Contacts of the helix formed by residues 295 - 311 (chain B) in PDB entry 3MP4
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 ASN 295 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B GLU 5.3 0.2 - - - +
66B ALA 2.7 18.0 + - - +
293B GLY 4.0 0.8 + - - +
294B VAL* 1.3 72.3 - - - +
296B LEU* 1.3 58.3 + - - +
297B GLN* 3.0 17.2 + - - +
298B LYS* 2.9 55.7 + - + +
299B LEU* 2.9 27.4 + - - +
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Residues in contact with LEU 296 (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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279B GLU* 3.9 21.8 - - + +
282B VAL* 3.1 33.4 - - + +
283B TYR* 4.5 15.9 - - + -
286B GLU* 4.4 21.2 + - - +
294B VAL* 3.6 7.2 + - - +
295B ASN* 1.3 69.3 + - - +
297B GLN* 1.3 64.5 + - - +
299B LEU* 3.4 7.8 - - + +
300B LEU* 3.0 37.1 + - + +
318B VAL* 4.2 17.7 - - + -
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Residues in contact with GLN 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ASN* 3.0 12.3 + - - +
296B LEU* 1.3 79.6 - - - +
298B LYS* 1.3 69.3 + - + +
300B LEU* 3.3 13.0 + - + +
301B GLU* 3.3 31.9 + - + +
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Residues in contact with LYS 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B MET* 4.9 2.5 - - - +
65B GLU* 3.6 35.7 - - + +
66B ALA* 3.8 14.8 - - + +
295B ASN* 2.9 35.8 + - + +
297B GLN* 1.3 80.7 - - + +
299B LEU* 1.3 66.7 + - - +
301B GLU* 3.1 23.8 + - - +
302B ALA* 3.1 21.5 + - - +
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Residues in contact with LEU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B GLU* 5.0 0.2 - - - +
63B LEU* 4.0 17.5 - - + -
66B ALA* 3.6 9.8 - - + +
68B LEU* 4.6 2.5 - - + -
260B VAL* 3.8 22.6 - - + +
278B THR* 3.8 20.0 - - + -
279B GLU* 3.5 41.0 - - + +
282B VAL* 4.1 15.3 - - + -
294B VAL* 4.1 11.7 - - + -
295B ASN 2.9 13.2 + - - +
296B LEU* 3.2 11.2 + - + +
298B LYS* 1.3 77.6 - - - +
300B LEU* 1.3 56.8 + - - +
302B ALA* 3.3 3.7 + - - +
303B GLY* 3.0 23.4 + - - -
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Residues in contact with LEU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B GLU* 3.8 26.2 - - + +
296B LEU* 3.0 34.6 + - + +
297B GLN* 3.6 10.1 - - - +
298B LYS 3.2 0.2 - - - -
299B LEU* 1.3 76.0 - - - +
301B GLU* 1.3 60.2 + - - +
303B GLY* 3.2 1.0 + - - +
304B ASN* 2.8 31.6 + - - +
318B VAL* 4.6 3.6 - - + -
319B ALA* 3.5 39.9 - - + +
322B THR* 4.1 28.5 - - + +
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Residues in contact with GLU 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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62B MET* 3.7 18.0 - - + +
297B GLN* 3.3 26.4 + - + +
298B LYS* 3.1 27.9 + - - +
300B LEU* 1.3 77.2 - - + +
302B ALA* 1.3 58.0 + - - +
304B ASN* 3.2 6.5 + - - +
305B PHE* 2.8 30.8 + - - +
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Residues in contact with ALA 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU* 4.0 7.2 - - + +
62B MET* 3.8 34.2 - - + +
63B LEU* 4.0 26.0 - - + -
260B VAL* 4.3 1.6 - - - -
298B LYS 3.1 8.5 + - - +
299B LEU* 3.4 9.9 - - - +
300B LEU 3.2 0.2 - - - -
301B GLU* 1.3 79.0 - - - +
303B GLY* 1.3 63.0 + - - +
305B PHE* 3.0 12.1 + - - +
306B ILE* 3.1 16.5 + - - +
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Residues in contact with GLY 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B VAL* 3.3 24.3 - - - +
261B ALA* 4.4 4.3 - - - -
279B GLU* 4.2 8.7 - - - -
299B LEU 3.0 11.6 + - - -
300B LEU 3.2 3.1 + - - -
302B ALA* 1.3 76.7 - - - +
304B ASN* 1.3 61.1 + - - +
306B ILE* 3.1 7.4 - - - +
307B CYS* 3.1 29.8 + - - -
314B THR* 5.7 0.9 - - - -
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Residues in contact with ASN 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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300B LEU 2.8 20.0 + - - +
301B GLU* 3.8 5.6 + - - +
303B GLY* 1.3 70.3 - - - +
305B PHE* 1.3 66.2 + - - +
307B CYS* 4.5 6.0 - - - +
308B GLN* 3.1 57.0 + - - +
314B THR* 6.2 1.1 - - - -
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Residues in contact with PHE 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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55B VAL* 3.5 47.6 - - + -
58B LYS* 3.4 41.3 - - + -
59B LEU* 3.7 20.2 - - + -
62B MET* 3.7 24.7 - - + -
301B GLU 2.8 14.3 + - - +
302B ALA 3.0 9.2 + - - +
304B ASN* 1.3 80.4 - - - +
306B ILE* 1.3 64.8 + - - +
308B GLN* 3.5 6.7 + - - +
309B ALA* 3.2 21.4 + - + +
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Residues in contact with ILE 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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44B LEU* 4.3 8.7 - - + -
51B VAL* 4.4 6.1 - - + -
55B VAL* 4.0 25.4 - - + -
56B LYS* 6.2 0.2 - - - -
59B LEU* 3.8 34.8 - - + -
260B VAL* 4.9 3.6 - - + -
261B ALA* 5.1 0.2 - - + -
263B LEU* 3.8 34.5 - - + -
302B ALA 3.1 7.4 + - - +
303B GLY* 3.1 21.5 - - - +
305B PHE* 1.3 81.5 - - + +
307B CYS* 1.3 62.0 + - - +
309B ALA* 3.2 4.7 + - + -
310B LEU* 2.8 40.4 + - + +
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Residues in contact with CYS 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B ALA* 3.3 33.7 - - - -
263B LEU* 4.6 1.1 - - - -
303B GLY 3.1 16.0 + - - +
304B ASN* 4.1 9.2 - - - +
305B PHE 3.4 0.2 - - - -
306B ILE* 1.3 79.6 - - - +
308B GLN* 1.3 53.1 + - + +
310B LEU* 3.3 0.8 + - - -
311B ASN 2.7 28.4 + - - -
312B ARG* 2.8 45.0 + - - +
314B THR* 3.5 24.5 - - - +
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Residues in contact with GLN 308 (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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304B ASN* 3.1 40.5 + - - +
305B PHE* 3.7 6.5 - - - +
306B ILE 3.2 0.4 - - - -
307B CYS* 1.3 74.8 - - + +
309B ALA* 1.3 61.2 + - - +
311B ASN* 2.9 21.2 + - - +
312B ARG 5.2 0.4 - - - -
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Residues in contact with ALA 309 (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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50B ILE 5.7 0.2 - - - +
51B VAL* 4.6 7.0 - - + +
55B VAL* 3.8 36.8 - - + -
305B PHE* 3.2 15.8 + - + +
306B ILE* 3.2 11.1 + - + +
308B GLN* 1.3 79.4 - - - +
310B LEU* 1.3 61.7 + - - +
311B ASN* 3.5 1.7 + - - +
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Residues in contact with LEU 310 (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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44B LEU* 4.0 15.9 - - + -
47B GLU* 4.3 17.0 - - + +
49B ASN* 3.5 45.8 + - + +
50B ILE 4.7 1.1 - - - +
51B VAL* 3.1 35.2 - - + -
263B LEU* 4.1 18.6 - - + -
306B ILE* 2.8 33.7 + - + +
309B ALA* 1.3 75.4 - - - +
311B ASN* 1.3 71.2 + - - +
312B ARG* 3.4 19.4 + - + +
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Residues in contact with ASN 311 (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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49B ASN* 5.5 1.1 - - - +
307B CYS 2.7 9.5 + - - -
308B GLN* 2.9 15.3 + - - +
309B ALA 3.2 1.8 - - - +
310B LEU* 1.3 82.1 - - - +
312B ARG* 1.3 56.4 + - - +
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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