Contacts of the helix formed by residues 313 - 326 (chain C) in PDB entry 1P4V
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 PHE 313 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310C THR 2.9 21.5 - - - -
311C TRP* 3.8 3.1 - - + +
312C ASN* 1.3 72.7 - - - +
314C GLY* 1.3 65.3 + - - +
315C LEU 3.0 6.4 + - - -
316C HIS* 3.2 32.3 + - + +
317C ALA* 3.1 21.5 + - - +
342C VAL* 4.3 12.9 - - + +
348C GLU* 2.8 41.5 - - + +
350C SER* 5.6 0.2 - - - -
351C VAL* 4.8 0.4 - - + -
451C ASN* 2.9 53.4 - - + -
452C THR 3.7 5.6 - - - -
453C ILE* 3.5 28.5 - - + -
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Residues in contact with GLY 314 (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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309C SER* 2.8 35.1 + - - -
310C THR 4.0 0.7 - - - -
311C TRP 2.9 12.7 + - - -
312C ASN 2.9 2.4 - - - -
313C PHE* 1.3 84.8 - - - +
315C LEU* 1.3 59.0 + - - +
317C ALA* 3.7 6.3 - - - -
318C ASN* 2.8 25.3 + - - -
453C ILE* 4.4 0.2 - - - -
578C ALA* 3.3 4.9 - - - -
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Residues in contact with LEU 315 (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 ASN 3.0 14.8 + - - +
313C PHE 3.0 0.2 - - - -
314C GLY* 1.3 81.3 - - - +
316C HIS* 1.3 62.8 + - - +
318C ASN 3.3 5.0 + - - -
319C VAL* 3.3 5.0 + - + +
578C ALA* 3.4 16.1 - - + +
585C ASN* 2.8 51.9 + - - +
586C ARG* 3.9 20.2 - - - +
587C LEU* 4.1 19.1 - - + +
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Residues in contact with HIS 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312C ASN 4.5 1.4 + - - -
313C PHE* 3.2 40.9 + - + +
315C LEU* 1.3 75.7 - - - +
317C ALA* 1.3 66.6 + - - +
319C VAL* 3.2 26.4 + - + +
320C GLU* 3.4 4.9 + - - +
341C LEU* 3.4 37.9 - - + +
342C VAL* 5.1 4.9 - - - +
345C ASP* 4.8 12.6 + - - +
348C GLU* 4.8 6.3 + - - +
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Residues in contact with ALA 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C PHE 3.1 18.3 + - - +
314C GLY 3.8 3.1 - - - +
316C HIS* 1.3 76.8 - - - +
318C ASN* 1.3 63.7 + - - +
320C GLU* 3.1 14.4 + - - +
321C ALA 3.1 9.7 + - - -
338C GLY* 3.5 23.6 - - - +
341C LEU* 3.7 11.4 - - - -
342C VAL* 4.1 5.6 - - + -
453C ILE* 3.6 24.0 - - + -
455C MET* 3.6 9.1 - - + +
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Residues in contact with ASN 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C VAL* 3.5 23.1 + - - +
309C SER* 2.6 25.2 + - - -
314C GLY 2.8 16.5 + - - +
315C LEU 3.3 6.7 - - - +
316C HIS 3.1 0.2 - - - -
317C ALA* 1.3 74.4 - - - +
319C VAL* 1.3 60.1 + - - +
321C ALA* 3.1 5.0 + - - +
322C TRP* 2.8 31.5 + - - +
455C MET* 3.5 8.6 - - - +
578C ALA* 3.1 33.3 + - - +
579C VAL 3.5 1.4 - - - +
580C HIS* 3.5 8.8 - - + +
585C ASN* 3.2 23.4 + - - +
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Residues in contact with VAL 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315C LEU 3.5 14.4 - - - +
316C HIS* 3.2 16.7 + - + +
318C ASN* 1.3 77.2 - - - +
320C GLU* 1.3 72.2 + - - +
322C TRP* 3.3 7.8 + - - +
323C LYS* 3.2 30.3 + - + +
580C HIS* 4.5 5.6 - - + +
585C ASN* 4.0 11.2 - - + +
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Residues in contact with GLU 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 HIS 3.4 1.5 + - - +
317C ALA 3.1 8.8 + - - +
319C VAL* 1.3 81.3 - - - +
321C ALA* 1.3 65.7 + - - +
323C LYS* 3.1 45.3 + - - +
324C VAL 3.8 0.2 + - - -
337C LYS* 3.2 45.9 - - + +
338C GLY* 4.2 11.2 - - - -
341C LEU* 3.5 43.2 - - + +
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Residues in contact with ALA 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C VAL* 4.1 16.4 - - + -
317C ALA 3.1 4.9 + - - +
318C ASN 3.1 8.4 + - - +
320C GLU* 1.3 79.2 - - - +
322C TRP* 1.3 58.4 + - - +
324C VAL* 3.1 7.1 + - - +
325C LEU* 2.9 29.7 + - - +
334C ALA* 3.5 32.4 - - + +
337C LYS* 5.2 0.2 - - - -
338C GLY* 4.2 1.0 - - - +
455C MET* 3.9 21.5 - - - -
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Residues in contact with TRP 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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305C PRO* 3.3 51.1 - - + -
306C ILE* 4.1 1.6 - - - -
307C VAL* 4.4 0.9 - - + -
318C ASN 2.8 17.7 + - - +
319C VAL* 3.5 6.5 - - - +
321C ALA* 1.3 73.1 - - - +
323C LYS* 1.3 53.5 + - - +
324C VAL 3.0 2.5 - - - -
325C LEU* 4.0 14.6 - - + +
326C SER* 2.7 62.0 + - - -
580C HIS* 3.4 55.2 - + + +
581C ASP 3.3 23.1 - - - -
582C GLN* 3.5 14.8 - - + -
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Residues in contact with LYS 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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319C VAL* 3.2 20.2 + - + +
320C GLU* 3.1 37.2 + - - +
322C TRP* 1.3 76.6 - - - +
324C VAL* 1.3 56.9 + - - +
326C SER* 4.0 4.0 - - - -
327C LYS* 3.1 31.4 + - - +
337C LYS* 2.9 30.9 - - - +
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Residues in contact with VAL 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321C ALA 3.1 7.3 + - - +
322C TRP 3.0 0.4 - - - -
323C LYS* 1.3 79.7 - - - +
325C LEU* 1.3 63.6 + - - +
327C LYS* 3.2 10.4 + - - +
329C GLY* 2.8 36.4 + - - -
330C LYS 3.6 24.9 - - - +
333C ASP* 4.1 13.5 - - + +
334C ALA* 3.8 16.8 - - + +
337C LYS* 3.6 31.2 - - + +
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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
----------------------------------------------------------
305C PRO* 3.6 24.2 - - + +
306C ILE 4.2 6.7 - - - +
307C VAL* 3.7 34.8 - - + -
321C ALA 2.9 19.7 + - - +
322C TRP* 4.0 16.2 - - + -
324C VAL* 1.3 76.4 - - - +
326C SER* 1.3 57.3 + - - +
328C GLY* 3.0 19.4 + - - -
329C GLY 4.3 6.5 - - - +
331C ALA* 4.2 6.5 - - - -
334C ALA* 3.5 20.9 - - + -
457C ALA* 4.0 12.6 - - + -
459C ASP* 3.9 33.2 - - + -
460C ALA* 4.9 2.4 + - - +
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Residues in contact with SER 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C PRO* 4.8 3.8 - - - -
322C TRP* 2.7 58.3 + - - +
323C LYS* 3.8 7.6 + - - -
325C LEU* 1.3 73.1 - - - +
327C LYS* 1.3 71.3 + - - +
328C GLY 3.2 2.6 + - - -
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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