Contacts of the helix formed by residues 1014 - 1032 (chain D) in PDB entry 5NPK
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 ILE1014 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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521D LEU* 4.2 15.0 - - + -
525D TYR* 4.6 2.7 - - + -
532D ILE* 3.5 34.1 - - + -
606D VAL* 3.7 21.5 - - + -
607D LYS 3.0 17.9 + - - +
608D LEU* 4.0 25.6 - - + -
609D GLU 5.3 0.2 - - - +
614D ALA* 4.5 6.5 - - + -
618D PHE* 3.9 29.8 - - + -
1012D ARG 3.3 2.2 + - - -
1013D ASN* 1.3 76.6 + - - +
1015D THR* 1.3 69.2 + - - +
1017D GLU* 3.3 5.4 + - - +
1018D MET* 2.9 30.8 + - + +
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Residues in contact with THR1015 (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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608D LEU* 5.7 0.2 - - - +
610D ASP 4.7 1.6 + - - -
613D GLU* 3.6 31.2 + - + +
614D ALA* 3.7 27.8 + - - +
617D THR* 3.5 22.8 + - - +
618D PHE* 6.1 0.9 - - - -
1013D ASN* 2.6 18.0 + - - -
1014D ILE* 1.3 75.5 - - - +
1016D SER* 1.3 63.5 + - - +
1018D MET* 3.3 5.4 + - - +
1019D ARG* 3.0 39.1 + - - +
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Residues in contact with SER1016 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012D ARG* 3.8 18.8 - - - -
1013D ASN* 3.4 27.8 + - - +
1014D ILE 3.4 0.4 - - - -
1015D THR* 1.3 79.3 - - - +
1017D GLU* 1.3 62.2 + - - +
1019D ARG* 3.4 5.5 + - - +
1020D GLU* 3.0 38.2 + - - +
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Residues in contact with GLU1017 (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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517D ARG* 2.7 23.0 + - + -
521D LEU* 3.8 24.5 - - + -
539D ILE* 3.8 14.7 - - + +
604D LEU* 4.8 3.8 - - - +
606D VAL* 6.1 0.9 - - + -
1012D ARG* 2.6 45.6 + - + +
1013D ASN 2.9 18.0 + - - +
1014D ILE* 3.7 8.7 - - - +
1016D SER* 1.3 75.4 - - - +
1018D MET* 1.3 57.9 - - - +
1021D SER* 2.5 61.9 + - - +
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Residues in contact with MET1018 (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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518D THR* 3.7 40.0 - - + +
521D LEU* 3.9 13.9 - - + -
522D THR* 3.7 11.9 - - - +
617D THR* 4.0 7.9 - - + -
618D PHE* 3.5 49.4 - - + -
621D LEU* 3.4 17.6 - - + +
622D MET* 3.7 16.4 - - + -
1014D ILE* 2.9 22.7 + - + +
1015D THR 3.8 3.6 - - - +
1017D GLU* 1.3 77.3 - - - +
1019D ARG* 1.3 61.0 + - - +
1022D PHE* 3.1 30.0 + - - +
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Residues in contact with ARG1019 (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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613D GLU* 5.4 3.0 - - - +
617D THR* 2.9 34.9 + - + +
620D MET* 3.5 30.8 - - - +
621D LEU* 3.8 9.2 - - + -
632D PHE* 3.6 31.9 - - + -
636D ASN* 5.7 0.2 - - - +
1015D THR* 3.0 29.0 + - - +
1016D SER* 4.1 5.4 - - - +
1018D MET* 1.3 76.3 - - - +
1020D GLU* 1.3 65.1 + - + +
1023D LEU* 3.2 26.7 + - - +
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Residues in contact with GLU1020 (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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1012D ARG* 2.8 41.5 + - - +
1016D SER* 3.0 25.2 + - - +
1019D ARG* 1.3 77.2 - - + +
1021D SER* 1.3 65.0 + - - +
1023D LEU* 4.0 5.8 - - - +
1024D ASP* 3.2 33.5 + - - +
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Residues in contact with SER1021 (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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514D ALA* 3.8 22.5 - - - +
517D ARG* 3.0 13.3 + - - -
518D THR* 3.6 18.8 - - - -
1012D ARG* 5.4 0.2 + - - -
1017D GLU* 2.5 42.2 + - - -
1020D GLU* 1.3 76.2 - - - +
1022D PHE* 1.3 64.6 + - - +
1024D ASP* 3.5 6.6 + - - +
1025D TYR* 3.2 21.8 + - - +
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Residues in contact with PHE1022 (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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515D HIS* 4.2 21.3 - + - -
518D THR* 3.8 15.8 - - + +
621D LEU* 3.7 31.2 - - + -
622D MET* 3.8 29.4 - - + -
629D ARG* 3.5 37.0 - - + -
632D PHE* 4.9 4.5 - + - -
633D ILE* 4.8 0.7 - - + -
1018D MET 3.1 19.4 + - - +
1019D ARG 4.5 0.2 - - - +
1021D SER* 1.3 74.4 - - - +
1023D LEU* 1.3 56.2 + - - +
1025D TYR* 3.3 8.5 + + - +
1026D ALA* 2.7 46.4 + - + +
1177D VAL* 3.8 20.6 - - + -
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Residues in contact with LEU1023 (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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632D PHE* 4.0 12.7 - - + -
633D ILE* 4.0 25.6 - - + +
636D ASN* 3.1 44.0 - - + +
639D TYR* 4.0 22.2 - - + +
640D ALA* 3.9 7.0 - - + -
1019D ARG 3.2 20.8 + - - +
1020D GLU* 4.0 5.8 - - - +
1022D PHE* 1.3 75.9 - - - +
1024D ASP* 1.3 59.4 + - - +
1026D ALA* 4.5 2.2 - - - -
1027D MET* 2.9 50.3 + - + +
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Residues in contact with ASP1024 (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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511D VAL* 3.8 6.1 - - + +
514D ALA* 5.0 5.9 - - + +
639D TYR 4.6 1.9 - - - +
640D ALA* 3.8 5.2 - - - -
641D ASN* 2.9 55.8 + - - +
1020D GLU* 3.2 22.2 + - - +
1021D SER* 3.6 8.9 - - - +
1023D LEU* 1.3 79.6 - - - +
1025D TYR* 1.3 61.9 + - - +
1028D SER* 3.1 21.7 + - - -
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Residues in contact with TYR1025 (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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460D LYS* 3.1 15.0 + - - -
511D VAL* 3.3 37.0 - - + +
512D ASP* 3.5 20.9 + - - -
515D HIS* 3.2 49.0 + + + +
1021D SER 3.2 13.9 + - - +
1022D PHE* 3.7 11.9 - + - +
1024D ASP* 1.3 78.1 - - - +
1026D ALA* 1.3 67.1 + - - +
1028D SER* 3.1 4.0 + - - -
1029D VAL* 3.0 49.2 + - + +
1033D ARG* 4.1 6.6 + - - -
1177D VAL* 4.1 13.4 - - + +
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Residues in contact with ALA1026 (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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633D ILE* 3.4 36.8 - - + -
1022D PHE* 2.7 27.3 + - + +
1023D LEU 4.0 2.2 - - - +
1025D TYR* 1.3 74.9 - - - +
1027D MET* 1.3 63.4 + - - +
1029D VAL* 3.4 1.9 + - - +
1030D ILE* 3.1 29.0 + - - +
1177D VAL* 3.9 24.2 - - + +
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Residues in contact with MET1027 (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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633D ILE* 3.8 15.3 - - + -
637D ALA* 3.6 37.2 - - + +
640D ALA* 3.5 23.3 - - + -
641D ASN* 4.1 3.8 - - - +
1023D LEU* 2.9 34.0 + - + +
1024D ASP 4.0 2.2 - - - +
1026D ALA* 1.3 76.4 - - - +
1028D SER* 1.3 58.4 + - - +
1030D ILE* 3.2 8.1 + - - +
1031D VAL* 2.9 60.3 + - + +
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Residues in contact with SER1028 (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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511D VAL* 3.7 32.4 - - - +
641D ASN* 4.2 6.0 + - - -
1024D ASP 3.1 17.8 + - - -
1025D TYR 3.1 5.2 + - - -
1027D MET* 1.3 74.5 - - - +
1029D VAL* 1.3 62.2 + - - +
1031D VAL* 4.4 5.4 - - - -
1032D ALA* 2.8 44.3 + - - +
1033D ARG* 4.7 4.0 + - - -
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Residues in contact with VAL1029 (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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1025D TYR* 3.0 54.7 + - + +
1026D ALA 3.8 4.0 - - - +
1028D SER* 1.3 78.5 - - - +
1030D ILE* 1.3 60.1 + - - +
1033D ARG* 3.6 23.7 + - + +
1034D ALA* 2.9 38.8 + - + +
1175D ILE 4.4 2.0 - - - +
1176D ALA* 3.6 33.2 - - - -
1177D VAL* 3.9 7.0 - - + -
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Residues in contact with ILE1030 (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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630D ARG* 6.3 0.2 - - + -
633D ILE* 3.9 28.3 - - + -
1026D ALA 3.1 19.5 + - - +
1027D MET* 3.2 8.0 + - - +
1029D VAL* 1.3 79.5 - - - +
1031D VAL* 1.3 71.4 + - + +
1032D ALA 3.9 0.2 + - - -
1035D LEU* 3.5 36.2 + - + +
1176D ALA* 4.3 5.2 - - + -
1177D VAL 3.2 34.3 - - - +
1179D MET* 4.5 14.4 - - + -
1338D LEU* 3.7 4.6 - - + +
1343D PRO* 3.7 29.6 - - + -
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Residues in contact with VAL1031 (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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1027D MET* 2.9 43.5 + - + +
1028D SER* 4.4 1.8 - - - -
1030D ILE* 1.3 89.7 - - + +
1032D ALA* 1.3 68.0 + - + +
1033D ARG 3.9 0.7 - - - -
1035D LEU 5.7 0.2 - - - -
1044D PRO* 4.9 2.5 - - - +
1338D LEU* 3.7 22.9 - - + +
1341D GLY 3.7 24.0 - - - +
1343D PRO* 4.9 3.4 - - + -
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Residues in contact with ALA1032 (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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1028D SER* 2.8 22.8 + - - +
1031D VAL* 1.3 88.0 - - + +
1033D ARG* 1.3 69.8 + - - +
1044D PRO* 3.6 23.3 - - + +
1048D ARG* 5.9 1.0 + - - +
1079D HIS* 6.0 1.2 - - - -
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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