Contacts of the helix formed by residues 1301 - 1312 (chain D) in PDB entry 3CMT
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 GLY1301 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3233A GLU* 4.6 8.7 - - - -
1289D ALA* 2.8 24.1 + - - -
1291D TYR* 3.5 9.2 - - - -
1300D GLN* 1.3 74.4 - - - +
1302D LYS* 1.3 67.2 + - - -
1303D ALA* 3.1 5.2 - - - -
1304D ASN 3.0 14.8 + - - -
1305D ALA 3.3 6.8 + - - -
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Residues in contact with LYS1302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3233A GLU* 3.7 32.7 + - - +
3234A GLY* 5.0 14.6 - - - +
1261D GLN* 5.6 8.2 - - - +
1269D ASN* 5.0 5.0 - - - +
1272D GLY* 2.9 41.4 + - - -
1275D VAL* 4.2 9.4 - - + -
1276D ASP* 3.2 31.0 + - - +
1291D TYR* 3.3 22.2 + - - +
1301D GLY* 1.3 71.5 - - - -
1303D ALA* 1.3 57.9 + - - +
1305D ALA* 3.4 3.3 + - - +
1306D THR* 2.8 38.2 + - - +
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Residues in contact with ALA1303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3233A GLU* 5.6 0.2 + - - -
3303A ALA* 4.8 19.1 - - + -
1300D GLN 5.5 0.2 - - - +
1301D GLY* 3.1 2.9 - - - +
1302D LYS* 1.3 79.2 - - - +
1304D ASN* 1.3 64.2 + - - +
1306D THR* 3.5 6.7 + - - -
1307D ALA* 3.3 19.6 + - - +
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Residues in contact with ASN1304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3303A ALA* 5.5 3.6 - - - +
3304A ASN* 2.9 44.1 + - - +
1298D ILE 4.1 1.2 - - - +
1299D GLY* 4.0 6.3 - - - -
1300D GLN* 2.9 37.8 + - - +
1301D GLY 3.0 2.6 + - - +
1303D ALA* 1.3 80.6 - - - +
1305D ALA* 1.3 60.4 + - - +
1307D ALA* 3.1 12.2 + - - +
1308D TRP* 2.9 27.7 + - - +
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Residues in contact with ALA1305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1275D VAL* 4.0 17.7 - - + -
1291D TYR* 3.8 38.4 - - + -
1298D ILE* 4.1 20.0 - - + +
1299D GLY* 4.3 1.7 - - - -
1301D GLY 3.3 3.4 + - - -
1302D LYS 3.4 7.4 + - - +
1304D ASN* 1.3 77.4 - - - +
1306D THR* 1.3 63.5 + - - +
1308D TRP* 3.3 4.3 + - - +
1309D LEU* 3.3 25.5 + - - +
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Residues in contact with THR1306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1269D ASN* 3.8 14.2 + - - +
1271D TYR* 3.6 11.1 - - + +
1272D GLY* 3.6 35.7 - - - +
1275D VAL* 3.9 10.8 - - - +
1302D LYS* 2.8 26.2 + - - +
1303D ALA* 3.5 7.7 - - - -
1305D ALA* 1.3 77.4 - - - +
1307D ALA* 1.3 60.4 + - - +
1309D LEU* 3.2 6.0 + - - +
1310D LYS* 3.2 32.1 + - - +
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Residues in contact with ALA1307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3300A GLN* 5.8 5.8 - - - +
1303D ALA 3.3 10.1 + - - +
1304D ASN* 3.1 17.7 + - - +
1306D THR* 1.3 79.2 - - - +
1308D TRP* 1.3 61.4 + - - +
1310D LYS* 3.4 15.9 + - + +
1311D ASP* 3.1 30.1 + - - +
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Residues in contact with TRP1308 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1293D TYR* 4.7 7.6 - + + -
1296D GLU* 3.8 26.4 + - - -
1297D LYS 5.1 0.8 + - - -
1298D ILE* 3.2 66.7 - - + +
1304D ASN 2.9 7.2 + - - +
1305D ALA 3.5 8.1 - - - +
1306D THR 3.2 0.2 - - - -
1307D ALA* 1.3 77.8 - - - +
1309D LEU* 1.3 81.5 + - + +
1311D ASP* 3.1 6.5 + - + +
1312D ASN* 2.8 69.4 + - + +
1315D THR* 4.0 25.8 - - + -
1319D ILE* 5.3 0.4 - - + -
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Residues in contact with LEU1309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1271D TYR* 3.8 22.2 - - + +
1274D LEU* 4.0 22.9 - - + -
1275D VAL* 3.7 31.4 - - + +
1284D ILE* 4.8 8.1 - - + -
1298D ILE* 5.0 3.6 - - + -
1305D ALA 3.3 5.3 + - - +
1306D THR 3.2 8.1 + - - +
1308D TRP* 1.3 95.5 - - + +
1310D LYS* 1.3 66.9 + - - +
1312D ASN 3.3 19.9 - - - +
1313D PRO* 3.7 1.2 - - - +
1316D ALA* 3.8 27.3 - - + +
1319D ILE* 3.9 24.2 - - + -
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Residues in contact with LYS1310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1266D GLU* 3.3 28.0 + - - +
1269D ASN* 5.7 2.6 + - - -
1271D TYR* 3.5 37.3 + - + -
1306D THR* 3.2 24.8 + - - +
1307D ALA* 3.4 16.4 - - + +
1309D LEU* 1.3 77.5 - - - +
1311D ASP* 1.3 64.7 + - - +
1313D PRO* 3.6 15.8 - - - +
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Residues in contact with ASP1311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1307D ALA* 3.1 16.3 + - - +
1308D TRP* 3.1 13.9 + - + +
1310D LYS* 1.3 83.9 - - - +
1312D ASN* 1.3 64.8 + - - +
1313D PRO* 3.2 10.0 - - - +
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Residues in contact with ASN1312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1308D TRP* 2.8 56.0 + - + +
1309D LEU* 3.3 8.7 - - - +
1310D LYS 3.4 0.2 - - - -
1311D ASP* 1.3 87.6 - - - +
1313D PRO* 1.3 60.6 - - - +
1314D GLU* 3.2 5.8 - - + +
1315D THR* 3.2 21.0 + - - +
1316D ALA* 3.0 22.5 + - - +
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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