Contacts of the helix formed by residues 915 - 932 (chain D) in PDB entry 4UN0
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 PRO 915 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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851D HIS* 3.5 51.0 - - + +
856D LEU* 3.5 25.8 - - + -
884D TYR* 3.7 28.0 - - + -
914D THR* 1.3 86.0 - - - +
916D ALA* 1.3 58.7 + - - +
917D ILE* 3.0 4.3 - - + -
918D ASP* 3.1 14.2 + - - +
919D VAL* 3.7 3.8 + - - +
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Residues in contact with ALA 916 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
905D GLU* 4.8 0.9 - - - +
914D THR* 2.8 19.4 + - - +
915D PRO* 1.3 76.5 - - - +
917D ILE* 1.3 58.5 + - - +
918D ASP 3.2 0.4 - - - -
919D VAL* 3.4 13.2 + - + +
920D TRP 3.3 10.9 + - - -
1005D PRO* 4.0 26.5 - - + +
1008D ARG* 2.7 39.8 + - + +
1009D CYS 5.3 2.0 - - - +
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Residues in contact with ILE 917 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856D LEU* 4.8 4.0 - - + -
858D ARG* 4.0 21.5 - - + -
896D VAL* 4.6 4.9 - - + -
897D ILE* 4.1 11.0 - - + +
903D PRO* 3.5 29.3 - - + +
905D GLU* 3.5 28.9 - - + +
906D LEU* 4.3 9.2 - - + -
913D TYR* 3.5 40.2 - - + -
914D THR 3.3 14.1 + - - +
915D PRO* 4.4 1.8 - - + -
916D ALA* 1.3 79.1 - - - +
918D ASP* 1.3 73.3 + - - +
921D SER* 3.1 21.3 + - - -
1008D ARG* 4.4 0.2 - - - +
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Residues in contact with ASP 918 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
847D LEU* 3.9 5.4 - - + -
851D HIS* 3.1 25.2 + - - +
856D LEU* 3.7 6.7 - - - +
857D HIS* 2.9 33.2 + - - +
858D ARG* 3.1 23.9 + - - -
860D ILE* 3.7 14.2 - - + +
897D ILE* 4.0 4.5 - - - +
915D PRO 3.1 10.0 + - - +
917D ILE* 1.3 86.1 - - - +
919D VAL* 1.3 63.7 + - - +
921D SER* 3.4 6.4 + - - -
922D CYS* 3.3 26.2 + - - -
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Residues in contact with VAL 919 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844D MET* 4.8 7.6 - - + -
847D LEU* 4.9 1.1 - - + -
851D HIS* 4.6 8.1 - - + -
915D PRO 3.8 14.1 - - - +
916D ALA* 3.4 11.4 + - - +
917D ILE 3.4 0.4 - - - -
918D ASP* 1.3 75.4 - - - +
920D TRP* 1.3 64.5 + - - +
922D CYS* 3.3 9.3 + - - +
923D GLY* 3.0 18.7 + - - -
1000D MET* 4.0 35.0 - - + +
1008D ARG* 4.4 4.9 - - - -
1009D CYS* 3.2 32.5 - - + +
1010D THR* 4.3 16.8 - - - +
1011D ALA* 4.5 2.7 - - - +
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Residues in contact with TRP 920 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901D TYR 3.4 19.7 - - - -
902D ARG 3.4 12.9 + - - -
903D PRO* 3.5 20.9 - - + -
904D PRO* 3.6 27.8 - - + -
916D ALA 3.3 4.0 + - - +
917D ILE 3.9 0.2 - - - +
918D ASP 3.3 0.2 - - - -
919D VAL* 1.3 78.2 - - - +
921D SER* 1.3 61.7 + - - +
923D GLY* 3.1 3.3 + - - -
924D CYS* 3.0 32.0 + - - -
936D PHE* 4.1 7.6 - + - -
948D ILE* 3.6 34.4 - - + +
952D CYS* 4.2 9.9 - - - -
1000D MET 3.9 8.2 + - - -
1001D LEU* 3.6 51.7 - - + +
1002D THR 3.8 8.5 - - - -
1003D LEU* 4.6 2.5 - - + -
1008D ARG* 3.4 34.0 - - - +
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Residues in contact with SER 921 (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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860D ILE* 3.6 30.3 - - - -
897D ILE* 3.2 26.2 - - - +
901D TYR* 3.5 13.2 + - - -
917D ILE 3.1 15.2 + - - -
918D ASP 3.4 8.9 + - - -
919D VAL 3.2 0.2 - - - -
920D TRP* 1.3 78.3 - - - +
922D CYS* 1.3 60.6 + - - +
924D CYS* 3.1 15.6 + - - +
925D ILE* 3.1 19.8 + - - +
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Residues in contact with CYS 922 (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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840D MET* 4.1 4.2 - - - +
843D LEU* 3.7 22.0 - - + -
844D MET* 3.7 25.4 - - - -
847D LEU* 3.6 23.1 - - - -
860D ILE* 4.1 12.1 - - - -
918D ASP 3.3 13.9 + - - -
919D VAL 3.3 8.8 + - - +
921D SER* 1.3 78.8 - - - +
923D GLY* 1.3 57.0 + - - +
925D ILE* 3.2 10.3 + - - +
926D LEU* 2.8 30.0 + - - +
1000D MET* 4.3 7.0 - - + -
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Residues in contact with GLY 923 (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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919D VAL 3.0 11.7 + - - -
920D TRP 3.1 6.0 + - - -
922D CYS* 1.3 77.3 - - - +
924D CYS* 1.3 60.2 + - - +
926D LEU* 4.4 2.0 - - - -
927D GLY* 3.2 19.1 + - - -
935D ILE* 4.3 0.2 - - - +
997D LEU* 3.2 12.2 - - - +
1000D MET* 3.8 26.6 - - - -
1001D LEU* 4.0 14.0 - - - +
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Residues in contact with CYS 924 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901D TYR* 4.1 33.1 - - + -
920D TRP* 3.0 44.8 + - - -
921D SER 3.1 8.5 + - - +
923D GLY* 1.3 76.5 - - - +
925D ILE* 1.3 59.7 + - - +
928D GLU* 3.2 23.9 + - - +
935D ILE* 3.7 19.5 + - + +
936D PHE* 3.9 26.0 - - + -
1001D LEU* 4.2 2.2 - - - -
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Residues in contact with ILE 925 (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 LEU* 4.2 18.8 - - + -
840D MET* 3.8 18.6 - - + -
843D LEU* 4.7 0.7 - - + -
860D ILE* 3.8 15.9 - - + -
861D LYS* 3.8 20.9 - - - -
862D CYS* 4.4 2.0 - - + +
865D ILE* 3.6 23.8 - - + -
901D TYR* 3.6 17.5 - - + -
921D SER 3.1 14.9 + - - +
922D CYS* 3.6 9.0 - - - +
923D GLY 3.1 0.2 - - - -
924D CYS* 1.3 77.8 - - - +
926D LEU* 1.3 64.8 + - - +
927D GLY 3.2 0.2 - - - -
928D GLU* 3.1 16.1 + - - +
929D LEU* 3.0 25.4 + - + +
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Residues in contact with LEU 926 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836D ILE* 3.9 5.8 - - + -
840D MET* 3.6 35.0 - - + -
922D CYS 2.8 17.6 + - - +
923D GLY 3.8 4.5 - - - +
925D ILE* 1.3 78.6 - - - +
927D GLY* 1.3 60.8 + - - +
929D LEU* 3.5 7.8 + - - +
930D PHE* 3.2 43.5 - - + -
989D ILE* 6.2 0.2 - - + -
993D ALA 4.2 5.4 - - - +
996D LEU* 3.8 27.4 - - + -
997D LEU* 3.8 34.5 - - + +
1000D MET* 4.2 7.2 - - - -
1019D PHE* 4.6 9.4 - - + -
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Residues in contact with GLY 927 (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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923D GLY 3.2 10.3 + - - -
924D CYS 4.5 0.4 - - - -
926D LEU* 1.3 76.7 - - - +
928D GLU* 1.3 62.8 + - - +
930D PHE* 3.4 6.4 + - - +
931D THR* 3.0 31.4 + - - +
935D ILE* 4.1 15.0 - - - -
986D PHE* 4.2 3.1 - - - -
989D ILE* 4.9 0.4 - - - -
997D LEU* 3.6 23.7 - - - +
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Residues in contact with GLU 928 (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 LEU* 4.6 2.6 - - - +
821D MET* 5.0 0.3 - - - -
824D LEU* 3.7 24.5 - - - +
862D CYS* 3.6 22.7 - - - +
901D TYR* 3.5 17.8 + - - +
924D CYS 3.2 20.9 + - - +
925D ILE* 3.1 18.7 + - - +
927D GLY* 1.3 77.9 - - - +
929D LEU* 1.3 60.2 + - - +
931D THR* 3.1 6.2 + - - -
932D LYS* 2.6 41.2 + - - +
933D LYS 3.7 22.9 - - - +
934D PRO* 3.7 11.9 - - + +
935D ILE* 4.4 2.2 - - - +
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Residues in contact with LEU 929 (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 LEU* 4.1 26.2 - - + +
831D PHE* 4.3 39.0 + - + +
836D ILE* 3.7 47.8 - - + +
839D PHE* 5.0 4.9 - - + -
840D MET* 3.8 27.8 - - + -
925D ILE* 3.0 16.6 + - + +
926D LEU* 3.7 6.1 - - - +
927D GLY 3.3 0.4 - - - -
928D GLU* 1.3 85.9 - - - +
930D PHE* 1.3 60.9 + - - +
931D THR 3.5 0.3 + - - -
932D LYS* 3.9 6.5 + - - +
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Residues in contact with PHE 930 (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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831D PHE 6.0 0.7 - - - -
832D SER 5.9 0.2 - - - -
833D GLU* 5.0 11.7 - - + -
836D ILE* 3.6 32.8 - - + -
926D LEU* 3.2 40.2 - - + -
927D GLY 3.4 4.8 + - - +
928D GLU 3.2 0.6 - - - -
929D LEU* 1.3 76.9 - - - +
931D THR* 1.3 58.3 + - + +
932D LYS 3.6 0.2 - - - -
988D PHE* 3.6 19.5 - + + -
989D ILE* 3.6 40.4 - - + -
990D PRO* 3.8 21.5 - - + -
993D ALA* 4.2 22.0 - - + -
1019D PHE* 4.4 6.7 - + - -
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Residues in contact with THR 931 (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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927D GLY 3.0 19.5 + - - +
928D GLU* 3.1 1.4 + - - -
930D PHE* 1.3 80.9 - - + +
932D LYS* 1.3 58.9 + - - +
933D LYS* 2.5 54.4 + - - +
935D ILE* 4.1 5.4 - - + +
986D PHE* 3.6 25.1 - - + -
988D PHE* 3.7 16.6 - - + -
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Residues in contact with LYS 932 (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 LEU* 3.5 34.0 - - + +
928D GLU* 2.6 21.2 + - - +
929D LEU* 3.9 6.5 + - - +
930D PHE 3.6 1.8 - - - -
931D THR* 1.3 73.1 - - - +
933D LYS* 1.3 56.7 + - + +
934D PRO* 4.4 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
------------------------------------------------------------
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