Contacts of the helix formed by residues 321 - 333 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318B GLU* 4.3 5.4 - - + +
319B LYS 4.7 0.9 - - - +
320B VAL* 1.3 81.8 - - - +
322B SER* 1.3 66.8 + - - +
323B GLU* 2.7 23.3 + - + +
324B GLN* 3.0 28.8 + - - +
325B LEU 3.2 4.5 + - - -
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Residues in contact with SER 322 (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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312B VAL* 5.1 10.3 - - - -
314B THR* 5.0 3.8 + - - -
318B GLU* 2.9 21.2 + - - -
320B VAL 3.0 4.0 + - - -
321B PRO* 1.3 69.3 - - - +
323B GLU* 1.3 51.1 + - - +
325B LEU* 2.6 18.1 + - - +
326B THR* 2.6 45.4 + - - -
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Residues in contact with GLU 323 (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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321B PRO* 2.7 26.3 + - + +
322B SER* 1.3 77.5 - - - +
324B GLN* 1.3 77.9 + - - +
326B THR* 3.0 6.3 + - - -
327B LEU* 3.0 35.8 + - + +
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Residues in contact with GLN 324 (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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320B VAL* 3.1 35.3 - - + +
321B PRO* 3.0 28.9 + - - +
323B GLU* 1.3 91.6 + - - +
325B LEU* 1.3 59.2 + - - +
327B LEU* 4.1 7.4 - - - +
328B LEU* 2.9 42.0 + - + +
331B GLU* 5.1 0.3 - - - +
379B ALA 4.5 3.9 - - - +
380B ALA* 3.9 18.0 - - + +
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Residues in contact with LEU 325 (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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285B ILE* 4.4 16.8 - - + -
290B LEU* 3.8 33.7 - - + +
312B VAL* 4.0 15.2 - - + +
314B THR* 3.5 32.8 - - + -
318B GLU* 4.4 12.1 - - + -
320B VAL* 3.7 23.3 - - + +
321B PRO 3.2 0.8 + - - -
322B SER* 2.6 26.3 + - - +
324B GLN* 1.3 79.7 - - - +
326B THR* 1.3 55.7 + - - -
328B LEU* 3.8 7.7 - - + +
329B VAL* 3.1 25.6 + - - +
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Residues in contact with THR 326 (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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310B ILE* 5.2 9.0 - - + +
311B MET* 5.1 5.4 - - - -
312B VAL* 3.5 32.0 - - + +
322B SER* 2.6 35.5 + - - -
323B GLU* 3.6 5.3 + - - -
325B LEU* 1.3 72.2 - - - +
327B LEU* 1.3 64.3 + - - +
328B LEU 3.1 2.2 + - - -
329B VAL* 3.4 11.8 + - + +
330B ARG* 2.9 23.9 - - + +
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Residues in contact with LEU 327 (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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323B GLU* 3.0 29.3 + - + +
324B GLN* 4.1 7.0 - - - +
326B THR* 1.3 77.8 - - - +
328B LEU* 1.3 54.4 + - - +
330B ARG* 2.5 44.7 + - + +
331B GLU* 2.8 32.4 - - - +
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Residues in contact with LEU 328 (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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285B ILE* 6.4 0.2 - - + -
290B LEU* 4.2 14.1 - - + -
324B GLN* 2.9 27.0 + - + +
325B LEU* 3.8 10.8 - - + +
327B LEU* 1.3 79.8 - - - +
329B VAL* 1.3 55.5 + - + +
331B GLU* 3.0 16.8 + - - +
332B PHE* 2.8 42.4 + - + +
376B LEU* 3.3 46.9 - - + +
379B ALA* 3.3 39.7 - - + +
380B ALA* 5.0 2.2 - - + -
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Residues in contact with VAL 329 (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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281B VAL* 4.7 5.6 - - + -
285B ILE* 4.4 19.1 - - + -
296B ILE* 4.5 9.9 - - + -
310B ILE* 4.6 19.3 - - + -
312B VAL* 3.9 19.5 - - + -
325B LEU 3.1 19.7 - - - +
326B THR* 3.5 8.5 - - + +
327B LEU 3.4 0.4 - - - -
328B LEU* 1.3 78.2 - - + +
330B ARG* 1.3 62.7 + - + +
331B GLU 3.1 0.5 + - - -
333B PHE* 3.0 51.2 + - + +
335B LEU* 4.7 12.8 - - + -
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Residues in contact with ARG 330 (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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310B ILE* 4.9 20.2 - - + -
326B THR* 2.9 22.7 - - + +
327B LEU* 2.5 48.3 + - + +
329B VAL* 1.3 79.3 - - + +
331B GLU* 1.3 107.7 + - - +
333B PHE 3.6 14.0 - - - +
335B LEU* 5.8 1.8 - - - -
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Residues in contact with GLU 331 (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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324B GLN 5.1 0.2 - - - +
327B LEU* 2.8 31.4 - - - +
328B LEU* 3.1 28.4 - - - +
329B VAL 3.0 0.2 - - - -
330B ARG* 1.3 101.6 + - - +
332B PHE* 1.3 65.6 + - + +
333B PHE 4.9 0.2 - - - +
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Residues in contact with PHE 332 (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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328B LEU* 2.8 22.9 + - + +
331B GLU* 1.3 82.2 - - + +
333B PHE* 1.3 69.9 + - + +
334B ASP 4.3 0.2 + - - -
372B LYS* 4.0 30.9 + - - -
375B LEU* 3.1 57.7 - - + -
376B LEU* 3.4 28.7 - - + -
379B ALA* 3.9 19.1 - - + -
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Residues in contact with PHE 333 (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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280B TYR* 3.7 38.6 - + - -
281B VAL* 3.6 36.3 - - + -
284B ASN* 4.5 2.0 - - + -
285B ILE* 5.5 1.3 - - + -
329B VAL* 3.0 32.1 + - + +
330B ARG* 3.6 19.6 - - - +
331B GLU 5.3 0.2 - - - -
332B PHE* 1.3 86.4 - - + +
334B ASP* 1.3 60.3 + - - +
335B LEU* 4.0 21.1 + - + +
343B MET* 4.3 8.1 - - - -
372B LYS* 3.7 21.8 - - + -
376B LEU* 3.5 34.3 - - + -
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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