Contacts of the helix formed by residues 1300 - 1320 (chain D) in PDB entry 1P3M
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 PRO1300 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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892C GLU* 3.4 28.9 - - + +
895C LYS* 4.0 38.8 - - + +
896C LEU* 4.5 12.1 - - + +
1298D LEU 3.5 8.5 - - - +
1299D LEU* 1.3 90.6 - - + +
1301D GLY* 1.3 70.1 + - - +
1302D GLU 3.6 1.3 - - - -
1303D LEU* 3.1 8.5 + - + +
1304D ALA 2.9 15.9 + - - -
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Residues in contact with GLY1301 (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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892C GLU* 4.5 2.8 + - - -
1300D PRO* 1.3 74.5 - - - +
1302D GLU* 1.3 62.8 + - - -
1304D ALA* 3.7 3.9 - - - +
1305D LYS* 3.1 30.2 + - - +
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Residues in contact with GLU1302 (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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857C TYR* 4.9 0.9 - - - +
892C GLU* 3.0 27.4 + - - +
1301D GLY* 1.3 71.8 - - - +
1303D LEU* 1.3 61.4 + - - +
1305D LYS* 2.6 35.0 + - - +
1306D HIS* 2.6 63.5 + - + +
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Residues in contact with LEU1303 (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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857C TYR* 3.6 24.7 - - + +
858C LEU* 3.8 20.4 - - + -
861C GLU* 4.2 17.9 - - + -
890C ASP* 5.3 0.7 - - - +
892C GLU* 2.6 45.2 + - + +
893C LEU* 3.7 26.0 - - + +
896C LEU* 4.4 14.8 - - + -
1299D LEU* 4.2 11.4 - - + -
1300D PRO* 3.1 10.9 + - + +
1302D GLU* 1.3 74.1 - - - +
1304D ALA* 1.3 58.3 + - - +
1306D HIS 3.3 0.3 + - - -
1307D ALA* 2.8 30.1 + - - +
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Residues in contact with ALA1304 (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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1295D VAL* 3.9 13.2 - - + +
1296D ARG* 4.5 17.0 - - - +
1299D LEU* 3.3 32.0 - - - +
1300D PRO 2.9 9.6 + - - +
1301D GLY* 3.7 3.8 - - - +
1303D LEU* 1.3 73.9 - - - +
1305D LYS* 1.3 68.1 + - - +
1307D ALA* 2.9 16.8 + - - +
1308D VAL* 2.9 20.0 + - - +
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Residues in contact with LYS1305 (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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1296D ARG* 5.3 3.1 - - - +
1301D GLY* 3.1 12.0 + - - +
1302D GLU* 2.6 45.2 + - - +
1304D ALA* 1.3 80.3 - - - +
1306D HIS* 1.3 70.6 + - + +
1308D VAL* 3.4 14.8 + - - +
1309D SER* 3.5 12.0 + - - -
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Residues in contact with HIS1306 (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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857C TYR* 3.0 37.5 + - + +
861C GLU* 5.6 1.0 + - - -
1302D GLU* 2.6 39.8 + - + +
1305D LYS* 1.3 85.1 - - + +
1307D ALA* 1.3 61.6 + - - +
1309D SER* 3.1 18.9 + - - -
1310D GLU* 3.1 16.9 + - + +
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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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854C VAL* 3.8 19.1 - - + +
857C TYR* 3.7 20.1 - - + -
1295D VAL* 3.6 22.0 - - + -
1299D LEU* 3.8 12.6 - - + -
1303D LEU 2.8 18.8 + - - +
1304D ALA 2.9 8.0 + - - +
1306D HIS* 1.3 69.7 - - - +
1308D VAL* 1.3 67.3 + - - +
1309D SER 3.3 0.2 + - - -
1310D GLU* 3.3 4.4 + - - +
1311D GLY* 3.1 17.2 + - - -
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Residues in contact with VAL1308 (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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850C TYR* 3.1 24.6 + - - +
1292D GLN* 3.2 23.8 - - + +
1295D VAL* 4.5 6.5 - - + +
1296D ARG* 3.4 43.7 - - + +
1304D ALA 2.9 17.0 + - - +
1305D LYS* 3.6 8.5 - - - +
1307D ALA* 1.3 74.8 - - - +
1309D SER* 1.3 54.6 + - - +
1311D GLY 3.1 1.4 + - - -
1312D THR* 2.7 42.3 + - - +
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Residues in contact with SER1309 (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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1305D LYS 3.5 7.6 + - - -
1306D HIS* 3.1 15.6 + - - -
1308D VAL* 1.3 79.2 - - - +
1310D GLU* 1.3 57.6 + - - +
1312D THR* 3.0 6.6 + - - -
1313D LYS* 2.7 39.9 + - - +
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Residues in contact with GLU1310 (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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823C LEU* 5.8 0.2 - - - +
853C ALA* 3.7 12.4 - - + +
857C TYR* 3.8 42.8 - - + +
1306D HIS* 3.1 13.8 + - + +
1307D ALA 3.7 6.1 - - - +
1309D SER* 1.3 81.4 - - - +
1311D GLY* 1.3 58.3 + - - +
1313D LYS* 3.1 19.2 + - - +
1314D ALA* 2.8 29.5 + - - +
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Residues in contact with GLY1311 (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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850C TYR* 3.7 28.4 - - - -
853C ALA* 3.7 17.2 - - - +
854C VAL* 4.8 0.4 - - - +
1307D ALA 3.1 7.1 + - - -
1308D VAL 3.6 2.2 - - - -
1309D SER 3.1 1.0 - - - -
1310D GLU* 1.3 76.1 - - - +
1312D THR* 1.3 65.6 + - - +
1314D ALA* 3.8 0.9 - - - +
1315D VAL* 2.9 29.6 + - - +
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Residues in contact with THR1312 (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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850C TYR* 3.7 6.5 - - - -
1292D GLN* 3.8 17.4 + - - +
1308D VAL* 2.7 32.7 + - - +
1309D SER* 3.6 5.5 - - - -
1311D GLY* 1.3 72.9 - - - +
1313D LYS* 1.3 66.0 + - - +
1315D VAL* 3.1 5.6 + - + +
1316D THR* 2.8 38.3 + - - +
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Residues in contact with LYS1313 (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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1309D SER* 2.7 24.2 + - - +
1310D GLU* 3.1 21.1 + - - +
1312D THR* 1.3 74.1 - - - +
1314D ALA* 1.3 64.4 + - - +
1316D THR* 3.2 6.0 + - - -
1317D LYS* 2.8 26.0 + - + +
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Residues in contact with ALA1314 (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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821C ALA 3.7 19.3 - - - +
823C LEU* 4.2 10.3 - - + -
849C VAL* 3.6 19.0 - - + +
853C ALA* 3.8 19.5 - - + -
1310D GLU 2.8 18.8 + - - +
1311D GLY 3.8 1.8 - - - +
1313D LYS* 1.3 72.5 - - - +
1315D VAL* 1.3 53.7 + - - +
1317D LYS* 3.2 2.8 + - - +
1318D TYR* 2.7 37.6 + - - +
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Residues in contact with VAL1315 (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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846C GLY* 4.1 13.7 - - - +
849C VAL* 3.7 13.9 - - + -
850C TYR* 3.7 31.4 - - + +
1288D SER* 4.2 14.6 - - - +
1311D GLY 2.9 22.3 + - - +
1312D THR* 3.6 6.1 - - - +
1314D ALA* 1.3 75.5 - - - +
1316D THR* 1.3 55.1 + - - +
1318D TYR* 3.1 5.8 + - + +
1319D THR* 2.7 48.1 + - - +
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Residues in contact with THR1316 (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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1312D THR* 2.8 34.8 + - - +
1313D LYS* 3.4 6.0 - - - -
1315D VAL* 1.3 73.0 - - - +
1317D LYS* 1.3 59.0 + - - +
1319D THR* 3.2 6.4 + - - -
1320D SER* 2.8 36.0 + - - +
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Residues in contact with LYS1317 (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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819C SER 3.8 6.9 + - - -
820C ARG* 3.4 13.5 - - - +
821C ALA 3.7 13.2 - - - +
822C GLY* 3.6 25.9 - - - +
1313D LYS* 2.8 21.4 + - + +
1314D ALA* 3.7 3.4 - - - +
1316D THR* 1.3 75.6 - - - +
1318D TYR* 1.3 61.0 + - - +
1320D SER* 3.6 8.8 + - - -
1321D ALA* 3.2 22.2 + - + +
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Residues in contact with TYR1318 (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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817C ARG* 3.2 59.7 + - + -
820C ARG* 2.9 78.6 + - + -
821C ALA* 3.9 8.1 - - + -
845C ALA* 4.4 20.8 - - + +
846C GLY* 6.0 1.6 - - - -
849C VAL* 3.6 26.7 - - + -
1314D ALA 2.7 20.8 + - - +
1315D VAL* 3.5 6.1 - - + +
1317D LYS* 1.3 71.2 - - - +
1319D THR* 1.3 70.4 + - - +
1321D ALA 3.7 2.4 + - - -
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Residues in contact with THR1319 (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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820C ARG* 4.7 4.5 + - - +
1315D VAL* 2.7 32.6 + - - +
1316D THR* 3.5 7.0 - - - +
1318D TYR* 1.3 76.6 - - - +
1320D SER* 1.3 56.7 + - - +
1321D ALA* 2.8 16.2 + - - -
1322D LYS* 4.0 8.1 + - - +
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Residues in contact with SER1320 (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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1316D THR* 2.8 27.1 + - - +
1317D LYS* 3.6 10.4 + - - -
1319D THR* 1.3 73.3 - - - +
1321D ALA* 1.3 55.7 + - - +
1322D LYS 3.8 2.5 + - - -
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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