Contacts of the helix formed by residues 314 - 324 (chain C) in PDB entry 2PI8
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 GLY 314 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102C TYR* 3.1 26.5 - - - -
103C THR 3.2 12.6 + - - -
104C PRO* 5.4 0.9 - - - -
105C VAL* 4.5 12.5 - - - +
313C ILE* 1.3 78.1 - - - +
315C PRO* 1.3 74.7 - - - +
316C GLU 3.5 1.3 - - - -
317C ALA 3.4 2.5 + - - -
318C GLY 3.2 4.0 + - - -
171D ASP* 6.1 3.4 - - - -
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Residues in contact with PRO 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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102C TYR* 5.1 2.2 - - + -
105C VAL* 5.9 2.2 - - + +
314C GLY* 1.3 81.3 - - - +
316C GLU* 1.3 62.8 + - + +
318C GLY* 2.8 22.4 + - - +
319C HIS* 3.0 35.4 + - + +
109D ARG* 5.3 15.0 - - - +
113D GLN* 5.2 10.3 - - - +
170D GLY 5.6 6.3 - - - +
171D ASP* 5.9 6.1 - - + -
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Residues in contact with GLU 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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314C GLY 3.5 0.4 - - - -
315C PRO* 1.3 84.2 - - + +
317C ALA* 1.3 61.4 + - - +
319C HIS* 3.5 14.5 + - + +
320C ARG* 3.3 34.8 + - - +
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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
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102C TYR* 3.8 3.7 - - + +
311C GLN* 3.4 6.8 - - - +
312C GLY* 3.6 40.6 - - - +
313C ILE 3.8 8.3 + - - +
314C GLY* 3.4 10.6 + - - +
315C PRO 3.1 0.6 - - - -
316C GLU* 1.3 78.3 - - - +
318C GLY* 1.3 57.3 + - - +
319C HIS 3.5 0.2 - - - -
320C ARG* 3.7 18.1 - - - +
321C ALA* 3.1 28.1 + - - +
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Residues in contact with GLY 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C TYR* 3.5 36.1 - - - -
209C GLN* 4.4 3.7 + - - +
314C GLY 3.2 5.9 + - - -
315C PRO 2.8 9.6 + - - -
317C ALA* 1.3 78.0 - - - +
319C HIS* 1.3 59.2 + - - -
321C ALA* 3.8 1.0 - - - +
322C GLY* 3.0 26.3 + - - -
2G NAG 5.1 0.7 - - - +
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Residues in contact with HIS 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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209C GLN* 2.9 36.4 + - + +
212C ARG* 5.5 12.3 - - - -
315C PRO* 3.0 34.3 + - + +
316C GLU* 3.9 14.1 - - + +
318C GLY* 1.3 76.9 - - - +
320C ARG* 1.3 61.5 + - - +
322C GLY 3.6 0.3 + - - -
323C TRP* 3.0 18.0 - - + +
113D GLN* 5.9 0.6 + - - -
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Residues in contact with ARG 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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69A ARG* 5.2 10.4 - - - +
255C ARG* 3.7 38.8 - - - +
278C LEU* 4.7 6.8 - - + +
311C GLN* 2.7 47.2 + - - +
316C GLU* 3.3 26.2 + - - +
317C ALA* 3.7 21.3 - - - +
318C GLY 3.3 0.4 - - - -
319C HIS* 1.3 81.9 - - - +
321C ALA* 1.3 58.8 + - - +
323C TRP* 3.8 10.9 + - - +
324C TYR* 2.9 39.1 + - + +
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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
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100C GLY* 3.7 7.3 - - - +
101C TYR* 3.8 27.1 - - - +
102C TYR* 4.3 2.9 - - + -
311C GLN* 3.4 20.4 - - + +
317C ALA 3.1 19.8 + - - +
318C GLY 3.8 3.4 - - - +
319C HIS 3.3 0.2 - - - -
320C ARG* 1.3 74.5 - - - +
322C GLY* 1.3 60.9 + - - +
323C TRP 3.2 2.8 + - - -
324C TYR* 3.4 12.4 + - - +
1G NAG 2.9 17.7 + - - -
2G NAG 4.1 7.2 - - + -
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Residues in contact with GLY 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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206C MSE 4.6 1.9 - - - +
207C SER* 4.3 3.5 - - - -
208C MSE 3.8 18.9 + - - -
209C GLN* 3.3 26.3 - - - +
318C GLY 3.0 14.0 + - - -
319C HIS 3.6 0.4 + - - -
320C ARG 3.5 0.2 - - - -
321C ALA* 1.3 75.6 - - - +
323C TRP* 1.3 57.7 + - - +
324C TYR 3.5 0.2 - - - -
325C ASN* 5.9 0.5 - - - +
1G NAG 3.2 14.9 + - - +
2G NAG 4.0 11.8 - - - +
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Residues in contact with TRP 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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202C LYS* 5.1 10.5 - - - -
207C SER* 3.0 28.5 - - - -
209C GLN* 3.3 28.9 - - + +
210C ALA* 5.9 1.8 - - + -
278C LEU* 3.9 16.8 - - + -
279C ASP 4.5 2.7 - - - -
280C ASN* 2.9 21.0 + - - -
281C ASN* 3.3 31.4 - - + -
282C GLY* 3.3 28.3 - - - -
319C HIS* 3.0 28.6 + - + +
320C ARG* 4.1 2.2 - - - +
321C ALA 3.2 0.8 - - - -
322C GLY* 1.3 78.5 - - - +
324C TYR* 1.3 64.5 + - - +
325C ASN* 3.1 8.0 + - - +
326C HIS* 3.7 13.9 - - - -
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Residues in contact with TYR 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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98C PHE* 3.5 24.0 - - + +
99C THR* 3.7 19.6 + - - -
100C GLY 3.9 0.2 - - - +
255C ARG* 5.9 1.9 - - - -
275C VAL* 3.7 24.5 - - + +
276C PRO* 3.3 33.8 + - + -
277C LEU* 4.7 9.9 - - - +
278C LEU* 4.1 22.5 + - + +
289C GLU* 5.1 2.3 + - - -
309C ILE* 5.0 1.6 - - + -
311C GLN* 3.6 27.6 - - - -
320C ARG* 2.9 40.7 - - + +
321C ALA* 3.4 10.1 + - - +
323C TRP* 1.3 74.1 - - - +
325C ASN* 1.3 60.9 + - - +
326C HIS* 5.1 1.8 - - - -
1G NAG 2.8 26.3 + - - +
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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