Contacts of the helix formed by residues 294 - 307 (chain B) in PDB entry 2PMW
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 294 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A GLU* 2.5 27.8 + - - -
147A SER* 5.4 1.8 - - - -
261B VAL* 3.9 12.8 - - - +
292B GLY 3.8 7.0 - - - -
293B TYR* 1.3 79.1 - - - +
295B ARG* 1.3 64.1 + - - +
296B VAL* 3.4 1.6 - - - +
297B LEU* 3.1 30.6 + - - +
298B ASN* 3.0 24.8 + - - +
326B SER* 2.7 12.4 + - - -
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Residues in contact with ARG 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A THR* 3.5 11.1 + - - -
65A HIS* 3.1 42.2 + - + +
141A ASP* 4.1 11.1 + - - -
142A TYR* 3.4 46.0 - - + +
144A GLU* 3.1 12.0 + - - +
293B TYR* 3.9 20.8 - - + +
294B SER* 1.3 71.9 - - - +
296B VAL* 1.3 58.7 + - - +
298B ASN* 3.4 4.1 + - - +
299B ALA* 3.0 28.7 + - + +
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Residues in contact with VAL 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A VAL* 4.0 8.5 - - + -
81A VAL* 3.7 24.9 - - + -
119A LEU* 4.0 13.4 - - + +
142A TYR* 3.6 16.6 - - + +
144A GLU* 3.0 35.9 + - + +
261B VAL* 3.9 14.8 - - + -
265B LEU* 3.5 23.6 - - + -
294B SER* 3.4 1.6 - - - +
295B ARG* 1.3 75.6 - - - +
297B LEU* 1.3 69.4 + - - +
299B ALA* 3.3 1.9 + - - +
300B ALA* 2.9 23.0 + - - +
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Residues in contact with LEU 297 (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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149A VAL* 4.7 10.1 - - + -
261B VAL* 4.1 21.8 - - + -
264B THR* 4.0 28.7 - - + -
265B LEU* 3.9 21.8 - - + -
268B LEU* 4.2 10.3 - - + -
287B LEU* 6.4 0.4 - - + -
294B SER* 3.1 18.2 + - - +
296B VAL* 1.3 82.7 - - - +
298B ASN* 1.3 64.0 + - - +
300B ALA* 3.4 0.7 + - - +
301B CYS* 3.1 30.7 + - - -
326B SER* 4.2 9.4 - - - +
327B PRO* 4.0 37.5 - - + -
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Residues in contact with ASN 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B TYR* 3.6 21.4 + - - +
294B SER 3.0 17.6 + - - +
295B ARG* 3.8 4.9 - - - +
297B LEU* 1.3 76.6 - - - +
299B ALA* 1.3 58.6 + - - +
301B CYS* 3.3 2.8 + - - +
302B GLN* 2.9 30.2 + - - +
326B SER* 2.8 24.8 + - - -
327B PRO* 4.0 2.1 - - - +
329B SER* 3.0 25.4 + - - -
330B ALA* 3.6 33.2 + - + +
331B PRO* 4.9 4.5 - - + +
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Residues in contact with ALA 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 4.2 9.6 - - + -
142A TYR* 3.8 14.8 - - - +
295B ARG* 3.0 19.7 + - + +
296B VAL 3.3 4.5 + - - +
298B ASN* 1.3 78.5 - - - +
300B ALA* 1.3 56.6 - - - +
302B GLN* 3.3 16.3 + - - +
303B ARG* 2.8 31.6 + - - +
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Residues in contact with ALA 300 (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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118A LEU* 4.0 15.7 - - + +
119A LEU* 4.2 12.7 - - + +
265B LEU* 3.4 33.0 - - + +
268B LEU* 4.3 11.2 - - + +
296B VAL 2.9 9.5 + - - +
297B LEU 3.7 3.4 - - - +
299B ALA* 1.3 78.5 - - - +
301B CYS* 1.3 57.0 + - - +
303B ARG* 3.5 6.4 + - - +
304B LEU* 2.9 29.5 + - - +
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Residues in contact with CYS 301 (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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268B LEU* 4.1 15.3 - - - -
287B LEU* 4.3 5.4 - - - -
297B LEU* 3.1 23.5 + - - +
298B ASN 3.7 3.8 - - - +
300B ALA* 1.3 74.0 - - - +
302B GLN* 1.3 62.2 + - - +
304B LEU* 3.3 1.4 + - - +
305B ALA* 2.9 31.4 + - - +
311B LEU* 3.6 30.1 - - + +
327B PRO* 3.8 27.6 - - - -
330B ALA* 4.2 4.7 - - + -
333B VAL* 3.7 16.4 - - + -
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Residues in contact with GLN 302 (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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298B ASN 2.9 15.5 + - - +
299B ALA* 3.5 16.2 + - - +
301B CYS* 1.3 76.4 - - - +
303B ARG* 1.3 57.6 + - - +
305B ALA* 3.2 7.3 + - - +
306B ARG* 2.7 73.4 + - - +
330B ALA* 5.4 1.7 - - + +
331B PRO* 6.2 6.1 - - + -
332B GLU* 4.2 19.7 - - + +
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Residues in contact with ARG 303 (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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84A GLU* 5.3 13.8 + - - +
117A GLY 4.3 9.2 + - - -
118A LEU* 2.5 61.2 + - + +
119A LEU* 4.7 2.1 - - + +
120A PRO* 4.8 6.9 - - - +
299B ALA 2.8 18.5 + - - +
300B ALA* 3.7 7.6 - - - +
302B GLN* 1.3 77.6 - - - +
304B LEU* 1.3 61.7 + - - +
306B ARG* 3.2 9.5 + - - +
307B ALA* 3.0 23.7 + - - +
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Residues in contact with LEU 304 (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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118A LEU* 3.7 22.0 - - + +
268B LEU* 4.0 40.2 - - + +
271B ILE* 5.0 5.4 - - + -
272B ARG* 4.1 24.2 - - + +
285B VAL* 4.6 7.0 - - + -
300B ALA 2.9 18.5 + - - +
301B CYS* 3.9 4.7 - - - +
303B ARG* 1.3 76.0 - - - +
305B ALA* 1.3 61.7 + - - +
307B ALA* 3.4 9.4 + - + +
309B VAL* 3.3 43.6 + - + +
311B LEU* 4.3 14.4 - - + -
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Residues in contact with ALA 305 (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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301B CYS 2.9 18.2 + - - +
302B GLN 3.5 4.0 - - - +
304B LEU* 1.3 74.5 - - - +
306B ARG* 1.3 53.2 + - - +
307B ALA 3.1 4.9 - - - -
308B GLY* 2.7 26.5 + - - -
309B VAL 3.4 19.0 + - - +
311B LEU* 4.3 5.3 - - + +
332B GLU* 3.8 38.6 - - + +
408B LEU* 4.6 7.6 - - + +
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Residues in contact with ARG 306 (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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84A GLU* 5.9 0.8 + - - -
302B GLN* 2.7 54.1 + - - +
303B ARG* 3.2 8.9 + - - +
305B ALA* 1.3 70.3 - - - +
307B ALA* 1.3 56.7 + - - +
308B GLY* 3.0 8.4 + - - -
332B GLU* 2.7 29.3 + - - +
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Residues in contact with ALA 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A LEU* 5.2 2.7 - - + -
272B ARG* 3.7 43.8 + - - +
275B GLN* 4.9 2.8 + - - +
303B ARG* 3.0 15.1 + - + +
304B LEU* 3.6 14.6 - - + +
305B ALA 3.1 0.4 - - - -
306B ARG* 1.3 76.2 - - - +
308B GLY* 1.3 58.9 + - - +
309B VAL* 3.6 3.9 - - + +
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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