Contacts of the helix formed by residues 331 - 340 (chain A) in PDB entry 2PFP
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 SER 331 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270A GLN* 4.9 1.7 + - - -
329A SER* 2.8 23.5 + - - -
330A GLU* 1.3 80.7 - - - +
332A VAL* 1.3 62.9 + - - +
333A PRO 3.4 0.2 - - - -
334A VAL* 3.0 8.3 + - - +
335A LEU* 2.8 40.9 + - - +
353A TYR* 3.3 43.1 - - - -
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Residues in contact with VAL 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A VAL 5.9 0.2 - - - +
265A LYS* 5.3 1.1 - - + -
266A ALA* 4.1 23.6 - - + +
269A VAL* 4.1 7.7 - - + +
270A GLN* 4.0 33.0 - - + +
328A ILE* 3.5 27.4 - - + -
329A SER* 3.2 7.8 + - - +
331A SER* 1.3 78.1 + - - +
333A PRO* 1.3 74.0 - - + +
335A LEU* 3.0 8.6 + - - +
336A GLU* 2.9 29.6 + - + +
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Residues in contact with PRO 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A ILE* 5.9 0.4 - - + -
329A SER 4.1 2.0 - - - +
330A GLU* 3.2 20.2 - - - +
332A VAL* 1.3 97.5 - - + +
334A VAL* 1.3 58.8 + - + +
336A GLU* 3.5 10.0 + - + +
337A LEU* 3.0 26.7 + - - +
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Residues in contact with VAL 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330A GLU 4.7 7.0 - - - +
331A SER 3.0 9.0 + - - +
333A PRO* 1.3 79.4 - - + +
335A LEU* 1.3 60.1 + - - +
337A LEU* 3.2 7.1 + - + +
338A PHE* 3.0 55.6 + - + -
353A TYR* 3.5 31.9 - - + -
358A ARG* 3.9 30.3 - - + +
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Residues in contact with LEU 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A VAL* 4.1 22.6 - - + +
270A GLN* 4.2 23.1 - - + -
331A SER* 2.8 36.4 + - - +
332A VAL* 3.0 7.6 + - - +
334A VAL* 1.3 75.8 - - - +
336A GLU* 1.3 57.5 + - - +
338A PHE* 3.5 1.1 + - + -
339A SER* 2.8 32.3 + - - -
349A ALA* 3.6 39.4 - - + +
350A GLN* 3.8 19.1 - - + +
353A TYR* 3.8 20.0 - - + -
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Residues in contact with GLU 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A LYS* 4.3 18.4 - - - +
269A VAL* 4.0 16.4 - - + +
332A VAL* 2.9 20.2 + - + +
333A PRO* 3.6 8.5 - - + +
335A LEU* 1.3 76.4 - - - +
337A LEU* 1.3 66.2 + - - +
339A SER* 3.4 8.5 + - - +
340A ASN* 3.1 44.7 + - - +
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Residues in contact with LEU 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333A PRO 3.0 15.8 + - - +
334A VAL* 3.4 9.6 - - - +
336A GLU* 1.3 78.5 - - - +
338A PHE* 1.3 82.2 + - + +
340A ASN* 3.3 5.9 + - - +
341A ILE* 4.3 0.3 - - - +
358A ARG 4.1 6.5 - - - +
359A SER* 4.1 7.6 - - - -
360A LEU* 4.0 31.8 - - + +
380A TYR* 2.7 53.7 + - + +
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Residues in contact with PHE 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A VAL* 3.0 33.4 + - + +
335A LEU* 3.8 4.5 - - - +
337A LEU* 1.3 85.2 - - + +
339A SER* 1.3 57.1 + - - +
340A ASN 3.0 4.7 - - - -
341A ILE* 3.0 33.3 + - - +
344A ALA* 3.8 6.8 - - - +
349A ALA* 3.8 28.7 - - + -
352A TRP* 3.8 30.5 - + + -
353A TYR* 4.1 4.3 - - + -
357A PHE* 3.5 35.7 - - + -
358A ARG 3.7 2.7 - - - -
359A SER 3.7 16.6 - - - -
360A LEU* 4.5 2.5 - - + -
363A ILE* 3.5 32.1 - - + -
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Residues in contact with SER 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A VAL* 4.1 13.0 - - - +
335A LEU 2.8 27.5 + - - -
336A GLU* 3.4 12.3 + - - +
337A LEU 3.5 0.2 - - - -
338A PHE* 1.3 71.7 - - - +
340A ASN* 1.3 57.2 + - - +
341A ILE 3.1 2.5 - - - -
344A ALA 3.7 13.9 - - - -
345A GLY* 4.3 17.7 - - - -
346A THR* 4.7 2.5 - - - -
349A ALA* 4.2 4.8 - - - +
752A NA 2.4 26.0 - - - -
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Residues in contact with ASN 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A GLU* 3.1 37.3 + - - +
337A LEU* 4.6 0.6 - - - +
338A PHE 3.0 2.2 - - - -
339A SER* 1.3 77.5 + - - +
341A ILE* 1.3 61.6 + - - +
342A TRP 3.6 2.3 + - - -
380A TYR* 3.3 37.7 + - + +
383A PHE* 5.6 4.7 - - - +
384A LEU* 4.1 33.1 - - + +
752A NA 4.2 0.4 - - - -
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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