Contacts of the helix formed by residues 1500 - 1520 (chain H) 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 PRO1500 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092G GLU* 3.7 41.5 - - + +
1095G LYS* 3.8 33.9 - - + +
1096G LEU* 4.5 9.4 - - + +
1498H LEU 4.1 4.7 - - - +
1499H LEU* 1.3 85.6 - - + +
1501H GLY* 1.3 57.9 + - - +
1502H GLU 3.4 1.8 - - - -
1503H LEU* 2.8 21.2 + - + +
1504H ALA 2.6 30.3 + - - -
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Residues in contact with GLY1501 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1092G GLU* 4.1 1.2 + - - -
1499H LEU 3.4 2.6 + - - -
1500H PRO* 1.3 69.1 - - - +
1502H GLU* 1.3 65.5 + - - -
1504H ALA* 3.2 5.9 + - - +
1505H LYS* 2.9 23.8 + - - +
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Residues in contact with GLU1502 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1092G GLU* 2.9 26.7 + - - +
1501H GLY* 1.3 72.9 - - - -
1503H LEU* 1.3 62.5 + - - +
1505H LYS* 3.1 49.2 + - - +
1506H HIS* 3.2 32.4 + - + +
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Residues in contact with LEU1503 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1057G TYR* 3.9 23.9 - - - +
1058G LEU* 3.9 26.9 - - + -
1061G GLU* 4.3 16.8 - - + +
1090G ASP* 5.1 1.8 - - - +
1092G GLU* 2.6 33.9 + - + +
1093G LEU* 4.0 25.6 - - + +
1096G LEU* 4.2 10.1 - - + -
1499H LEU* 4.3 5.4 - - + -
1500H PRO* 2.8 30.0 + - + +
1502H GLU* 1.3 71.6 - - - +
1504H ALA* 1.3 63.5 + - - +
1506H HIS* 3.7 0.7 + - - -
1507H ALA* 3.1 22.5 + - - +
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Residues in contact with ALA1504 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1495H VAL* 4.4 9.4 - - + +
1496H ARG* 4.7 12.6 - - + +
1499H LEU* 3.3 35.2 - - + +
1500H PRO 2.6 8.8 + - - +
1501H GLY* 3.3 11.0 - - - +
1503H LEU* 1.3 71.7 - - - +
1505H LYS* 1.3 66.9 + - - +
1507H ALA* 3.0 6.4 + - - +
1508H VAL* 2.8 29.9 + - + +
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Residues in contact with LYS1505 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1501H GLY 2.9 15.5 + - - +
1502H GLU* 3.1 40.3 + - - +
1504H ALA* 1.3 72.1 - - - +
1506H HIS* 1.3 87.3 + - + +
1508H VAL* 3.0 12.3 + - - +
1509H SER* 3.0 21.2 + - - -
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Residues in contact with HIS1506 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1057G TYR* 3.3 37.4 + - + +
1502H GLU* 3.2 47.2 + - + +
1503H LEU* 3.9 1.8 - - - +
1505H LYS* 1.3 100.4 + - + +
1507H ALA* 1.3 53.9 + - - +
1509H SER* 2.8 12.3 + - - -
1510H GLU* 2.7 36.8 + - + +
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Residues in contact with ALA1507 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1050G TYR* 4.4 0.2 - - - -
1054G VAL* 3.5 26.3 - - + +
1057G TYR* 3.8 18.0 - - + -
1058G LEU* 5.4 0.2 - - + -
1495H VAL* 3.9 9.0 - - + -
1499H LEU* 3.7 23.6 - - + -
1503H LEU 3.1 12.6 + - - +
1504H ALA 3.0 10.6 + - - +
1506H HIS* 1.3 78.7 - - - +
1508H VAL* 1.3 61.2 + - - +
1510H GLU* 4.0 2.5 - - - +
1511H GLY 3.1 15.2 + - - -
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Residues in contact with VAL1508 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1050G TYR* 3.3 10.0 + - - +
1492H GLN* 3.4 31.9 - - + +
1495H VAL* 4.3 14.1 - - + -
1496H ARG* 4.1 36.6 - - + +
1504H ALA 2.8 23.4 + - - +
1505H LYS* 3.2 10.1 - - - +
1507H ALA* 1.3 73.8 - - - +
1509H SER* 1.3 55.2 + - - +
1511H GLY 3.1 1.9 + - - -
1512H THR* 2.6 42.9 + - - +
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Residues in contact with SER1509 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1505H LYS* 3.0 13.5 + - - -
1506H HIS* 2.8 14.5 + - - -
1508H VAL* 1.3 72.6 - - - +
1510H GLU* 1.3 75.2 + - - -
1511H GLY 3.0 0.7 + - - -
1512H THR* 3.0 6.9 + - - -
1513H LYS* 2.8 27.9 + - - +
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Residues in contact with GLU1510 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1023G LEU* 5.8 5.0 - - - +
1053G ALA* 3.8 16.6 - - + +
1057G TYR* 3.6 41.7 - - + +
1506H HIS* 2.7 21.0 + - + +
1507H ALA 4.0 3.8 - - - +
1509H SER* 1.3 79.2 + - - +
1511H GLY* 1.3 62.1 + - - +
1513H LYS* 3.3 31.8 + - - +
1514H ALA* 3.2 16.3 + - - +
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Residues in contact with GLY1511 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1050G TYR* 3.9 22.5 - - - -
1053G ALA* 3.6 16.4 - - - +
1054G VAL* 4.1 0.4 - - - +
1507H ALA 3.1 9.5 + - - -
1508H VAL 3.1 5.1 + - - -
1509H SER 3.1 1.2 - - - -
1510H GLU* 1.3 76.3 - - - +
1512H THR* 1.3 66.2 + - - +
1513H LYS 3.0 2.4 + - - -
1514H ALA* 3.0 13.7 + - - +
1515H VAL* 3.3 14.6 + - - +
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Residues in contact with THR1512 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1050G TYR* 3.7 10.3 - - + -
1492H GLN* 3.3 22.9 + - - +
1508H VAL* 2.6 35.1 + - - +
1509H SER* 3.8 5.0 + - - -
1511H GLY* 1.3 71.0 - - - -
1513H LYS* 1.3 61.2 + - - +
1515H VAL* 3.7 5.8 + - + +
1516H THR* 3.2 24.9 + - - +
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Residues in contact with LYS1513 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1021G ALA 6.1 0.9 - - - -
1509H SER* 2.8 15.1 + - - +
1510H GLU* 3.3 37.3 + - - +
1512H THR* 1.3 75.9 - - - +
1514H ALA* 1.3 61.9 + - - +
1516H THR* 3.1 10.0 + - + -
1517H LYS* 2.8 35.4 + - + +
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Residues in contact with ALA1514 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1021G ALA* 4.1 13.6 - - + +
1023G LEU* 3.9 13.7 - - + -
1049G VAL* 3.4 20.4 - - + -
1053G ALA* 3.5 23.1 - - + -
1510H GLU 3.2 3.3 + - - +
1511H GLY 3.0 8.4 + - - +
1513H LYS* 1.3 77.0 - - - +
1515H VAL* 1.3 68.5 + - - +
1517H LYS* 3.1 3.4 + - - +
1518H TYR* 2.7 26.0 + - - +
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Residues in contact with VAL1515 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1046G GLY* 4.0 15.0 - - - +
1049G VAL* 3.5 14.1 - - + +
1050G TYR* 3.7 40.2 - - + -
1488H SER* 4.4 11.9 - - - +
1511H GLY 3.3 4.8 + - - +
1512H THR* 4.0 8.1 - - + +
1514H ALA* 1.3 75.0 - - - +
1516H THR* 1.3 64.0 + - - +
1518H TYR* 3.4 4.2 + - + +
1519H THR* 2.8 38.0 + - - +
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Residues in contact with THR1516 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1512H THR* 3.2 14.7 + - - +
1513H LYS* 3.1 15.2 + - + +
1514H ALA 3.1 0.6 - - - -
1515H VAL* 1.3 81.8 - - - +
1517H LYS* 1.3 73.4 + - + +
1519H THR* 3.1 11.5 + - - -
1520H SER* 3.1 19.2 + - - +
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Residues in contact with LYS1517 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1019G SER 4.4 4.6 + - - -
1020G ARG 3.4 16.6 - - - +
1021G ALA 4.1 13.0 - - - +
1022G GLY* 3.8 21.0 - - - +
1513H LYS* 2.8 18.1 + - + +
1514H ALA* 3.5 7.2 - - - +
1516H THR* 1.3 83.4 - - + +
1518H TYR* 1.3 65.4 + - - +
1520H SER* 3.1 23.8 + - - +
1521H ALA* 4.2 0.3 - - - +
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Residues in contact with TYR1518 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1017G ARG* 3.2 49.5 + - + -
1020G ARG* 3.2 41.9 + - + +
1021G ALA* 4.1 7.0 - - + -
1045G ALA* 4.2 24.7 + - + +
1046G GLY* 5.3 3.6 - - - -
1049G VAL* 3.9 23.3 - - + -
1514H ALA 2.7 22.2 + - - +
1515H VAL* 3.6 6.3 - - + +
1517H LYS* 1.3 74.1 - - - +
1519H THR* 1.3 68.8 + - - +
1520H SER 3.1 0.9 + - - -
1521H ALA* 3.6 17.5 + - - +
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Residues in contact with THR1519 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1515H VAL* 2.8 33.6 + - - +
1516H THR* 3.7 5.4 - - - -
1518H TYR* 1.3 79.3 - - - +
1520H SER* 1.3 59.7 + - - +
1521H ALA 3.3 8.4 + - - +
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Residues in contact with SER1520 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1516H THR* 3.1 20.2 + - - +
1517H LYS* 3.1 10.4 + - - +
1519H THR* 1.3 79.0 - - - +
1521H ALA* 1.3 62.8 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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