Contacts of the helix formed by residues 314 - 322 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A GLY 3.6 10.8 - - - -
171A ASP* 3.9 3.6 - - - -
102B TYR* 3.2 15.6 - - - -
103B THR 3.1 12.7 + - - -
104B PRO* 5.4 1.3 - - - -
105B VAL* 4.5 5.3 - - - +
313B ILE* 1.3 76.7 - - - +
315B PRO* 1.3 74.7 - - - +
316B GLU 3.5 1.6 - - - -
317B ALA* 3.4 2.7 + - - +
318B GLY 3.1 15.4 + - - -
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Residues in contact with PRO 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ARG* 3.1 43.3 - - - +
113A GLN* 5.0 3.4 - - - +
170A GLY 3.1 17.9 - - - +
171A ASP* 4.4 6.5 - - + -
102B TYR* 5.1 2.5 - - + -
105B VAL 6.2 0.2 - - - +
314B GLY* 1.3 80.5 - - - +
316B GLU* 1.3 65.4 + - + +
318B GLY* 2.9 17.8 + - - +
319B HIS* 2.9 38.7 + - + +
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Residues in contact with GLU 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ARG* 5.5 8.1 - - - -
110A HIS* 5.5 4.9 + - - -
111A THR* 6.2 0.2 - - - -
113A GLN* 5.2 13.5 - - - +
171A ASP* 5.1 11.0 - - + +
314B GLY 3.5 0.2 - - - -
315B PRO* 1.3 80.7 - - + +
317B ALA* 1.3 61.9 + - - +
319B HIS* 3.6 14.2 + - + +
320B ARG* 3.2 35.6 + - - +
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Residues in contact with ALA 317 (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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102B TYR* 3.7 4.6 - - + +
311B GLN* 3.3 6.9 - - - +
312B GLY* 3.6 40.4 - - - +
313B ILE 3.7 8.7 + - - +
314B GLY 3.4 10.8 + - - +
315B PRO 3.1 0.4 - - - -
316B GLU* 1.3 78.9 - - - +
318B GLY* 1.3 57.6 + - - +
320B ARG* 3.7 19.1 + - - +
321B ALA* 3.1 27.5 + - - +
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Residues in contact with GLY 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B TYR* 3.5 37.6 - - - -
208B MSE 5.8 0.5 - - - +
314B GLY 3.1 5.5 + - - -
315B PRO* 2.9 8.2 + - - -
317B ALA* 1.3 77.3 - - - +
319B HIS* 1.3 60.7 + - - +
320B ARG 3.3 0.2 - - - -
321B ALA* 3.7 0.5 - - - +
322B GLY* 2.9 27.4 + - - -
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Residues in contact with HIS 319 (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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113A GLN* 3.7 20.7 + - - -
209B GLN* 6.2 2.4 - - - +
212B ARG* 5.9 7.4 - - - -
280B ASN 6.1 0.4 - - - +
315B PRO* 2.9 35.6 + - + +
316B GLU* 3.9 13.5 - - + +
318B GLY* 1.3 78.2 - - - +
320B ARG* 1.3 59.4 + - - +
321B ALA 3.4 0.5 + - - -
322B GLY* 3.6 5.0 + - - -
323B TRP* 2.9 32.4 + - - +
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Residues in contact with ARG 320 (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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255B ARG* 3.7 39.2 - - - +
278B LEU* 4.7 6.8 - - + +
311B GLN* 2.8 48.0 + - - +
312B GLY* 5.2 0.2 - - - -
316B GLU* 3.2 31.7 + - - +
317B ALA* 3.7 19.4 - - - +
318B GLY 3.3 0.2 - - - -
319B HIS* 1.3 81.0 - - - +
321B ALA* 1.3 58.3 + - - +
323B TRP* 4.2 9.4 + - - +
324B TYR* 3.2 35.3 - - + +
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Residues in contact with ALA 321 (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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100B GLY* 3.7 7.0 - - - +
101B TYR 3.9 16.2 - - - +
102B TYR* 4.2 3.4 - - + -
311B GLN* 3.5 19.1 - - + -
317B ALA 3.1 20.5 + - - +
318B GLY 3.7 3.4 - - - +
319B HIS 3.2 0.2 - - - -
320B ARG* 1.3 74.1 - - - +
322B GLY* 1.3 49.9 + - - +
323B TRP 2.8 7.2 + - - -
324B TYR* 3.6 4.8 + - - +
1F NAG 2.5 31.4 + - - -
2F NAG 3.8 18.2 - - + -
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Residues in contact with GLY 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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207B SER* 4.1 1.9 - - - -
208B MSE 3.8 38.0 + - - +
209B GLN* 4.5 3.5 + - - +
318B GLY 2.9 15.7 + - - -
319B HIS* 3.6 2.5 + - - +
320B ARG 3.6 0.4 - - - -
321B ALA* 1.3 72.2 - - - +
323B TRP* 1.3 76.9 + - - -
1F NAG 3.6 7.0 - - - -
2F NAG 4.0 5.7 - - - +
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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