Contacts of the helix formed by residues 1117 - 1135 (chain B) in PDB entry 5YWB
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 PRO1117 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825B GLU* 3.8 28.3 - - - +
828B ILE* 5.2 4.0 - - + -
1115B THR 3.6 7.9 - - - +
1116B THR* 1.3 92.0 - - + +
1118B LEU* 1.3 62.7 + - - +
1119B GLY 3.3 0.2 - - - -
1120B SER* 2.5 38.7 + - - +
1121B ILE* 3.4 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B LEU* 4.2 33.1 - - + +
504B ARG* 4.6 9.2 - - + +
825B GLU* 5.3 3.3 + - + +
826B ARG* 3.4 28.9 - - - +
828B ILE* 3.7 22.8 - - + +
1113B PHE* 3.9 29.6 - - + +
1116B THR 3.3 2.9 + - - +
1117B PRO* 1.3 69.5 - - - +
1119B GLY* 1.3 66.9 + - - +
1121B ILE* 3.1 20.9 + - + +
1122B LEU* 2.9 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY1119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
825B GLU* 5.2 15.1 - - - +
1117B PRO* 3.3 2.0 - - - +
1118B LEU* 1.3 78.3 - - - +
1120B SER* 1.3 56.5 + - - +
1122B LEU* 3.4 6.4 + - - +
1123B ASN* 2.9 32.9 + - - +
1198B LEU* 6.0 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER1120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1116B THR* 4.1 8.8 - - - +
1117B PRO* 2.5 38.0 + - - +
1119B GLY* 1.3 75.6 - - - +
1121B ILE* 1.3 62.2 + - - +
1123B ASN* 4.8 2.2 - - - -
1124B ARG* 2.9 52.3 + - - +
1198B LEU* 5.6 12.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B LEU* 3.7 23.6 - - + -
1105B ILE* 5.1 15.3 - - + -
1112B PHE* 4.8 15.3 - - + -
1113B PHE* 5.0 10.8 - - + +
1116B THR* 3.7 37.2 - - + +
1117B PRO 3.4 2.7 + - - +
1118B LEU* 3.1 27.6 + - + +
1120B SER* 1.3 81.5 + - - +
1122B LEU* 1.3 58.4 + - - +
1124B ARG* 3.7 4.3 - - - +
1125B PHE* 2.9 37.1 + - + +
1318B LEU* 4.8 19.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B ASN* 5.1 9.6 - - - +
496B LEU* 4.7 16.2 - - + +
499B THR* 3.9 22.9 - - + -
500B ASN* 3.1 39.0 - - - +
503B LEU* 4.9 8.7 - - + -
1118B LEU 2.9 15.8 + - - +
1119B GLY* 4.0 5.4 - - - +
1121B ILE* 1.3 78.1 - - - +
1123B ASN* 1.3 61.6 + - - +
1125B PHE* 3.2 7.0 - - + +
1126B SER* 2.9 28.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B ALA* 5.4 7.6 - - - +
1119B GLY 2.9 18.5 + - - +
1120B SER* 4.2 2.7 - - - +
1122B LEU* 1.3 75.9 - - + +
1124B ARG* 1.3 61.8 + - - +
1126B SER* 4.5 4.1 - - - +
1127B SER* 2.9 46.4 + - - -
1198B LEU* 4.9 15.3 - - + +
1201B LEU* 4.6 18.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1120B SER* 2.9 44.4 + - - +
1121B ILE 3.7 3.1 - - - +
1123B ASN* 1.3 75.6 - - - +
1125B PHE* 1.3 67.0 + - - +
1127B SER* 5.0 1.1 - - - -
1128B ASP* 2.9 49.7 + - - +
1314B ARG* 3.2 53.2 - - + +
1315B ILE* 4.8 6.1 - - + +
1318B LEU* 3.6 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B ARG* 3.5 28.7 - - - -
496B LEU* 5.4 2.2 - - + -
499B THR* 4.8 24.9 - - + -
503B LEU* 5.7 1.6 - - + -
522B VAL* 6.2 0.2 - - + -
1098B HIS* 3.9 16.4 - + - -
1101B LEU* 3.5 34.5 - - + -
1102B LEU* 3.6 38.1 - - + -
1105B ILE* 5.2 5.4 - - + -
1121B ILE* 2.9 24.1 + - + +
1122B LEU* 3.2 15.9 - - + +
1124B ARG* 1.3 79.8 - - - +
1126B SER* 1.3 64.5 + - - +
1128B ASP* 5.2 0.7 - - - -
1129B CYS* 3.0 31.9 + - - -
1315B ILE* 5.3 1.1 - - - +
1318B LEU* 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B ASN* 5.9 0.9 - - - -
423B ILE* 5.3 5.9 - - - +
495B ARG* 5.5 1.3 - - - +
496B LEU* 3.2 42.5 - - - +
1122B LEU* 2.9 21.1 + - - -
1123B ASN* 4.2 5.2 - - - -
1125B PHE* 1.3 75.7 - - - +
1127B SER* 1.3 65.0 + - - +
1129B CYS* 3.9 2.0 - - - -
1130B ASN* 2.9 41.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1123B ASN* 2.9 32.0 + - - -
1124B ARG* 5.0 1.3 - - - -
1126B SER* 1.3 74.1 - - - +
1128B ASP* 1.3 62.9 + - - +
1130B ASN* 3.8 3.9 - - - +
1131B THR* 2.9 38.2 + - - -
1314B ARG* 5.8 2.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1124B ARG* 2.9 44.4 + - - +
1125B PHE 4.1 0.7 - - - +
1127B SER* 1.3 79.8 + - - +
1129B CYS* 1.3 57.8 + - - +
1131B THR* 3.3 4.7 + - - -
1132B ILE* 2.9 38.6 + - + +
1311B ALA* 3.0 38.0 - - - +
1314B ARG* 3.2 19.1 + - - +
1315B ILE* 3.4 21.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS1129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B ARG* 4.4 17.7 - - - +
526B ARG* 4.6 9.2 - - - +
1098B HIS* 4.5 17.5 - - - -
1101B LEU* 4.5 11.2 - - - -
1125B PHE* 3.0 46.2 + - - +
1126B SER 4.0 1.8 - - - +
1128B ASP* 1.3 78.4 - - - +
1130B ASN* 1.3 59.0 + - - +
1132B ILE* 3.4 7.1 + - - -
1133B ASP* 2.9 36.6 + - - +
1315B ILE* 5.4 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN1130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B ILE* 5.4 10.3 - - - +
427B GLN* 5.8 1.6 - - - +
492B SER* 4.1 17.5 + - - -
495B ARG* 4.1 9.5 + - - -
496B LEU* 5.7 2.5 - - - +
602B LYS* 4.9 15.4 - - - +
1126B SER* 2.9 32.2 + - - +
1127B SER* 3.8 5.1 - - - +
1129B CYS* 1.3 78.1 - - - +
1131B THR* 1.3 61.8 + - - +
1133B ASP* 3.3 5.4 + - - +
1134B GLN* 2.9 34.8 + - - +
1135B HIS* 4.1 5.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1127B SER* 2.9 22.9 + - - -
1128B ASP* 3.7 5.8 + - - -
1130B ASN* 1.3 75.4 - - - +
1132B ILE* 1.3 61.9 + - + +
1135B HIS* 2.7 47.7 + - + +
1136B ILE* 3.0 9.4 + - + -
1308B GLN* 3.8 37.0 - - + +
1311B ALA* 5.1 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1004B TYR* 6.1 0.4 - - + -
1090B GLY 5.3 2.6 - - - +
1093B VAL* 4.4 14.4 - - + -
1094B ALA* 4.2 26.3 - - + +
1097B LEU* 3.6 27.6 - - + -
1128B ASP* 2.9 30.0 + - + +
1129B CYS* 3.9 7.0 - - - +
1131B THR* 1.3 78.5 - - + +
1133B ASP* 1.3 63.8 + - - +
1136B ILE* 3.2 36.8 - - + +
1137B PRO* 3.8 2.1 - - - +
1308B GLN 5.7 0.2 - - - +
1311B ALA* 6.0 1.3 - - + -
1312B VAL* 4.1 29.8 - - + +
1315B ILE* 5.1 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP1133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B ARG* 5.1 2.6 + - - -
526B ARG* 3.0 31.3 + - - -
529B GLU* 4.2 4.2 - - - +
533B LEU* 3.7 32.6 - - + +
536B PHE* 5.9 2.6 - - - -
1091B LEU* 6.1 0.7 - - - +
1094B ALA* 3.1 29.1 - - - +
1129B CYS* 2.9 26.1 + - - +
1130B ASN* 3.9 5.8 - - - +
1131B THR 3.3 0.2 - - - -
1132B ILE* 1.3 79.4 - - - +
1134B GLN* 1.3 69.6 + - + +
1137B PRO* 4.0 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN1134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B GLN* 5.0 5.0 - - - +
488B THR* 4.7 13.9 - - - +
489B LEU* 4.3 11.3 - - - +
529B GLU* 5.4 1.6 + - - -
533B LEU* 4.8 9.5 - - + +
536B PHE* 6.0 4.4 - - + -
598B ARG* 3.2 47.0 + - - +
602B LYS* 2.4 45.2 + - - +
1130B ASN* 2.9 20.1 + - - +
1133B ASP* 1.3 90.6 - - + +
1135B HIS* 1.3 63.3 + - - +
1136B ILE 3.8 0.4 - - - -
1137B PRO* 3.9 5.9 - - - +
1138B SER* 4.0 6.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B GLN* 5.5 6.3 - - - -
430B TRP* 4.9 20.4 + + - -
598B ARG* 3.6 31.4 + - - -
599B SER* 5.9 0.4 + - - -
602B LYS* 5.3 5.2 - - - -
1130B ASN* 4.1 4.1 + - + -
1131B THR* 2.7 43.7 + - + +
1134B GLN* 1.3 78.8 - - + +
1136B ILE* 1.3 60.2 + - - +
1137B PRO* 3.4 1.3 - - - -
1138B SER* 3.5 4.1 + - - -
1139B THR* 3.2 30.0 + - - -
1304B ASP* 5.8 1.8 - - - -
1308B GLN* 3.4 17.7 - - - +
----------------------------------------------------------
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