - +
328C LEU* 1.3 52.6 + - - +
330C ARG* 2.6 43.7 + - - +
331C GLU* 2.6 32.7 - - - +
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Residues in contact with LEU 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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285C ILE* 6.4 0.7 - - + -
290C LEU* 4.3 12.8 - - + -
324C GLN* 2.9 24.7 + - + +
325C LEU* 3.8 9.6 - - + +
326C THR 3.1 0.2 - - - -
327C LEU* 1.3 78.7 - - - +
329C VAL* 1.3 60.2 + - + +
331C GLU* 3.0 16.5 + - - +
332C PHE* 2.8 37.1 + - + +
376C LEU* 3.2 47.8 - - + +
379C ALA* 3.2 39.0 - - + +
380C ALA* 5.0 3.4 - - + -
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Residues in contact with VAL 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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281C VAL* 4.7 10.5 - - + -
285C ILE* 4.4 19.5 - - + -
296C ILE* 4.5 5.4 - - + -
310C ILE* 4.6 19.7 - - + -
312C VAL* 3.9 19.7 - - + -
325C LEU 3.1 19.7 - - - +
326C THR* 3.5 8.3 - - + +
328C LEU* 1.3 77.3 - - + +
330C ARG* 1.3 65.7 + - + +
331C GLU 3.0 1.0 + - - -
333C PHE* 3.0 46.4 + - + +
335C LEU* 4.7 12.7 - - + +
376C LEU* 5.8 0.2 - - - -
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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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310C ILE* 5.0 18.6 - - + -
326C THR* 3.0 26.0 - - + +
327C LEU* 2.6 43.0 + - + +
329C VAL* 1.3 77.6 - - + +
331C GLU* 1.3 102.8 + - - +
333C PHE 3.7 14.3 - - - +
335C LEU* 5.7 2.2 - - - -
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Residues in contact with GLU 331 (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 GLN 5.0 0.2 - - - +
327C LEU* 2.6 36.4 - - - +
328C LEU* 3.0 24.8 - - + +
329C VAL 2.9 0.2 - - - -
330C ARG* 1.3 102.3 + - - +
332C PHE* 1.3 65.6 + - + +
333C PHE 5.4 0.2 - - - -
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Residues in contact with PHE 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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328C LEU* 2.8 19.5 + - + +
331C GLU* 1.3 84.7 - - + +
333C PHE* 1.3 71.0 + - + +
372C LYS* 4.0 31.6 + - - -
375C LEU* 3.3 58.6 - - + -
376C LEU* 3.5 28.3 - - + -
379C ALA* 3.9 19.5 - - + -
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Residues in contact with PHE 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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280C TYR* 3.7 32.1 - + - -
281C VAL* 3.5 35.2 - - + -
284C ASN* 4.6 2.0 - - + -
285C ILE* 5.5 0.9 - - + -
329C VAL* 3.0 32.0 + - + +
330C ARG* 3.7 19.8 - - - +
332C PHE* 1.3 86.1 - - + +
334C ASP* 1.3 61.1 + - - +
335C LEU* 3.9 21.9 + - + +
343C MET* 4.4 7.6 - - - -
372C LYS* 3.5 29.8 - - + -
376C LEU* 3.5 35.4 - - + -
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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