Contacts of the helix formed by residues 1014 - 1032 (chain B) in PDB entry 2XCR
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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B LEU* 4.4 18.3 - - + +
525B TYR* 4.6 11.7 - - + -
532B ILE* 3.9 28.5 - - + -
606B VAL* 4.1 13.5 - - + -
607B LYS 3.1 12.9 + - - +
608B LEU* 3.3 34.1 - - + -
614B ALA* 4.7 7.4 - - + -
618B PHE* 4.4 18.8 - - + -
1012B ARG 3.6 0.9 + - - -
1013B ASN* 1.3 79.4 + - - +
1015B THR* 1.3 67.9 + - - +
1017B GLU* 3.6 3.4 + - - +
1018B MET* 3.0 45.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1015 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609B GLU 4.2 8.1 + - - -
613B GLU* 3.7 27.4 + - - +
614B ALA* 4.3 10.7 + - - -
617B THR* 3.0 40.2 - - + +
1013B ASN* 3.1 12.8 + - - -
1014B ILE* 1.3 82.7 - - - +
1016B SER* 1.3 54.8 + - - +
1017B GLU 2.8 15.4 + - - -
1018B MET* 4.6 4.0 - - - -
1019B ARG* 3.0 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1016 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012B ARG* 4.2 16.3 + - - -
1013B ASN* 3.4 31.4 + - - +
1015B THR* 1.3 78.2 - - - +
1017B GLU* 1.3 56.0 + - - +
1019B ARG* 4.5 6.1 - - - +
1020B GLU* 3.2 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1017 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B ARG* 3.6 19.6 + - - +
521B LEU* 5.0 8.5 - - + -
539B ILE* 3.7 27.1 - - + +
604B LEU* 5.2 4.8 - - - +
1012B ARG* 2.7 49.4 + - + +
1013B ASN 3.1 15.1 + - - +
1014B ILE* 4.0 3.6 - - - +
1015B THR 2.8 2.6 + - - -
1016B SER* 1.3 75.3 - - - +
1018B MET* 1.3 68.3 + - - +
1019B ARG 3.1 1.6 - - - -
1020B GLU* 3.1 2.3 + - - -
1021B SER* 2.8 44.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1018 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B THR* 3.5 35.7 - - - +
521B LEU* 3.9 14.8 - - + -
522B THR* 3.2 22.9 - - - +
617B THR* 4.6 6.3 - - + -
618B PHE* 3.0 41.7 - - + -
621B LEU* 4.3 13.7 - - + -
622B MET* 4.2 10.1 - - + -
1014B ILE* 3.0 32.5 + - + +
1015B THR* 4.0 4.7 - - - +
1017B GLU* 1.3 73.8 - - - +
1019B ARG* 1.3 64.7 + - - +
1022B PHE* 3.0 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1019 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613B GLU* 5.4 4.8 + - - +
617B THR* 3.8 27.4 + - + +
620B MET* 3.9 21.2 - - - +
621B LEU* 4.2 11.9 - - - -
632B PHE* 3.8 34.8 - - + -
636B ASN* 4.4 17.7 + - - +
1015B THR* 3.0 21.6 + - - +
1016B SER* 4.5 5.4 - - - +
1018B MET* 1.3 83.0 - - - +
1020B GLU* 1.3 67.7 + - + +
1022B PHE* 4.3 0.7 - - - +
1023B LEU* 3.5 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU1020 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1012B ARG* 2.5 42.7 + - - +
1016B SER* 3.2 16.0 + - - +
1017B GLU* 3.1 8.7 + - - +
1019B ARG* 1.3 81.4 - - + +
1021B SER* 1.3 57.0 + - - +
1023B LEU* 2.7 31.9 + - - +
1024B ASP* 3.0 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1021 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B ALA* 3.8 17.4 - - - +
517B ARG* 3.0 31.4 + - - -
518B THR* 4.2 14.4 - - - -
1017B GLU* 2.8 34.7 + - - -
1020B GLU* 1.3 72.9 - - - +
1022B PHE* 1.3 60.1 + - - -
1024B ASP* 3.6 10.0 + - - +
1025B TYR* 3.3 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1022 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515B HIS* 5.0 14.8 - + - +
518B THR* 4.0 13.4 - - + +
621B LEU* 3.3 51.1 - - + -
622B MET* 3.9 24.7 - - + -
629B ARG* 3.8 26.7 - - + -
632B PHE* 5.0 3.6 - + - -
633B ILE* 5.4 3.4 - - + -
1018B MET 3.0 18.7 + - - +
1019B ARG 4.3 2.5 - - - +
1021B SER* 1.3 76.0 - - - +
1023B LEU* 1.3 59.9 + - - +
1025B TYR* 3.1 13.3 - + - +
1026B ALA* 2.9 31.4 + - + +
1177B VAL* 4.2 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1023 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560B ARG* 5.8 2.0 - - - +
632B PHE* 4.2 18.2 - - + +
633B ILE* 4.7 9.4 - - + +
636B ASN* 3.5 46.4 - - + +
637B ALA* 4.2 5.8 - - - +
1019B ARG 3.5 11.0 + - - +
1020B GLU* 2.7 16.0 + - - +
1022B PHE* 1.3 73.3 - - - +
1024B ASP* 1.3 70.8 + - - +
1025B TYR 2.8 5.6 - - - -
1026B ALA* 4.1 5.6 - - - +
1027B MET* 2.8 45.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1024 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B VAL* 4.2 6.5 - - + +
514B ALA* 5.6 4.3 - - + -
558B ASN* 4.5 14.6 + - - +
560B ARG* 3.3 42.7 + - - +
1020B GLU* 3.0 25.2 + - - +
1021B SER* 3.9 12.3 + - - +
1022B PHE 3.5 0.2 - - - -
1023B LEU* 1.3 88.5 - - - +
1025B TYR* 1.3 59.0 + - - +
1027B MET* 4.6 0.2 - - - -
1028B SER* 3.5 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1025 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B LYS* 3.4 15.0 + - - -
511B VAL* 3.8 25.1 - - + +
512B ASP* 4.0 19.2 + - - -
514B ALA* 5.7 0.4 - - - +
515B HIS* 2.7 54.7 + + + +
1021B SER 3.3 11.8 + - - +
1022B PHE* 3.1 18.6 - + - +
1023B LEU 2.8 0.4 - - - -
1024B ASP* 1.3 78.1 - - - +
1026B ALA* 1.3 71.4 + - + +
1027B MET 3.1 1.1 - - - -
1028B SER* 2.9 22.9 + - - -
1029B VAL* 3.0 36.9 + - + +
1033B ARG* 5.2 1.7 + - - -
1177B VAL* 4.7 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1026 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633B ILE* 3.9 27.1 - - + -
1022B PHE* 2.9 27.2 + - + +
1023B LEU* 4.0 2.5 - - - +
1025B TYR* 1.3 75.4 - - + +
1027B MET* 1.3 61.2 + - - +
1029B VAL* 3.8 1.3 + - - +
1030B ILE* 3.1 32.4 + - + +
1177B VAL* 3.7 30.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET1027 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560B ARG* 4.8 11.2 - - - +
633B ILE* 4.6 10.3 - - + -
637B ALA* 3.6 27.1 - - - -
638B VAL 3.9 19.1 - - - +
639B TYR* 3.4 40.2 - - + -
1023B LEU* 2.8 38.9 + - + +
1024B ASP* 4.4 4.7 - - - +
1026B ALA* 1.3 76.7 - - + +
1028B SER* 1.3 59.2 + - - +
1030B ILE* 3.1 6.6 + - - +
1031B VAL* 2.9 45.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1028 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B VAL* 3.7 31.8 - - - +
560B ARG* 4.6 6.0 - - - +
1024B ASP 3.5 13.2 + - - -
1025B TYR 2.9 9.7 + - - -
1027B MET* 1.3 76.1 - - - +
1029B VAL* 1.3 56.5 + - - +
1030B ILE 3.0 9.5 + - - -
1031B VAL* 3.8 7.5 - - - +
1032B ALA* 3.1 33.1 + - - +
1033B ARG* 4.6 4.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1029 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B VAL* 6.3 0.4 - - + -
1025B TYR* 3.0 48.7 + - + +
1026B ALA 3.9 0.4 - - - +
1028B SER* 1.3 74.3 - - - +
1030B ILE* 1.3 56.2 + - - +
1033B ARG* 3.5 39.0 - - + +
1034B ALA* 3.1 26.5 + - + +
1175B ILE 4.9 0.9 - - - +
1176B ALA* 3.8 18.4 - - + +
1177B VAL* 3.5 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1030 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633B ILE* 4.8 18.2 - - + -
639B TYR* 5.0 3.1 - - + +
1026B ALA* 3.1 22.0 - - + +
1027B MET* 3.1 7.1 + - - +
1028B SER 3.0 1.0 - - - -
1029B VAL* 1.3 81.7 - - - +
1031B VAL* 1.3 71.1 + - + +
1032B ALA 3.3 1.5 + - - -
1033B ARG 4.5 0.3 + - - -
1035B LEU* 3.8 18.3 + - + +
1176B ALA* 4.1 15.9 - - + -
1177B VAL* 3.9 17.5 - - + +
1179B MET* 3.6 23.3 - - - -
1338B LEU* 3.5 19.3 - - + +
1343B PRO* 3.8 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL1031 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639B TYR* 3.8 24.9 - - + +
1027B MET* 2.9 29.0 + - + +
1028B SER* 3.8 8.1 - - - +
1030B ILE* 1.3 76.4 - - + +
1032B ALA* 1.3 68.2 + - + +
1033B ARG 4.1 0.2 - - - -
1035B LEU 5.0 1.6 - - - +
1338B LEU* 3.7 21.7 - - + +
1341B GLY* 3.6 23.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1032 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1028B SER* 3.1 14.6 + - - +
1031B VAL* 1.3 86.3 - - + +
1033B ARG* 1.3 67.0 + - - +
1035B LEU 5.6 0.4 - - - -
1044B PRO* 3.2 26.3 - - + +
1048B ARG* 5.5 6.5 - - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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