Contacts of the strand formed by residues 972 - 989 (chain D) in PDB entry 5D6Y
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 VAL 972 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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987A GLN* 4.0 15.0 - - - +
995A GLN* 2.8 45.0 + - + +
996A LEU 4.1 1.8 - - - -
997A VAL* 3.6 31.0 - - + -
947D VAL* 4.4 2.5 - - + -
964D GLN* 3.7 32.5 - - + -
965D VAL 3.3 8.3 - - - +
966D ARG* 4.5 4.9 - - - -
971D GLN* 1.3 80.2 - - - +
973D TYR* 1.3 69.3 + - - +
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Residues in contact with TYR 973 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932D PHE* 3.9 22.2 - + + -
934D ASP* 5.8 0.7 - - - -
964D GLN* 3.5 4.3 - - - -
965D VAL* 2.8 34.9 + - - +
967D TRP* 3.4 24.9 - - + -
969D ASP* 2.8 23.5 + - - -
971D GLN* 3.3 46.3 + - + -
972D VAL* 1.3 77.3 - - - +
974D GLY* 1.3 64.1 + - - +
23d M3L 3.8 38.0 - - - -
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Residues in contact with GLY 974 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932D PHE* 3.6 5.9 - - - -
933D ASP* 3.0 42.6 + - - +
962D VAL* 6.1 1.6 - - - -
963D VAL 3.7 5.4 - - - -
964D GLN* 4.8 4.7 - - - -
973D TYR* 1.3 72.7 - - - +
975D ALA* 1.3 63.9 + - - +
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Residues in contact with ALA 975 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
930D VAL* 4.1 7.4 - - + -
931D ASN 3.3 16.2 - - - +
932D PHE* 3.8 17.9 - - + +
933D ASP* 4.0 6.4 + - - -
962D VAL* 3.5 8.9 - - - +
963D VAL* 2.8 34.2 + - + +
965D VAL* 4.0 19.3 - - + -
974D GLY* 1.3 75.9 - - - +
976D LYS* 1.3 65.2 + - - +
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Residues in contact with LYS 976 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
930D VAL* 3.6 1.3 - - - -
931D ASN* 2.8 43.0 + - + +
933D ASP* 4.9 6.5 + - - +
960D GLY* 3.9 25.6 - - - +
961D GLU 3.3 5.4 - - - +
962D VAL* 4.0 22.7 - - + -
963D VAL* 4.4 2.7 - - - -
975D ALA* 1.3 78.3 - - - +
977D PHE* 1.3 63.7 + - - +
978D VAL* 3.9 0.5 - - - +
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Residues in contact with PHE 977 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928D TYR* 3.6 28.3 - + + -
929D GLU 3.8 12.1 - - - -
930D VAL* 4.1 11.7 - - + -
946D ILE* 4.7 2.7 - - + -
956D PRO* 3.9 2.5 - - + -
957D PRO* 3.1 59.2 - - + -
958D ALA 3.6 17.3 - - - +
959D GLU* 3.7 2.3 - - + +
960D GLY* 2.7 29.3 + - - -
961D GLU 2.9 14.8 + - - +
963D VAL* 4.2 5.4 - - + +
976D LYS* 1.3 73.4 - - - +
978D VAL* 1.3 61.3 + - - +
979D ALA* 3.4 32.3 - - - -
980D SER* 3.4 17.5 - - - -
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Residues in contact with VAL 978 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
929D GLU* 2.9 41.6 + - + +
930D VAL 3.9 1.6 - - - -
931D ASN* 3.2 50.9 - - - +
959D GLU* 3.1 32.7 - - + +
976D LYS 3.9 0.9 - - - +
977D PHE* 1.3 78.6 - - - +
979D ALA* 1.3 65.9 + - + +
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Residues in contact with ALA 979 (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 PHE 3.9 0.2 - - - +
928D TYR* 3.5 1.7 - - - -
929D GLU* 2.8 34.8 + - - +
977D PHE* 3.4 14.1 - - - -
978D VAL* 1.3 87.3 - - + +
980D SER* 1.3 62.5 + - - +
981D HIS* 3.8 25.2 - - + +
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Residues in contact with SER 980 (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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926D THR* 4.9 6.3 - - - -
927D PHE 3.5 4.3 - - - -
928D TYR* 3.2 21.4 - - - -
956D PRO* 3.0 37.1 - - - +
977D PHE* 3.4 3.3 - - - -
979D ALA* 1.3 74.1 - - - +
981D HIS* 1.3 63.2 + - - +
982D PRO* 3.3 12.8 - - - +
959E GLU* 4.0 3.3 - - - +
979E ALA* 5.8 3.5 - - - +
980E SER* 6.2 0.2 - - - -
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Residues in contact with HIS 981 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
925D GLU 3.4 0.7 - - - +
926D THR* 4.5 1.8 - - - -
927D PHE* 2.6 42.4 + - + +
929D GLU* 2.7 46.7 + - + +
939D ASP* 4.4 12.3 - - + -
979D ALA* 3.8 20.1 - - + +
980D SER* 1.3 72.9 + - - +
982D PRO* 1.3 64.2 - - - +
983D ILE* 3.2 30.6 + - + +
959E GLU* 3.1 26.1 + - - +
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Residues in contact with PRO 982 (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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925D GLU 3.4 7.2 - - - +
926D THR* 4.5 10.7 - - + +
980D SER* 3.3 14.1 - - - +
981D HIS* 1.3 81.3 - - - +
983D ILE* 1.3 53.7 + - - +
956E PRO* 4.6 18.6 - - + +
957E PRO 4.2 17.9 - - - +
958E ALA* 4.2 3.4 - - - -
959E GLU* 2.6 51.3 + - - +
977E PHE* 4.7 9.2 - - + -
979E ALA* 5.8 0.4 - - - -
980E SER* 4.8 12.1 - - - +
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Residues in contact with ILE 983 (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 THR 3.7 2.1 - - - +
924D THR* 3.9 2.9 - - - +
925D GLU* 2.8 37.1 + - + +
927D PHE* 3.7 24.5 - - + -
939D ASP 5.4 1.8 - - - +
981D HIS* 3.6 30.5 - - + +
982D PRO* 1.3 76.0 - - - +
984D GLN* 1.3 75.4 + - - +
985D MET* 3.7 22.8 + - + -
999D LYS* 5.6 5.2 - - + -
1000D ARG 6.1 0.2 - - - +
958E ALA* 3.8 4.6 - - - +
959E GLU* 4.4 9.9 - - + +
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Residues in contact with GLN 984 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922D LEU* 3.2 39.8 - - + +
923D THR 3.2 20.9 - - - +
924D THR* 5.3 7.0 - - - +
983D ILE* 1.3 78.6 - - - +
985D MET* 1.3 63.6 - - - +
986D TYR* 3.2 38.8 - - + +
1000D ARG* 4.2 9.9 + - + +
958E ALA* 3.3 27.2 - - + +
959E GLU 4.8 6.2 + - - +
961E GLU* 4.4 18.2 + - + +
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Residues in contact with MET 985 (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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966A ARG* 4.2 4.7 - - - +
922D LEU* 3.4 5.4 - - - -
923D THR* 2.8 47.7 + - - +
925D GLU* 4.1 12.1 - - + +
927D PHE* 3.8 33.4 - - + -
983D ILE* 3.7 14.6 + - + +
984D GLN* 1.3 79.3 - - - +
986D TYR* 1.3 66.7 + - - +
997D VAL* 3.4 34.3 - - + +
998D VAL* 3.6 18.4 - - - +
999D LYS* 3.9 19.1 - - + +
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Residues in contact with TYR 986 (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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898D SER* 5.2 2.8 - - - -
899D ILE* 3.5 37.4 + - + +
919D VAL* 4.4 6.7 - - + -
921D ARG 3.5 3.4 - - - +
922D LEU* 3.7 34.0 - - + +
984D GLN* 3.2 33.0 - - + +
985D MET* 1.3 73.4 - - - +
987D GLN* 1.3 62.7 + - - +
988D VAL* 3.5 15.9 + - + -
997D VAL* 3.4 2.8 - - - -
998D VAL* 2.9 45.2 + - - +
999D LYS 4.2 1.6 - - - -
1000D ARG* 3.1 53.9 + - + +
1003D VAL* 4.5 12.1 - - + -
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Residues in contact with GLN 987 (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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947A VAL* 3.9 13.7 - - - +
964A GLN* 3.1 24.3 + - - +
972A VAL* 3.8 18.9 - - + +
919D VAL* 3.7 2.9 - - - +
920D VAL* 2.8 42.9 + - + +
921D ARG* 2.8 37.8 + - + +
923D THR* 4.5 4.8 - - + +
985D MET 4.1 0.8 + - - -
986D TYR* 1.3 69.4 - - - +
988D VAL* 1.3 61.1 + - - +
995D GLN* 2.3 35.7 + - + +
996D LEU 3.3 11.2 - - - +
997D VAL* 4.0 13.4 - - + +
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Residues in contact with VAL 988 (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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905D VAL* 4.6 0.2 - - + -
907D SER* 3.7 20.2 - - - +
917D CYS* 3.9 11.2 - - - -
918D GLU 3.1 6.3 - - - +
919D VAL* 4.2 17.9 - - + -
920D VAL* 5.1 0.4 - - - -
986D TYR* 3.7 21.1 - - + +
987D GLN* 1.3 79.8 - - - +
989D GLU* 1.3 61.0 + - - +
990D PHE* 3.7 17.4 - - + -
994D SER 3.7 0.7 - - - +
995D GLN* 3.1 7.1 - - - -
996D LEU 2.7 40.9 + - - +
998D VAL* 4.1 21.8 - - + -
1003D VAL* 4.4 4.3 - - + -
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Residues in contact with GLU 989 (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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917D CYS* 3.4 3.1 - - - +
918D GLU* 2.6 40.3 + - + +
920D VAL* 4.0 22.0 - - + +
987D GLN 4.4 0.2 + - - -
988D VAL* 1.3 72.8 - - - +
990D PHE* 1.3 64.5 + - - +
993D GLY* 3.3 31.5 - - - +
994D SER 3.5 2.0 - - - +
995D GLN* 3.6 32.8 + - + -
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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
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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