Contacts of the helix formed by residues 938 - 947 (chain D) in PDB entry 2X36
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 HIS 938 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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757C TYR* 4.4 10.9 + + - -
820D PHE* 4.4 8.2 - + - -
824D PHE* 5.4 2.0 - + - -
886D THR 2.9 28.5 + - - -
887D GLY* 3.2 20.2 + - - -
888D LYS* 3.7 8.0 + - - +
889D ILE* 2.9 11.1 - - - +
937D GLU* 1.3 81.5 + - + +
939D TYR* 1.3 69.0 + - + +
940D ARG* 2.9 43.1 + - + +
941D GLU* 2.8 27.0 + - + +
942D ILE 3.8 0.3 + - - -
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Residues in contact with TYR 939 (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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820D PHE* 3.4 37.9 - + + -
824D PHE* 4.5 4.7 - + - -
858D CYS* 3.6 15.5 - - + -
861D VAL* 3.5 21.5 - - + -
862D THR* 2.6 44.5 + - - +
865D LEU* 3.5 19.6 - - + +
883D VAL* 4.7 3.4 - - + -
887D GLY 2.8 17.6 + - - +
889D ILE* 3.0 10.3 - - + +
938D HIS* 1.3 71.8 - - - +
940D ARG* 1.4 54.6 + - - +
941D GLU 3.2 0.2 - - - -
942D ILE* 3.1 32.9 + - + +
943D PHE* 2.9 35.0 + + + +
947D PHE* 4.4 4.2 - - - -
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Residues in contact with ARG 940 (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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824D PHE* 4.0 28.1 - - + -
828D HIS* 5.8 5.9 - - - -
938D HIS* 2.9 23.0 + - + -
939D TYR* 1.4 75.5 - - - +
941D GLU* 1.3 67.1 + - + +
943D PHE* 3.2 20.6 - - - +
944D ASP* 3.2 38.8 + - - +
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Residues in contact with GLU 941 (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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935D PHE 4.5 4.2 - - - +
936D VAL* 3.8 16.9 - - + -
937D GLU* 2.7 44.2 + - - +
938D HIS* 2.8 22.0 + - + +
940D ARG* 1.3 81.5 - - + +
942D ILE* 1.3 64.0 + - - +
944D ASP* 3.0 19.3 + - - +
945D ILE* 3.4 17.7 + - + +
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Residues in contact with ILE 942 (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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858D CYS* 3.8 21.1 - - + -
862D THR* 4.3 0.9 - - - +
879D MET* 3.8 28.7 - - + -
889D ILE* 3.3 28.0 - - + -
911D VAL* 3.8 16.6 - - + -
936D VAL* 3.7 27.4 - - + -
939D TYR* 3.1 35.3 + - + +
941D GLU* 1.3 74.4 - - - +
943D PHE* 1.3 58.7 + - - +
944D ASP 3.2 0.2 + - - -
945D ILE* 3.2 6.0 + - - +
946D ALA* 2.8 29.4 + - + +
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Residues in contact with PHE 943 (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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824D PHE* 3.7 27.1 - + + -
825D LEU* 6.1 0.4 - - + -
828D HIS* 3.5 41.3 - + - -
865D LEU* 4.0 17.3 - - + -
869D MET* 4.0 19.1 - - + -
939D TYR* 2.9 24.2 + - + +
940D ARG* 3.2 15.3 - - - +
941D GLU 3.1 0.2 - - - -
942D ILE* 1.3 79.3 - - - +
944D ASP* 1.3 73.8 + - - +
947D PHE* 3.0 61.4 + + + +
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Residues in contact with ASP 944 (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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940D ARG* 3.2 45.0 + - - +
941D GLU* 3.0 13.4 + - - +
943D PHE* 1.3 98.3 - - - +
945D ILE* 1.3 63.3 + - + +
947D PHE 4.3 2.6 - - - +
948D PRO* 3.7 23.0 - - - +
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Residues in contact with ILE 945 (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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874D ARG* 3.0 41.4 + - - +
877D LEU* 4.3 20.0 - - + -
911D VAL* 4.5 8.5 - - + -
934D HIS* 3.1 54.3 - - + +
936D VAL* 4.7 6.7 - - + -
941D GLU* 3.8 17.9 - - + +
942D ILE* 3.2 5.1 + - - +
944D ASP* 1.3 79.6 - - + +
946D ALA* 1.3 66.1 + - - +
947D PHE 3.3 0.7 + - - -
948D PRO* 3.6 7.8 - - - +
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Residues in contact with ALA 946 (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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862D THR* 4.0 22.7 - - + -
873D VAL* 3.1 28.2 - - + +
874D ARG 3.0 27.5 + - - -
877D LEU* 3.8 11.8 - - + +
879D MET* 4.5 4.9 - - + -
942D ILE* 2.8 18.5 + - + +
943D PHE* 4.7 0.2 - - - -
945D ILE* 1.3 79.7 - - - +
947D PHE* 1.3 63.6 + - + +
948D PRO* 3.7 0.9 - - - -
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Residues in contact with PHE 947 (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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862D THR* 3.7 30.5 - - + -
865D LEU* 4.3 7.6 - - + -
866D SER* 3.7 27.6 - - - -
869D MET* 3.7 15.0 - - + -
871D ARG* 3.5 53.2 - - - +
872D PRO 3.9 4.5 - - - -
873D VAL* 3.9 11.4 - - + -
939D TYR* 4.4 2.5 - - - -
943D PHE* 3.0 53.9 + + + +
944D ASP* 3.8 7.3 - - - +
946D ALA* 1.3 82.6 - - + +
948D PRO* 1.3 66.9 - - - +
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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