Contacts of the helix formed by residues 1117 - 1135 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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825D GLU* 3.8 26.2 - - - +
828D ILE* 5.2 4.3 - - + -
1115D THR 3.6 7.4 - - - +
1116D THR* 1.3 92.1 - - + +
1118D LEU* 1.3 62.6 + - - +
1119D GLY 3.3 0.2 - - - -
1120D SER* 2.5 38.0 + - - +
1121D ILE* 3.4 3.3 + - - +
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Residues in contact with LEU1118 (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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503D LEU* 4.2 32.3 - - + +
504D ARG* 4.6 9.0 - - + -
825D GLU* 5.3 3.3 + - + +
826D ARG* 3.4 28.5 - - - +
828D ILE* 3.7 21.8 - - + +
1113D PHE* 3.9 30.1 - - + +
1116D THR 3.3 2.9 + - - +
1117D PRO* 1.3 69.9 - - - +
1119D GLY* 1.3 65.2 + - - +
1121D ILE* 3.1 21.9 + - + +
1122D LEU* 2.9 25.1 + - - +
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Residues in contact with GLY1119 (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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825D GLU* 5.2 14.9 - - - +
1117D PRO* 3.3 2.0 - - - +
1118D LEU* 1.3 79.0 - - - +
1120D SER* 1.3 55.9 + - - +
1122D LEU* 4.0 6.6 - - - +
1123D ASN* 2.9 33.4 + - - +
1198D LEU* 6.0 3.1 - - - -
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Residues in contact with SER1120 (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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825D GLU* 6.3 0.2 - - - -
1116D THR* 4.1 9.9 - - - +
1117D PRO* 2.5 37.2 + - - +
1119D GLY* 1.3 75.8 - - - +
1121D ILE* 1.3 62.4 + - - +
1123D ASN* 4.8 2.7 - - - -
1124D ARG* 2.9 51.3 + - - +
1198D LEU* 5.6 12.0 - - - +
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Residues in contact with ILE1121 (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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503D LEU* 3.7 23.3 - - + -
1105D ILE* 5.1 15.5 - - + -
1112D PHE* 4.8 15.5 - - + -
1113D PHE* 5.0 10.3 - - + -
1116D THR* 3.7 37.7 - - + -
1117D PRO 3.7 2.2 - - - +
1118D LEU* 3.1 28.1 + - + +
1120D SER* 1.3 82.8 + - - +
1122D LEU* 1.3 56.1 + - - +
1124D ARG* 3.7 4.0 - - - +
1125D PHE* 2.9 37.8 + - + +
1318D LEU* 4.8 18.9 - - + +
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Residues in contact with LEU1122 (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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415D GLY* 6.2 0.2 - - - -
419D ASN* 5.1 9.6 - - - +
496D LEU* 4.7 15.3 - - + +
499D THR* 3.9 22.9 - - + -
500D ASN* 3.1 37.9 - - - +
503D LEU* 4.9 8.1 - - + -
1118D LEU 2.9 16.0 + - - +
1119D GLY* 4.0 5.6 - - - +
1121D ILE* 1.3 79.3 - - - +
1123D ASN* 1.3 61.6 + - + +
1125D PHE* 3.2 8.3 - - + +
1126D SER* 2.9 29.0 + - - -
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Residues in contact with ASN1123 (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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422D ALA* 5.4 7.8 - - - +
1119D GLY 2.9 19.6 + - - +
1120D SER* 4.2 2.7 - - - +
1122D LEU* 1.3 76.6 - - + +
1124D ARG* 1.3 60.9 + - - +
1126D SER* 4.5 4.3 - - - +
1127D SER* 2.9 46.7 + - - -
1198D LEU* 4.9 15.5 - - + +
1201D LEU* 4.6 18.2 - - - +
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Residues in contact with ARG1124 (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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1120D SER* 2.9 45.0 + - - +
1121D ILE 3.7 3.6 - - - +
1123D ASN* 1.3 75.4 - - - +
1125D PHE* 1.3 67.1 + - - +
1127D SER* 5.0 1.6 - - - -
1128D ASP* 2.9 50.2 + - - +
1314D ARG* 3.2 52.4 - - + +
1315D ILE* 4.8 6.1 - - + -
1318D LEU* 3.6 29.2 - - + +
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Residues in contact with PHE1125 (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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495D ARG* 3.5 28.3 - - - -
496D LEU* 5.4 3.1 - - + -
499D THR* 4.8 23.8 - - + -
503D LEU* 5.7 1.8 - - + -
522D VAL* 6.2 0.2 - - + -
1098D HIS* 3.9 15.9 - + - -
1101D LEU* 3.5 36.1 - - + -
1102D LEU* 3.6 38.6 - - + -
1105D ILE* 5.2 5.8 - - + -
1121D ILE* 2.9 25.5 + - + +
1122D LEU* 3.2 15.5 + - + +
1124D ARG* 1.3 79.7 - - - +
1126D SER* 1.3 64.3 + - - +
1128D ASP* 4.1 0.6 - - - +
1129D CYS* 3.0 31.2 + - - -
1315D ILE* 5.3 1.1 - - - +
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Residues in contact with SER1126 (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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419D ASN* 5.9 0.9 - - - -
423D ILE* 5.3 5.4 - - - +
495D ARG* 5.5 1.3 - - - +
496D LEU* 3.2 42.9 - - - +
1122D LEU* 2.9 21.1 + - - -
1123D ASN* 4.2 5.2 - - - -
1125D PHE* 1.3 73.8 - - - +
1127D SER* 1.3 65.0 + - - +
1129D CYS* 3.9 1.9 - - - +
1130D ASN* 2.9 40.8 + - - +
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Residues in contact with SER1127 (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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1123D ASN* 2.9 31.9 + - - -
1124D ARG* 4.4 1.6 - - - -
1126D SER* 1.3 74.4 - - - +
1128D ASP* 1.3 61.2 + - - +
1130D ASN* 3.8 4.1 - - - +
1131D THR* 2.9 38.3 + - - -
1314D ARG* 5.8 2.3 + - - -
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Residues in contact with ASP1128 (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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1124D ARG* 2.9 44.0 + - - +
1125D PHE 4.1 0.4 - - - +
1127D SER* 1.3 79.9 + - - +
1129D CYS* 1.3 59.0 + - - +
1131D THR* 3.3 4.4 + - - -
1132D ILE* 2.9 38.9 + - + +
1311D ALA* 3.0 37.1 - - - +
1314D ARG* 3.2 18.5 + - - +
1315D ILE* 3.4 21.4 - - + +
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Residues in contact with CYS1129 (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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495D ARG* 4.4 15.9 - - - +
526D ARG* 4.6 9.4 - - - +
1098D HIS* 4.5 17.9 - - - -
1101D LEU* 4.5 11.4 - - - -
1125D PHE* 3.0 46.6 + - - +
1126D SER 4.0 2.2 - - - +
1128D ASP* 1.3 79.2 - - - +
1130D ASN* 1.3 59.0 + - - +
1132D ILE* 3.8 7.1 - - - +
1133D ASP* 2.9 37.2 + - - +
1315D ILE* 5.4 2.7 - - - -
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Residues in contact with ASN1130 (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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423D ILE* 5.4 9.7 - - - +
427D GLN* 5.8 2.0 - - - +
492D SER* 4.1 17.2 + - - -
495D ARG* 4.1 10.0 + - - -
496D LEU* 5.7 2.7 - - - +
602D LYS* 4.9 15.1 - - - +
1126D SER* 2.9 32.8 + - - +
1127D SER* 3.8 5.1 - - - +
1129D CYS* 1.3 79.1 - - - +
1131D THR* 1.3 62.6 + - - +
1133D ASP* 3.3 5.6 + - - +
1134D GLN* 2.9 35.5 + - - +
1135D HIS* 4.1 4.1 + - + +
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Residues in contact with THR1131 (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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1127D SER* 2.9 23.3 + - - -
1128D ASP* 3.3 6.5 + - - -
1130D ASN* 1.3 75.8 - - - +
1132D ILE* 1.3 61.5 + - + +
1135D HIS* 2.7 49.3 + - + +
1136D ILE* 3.0 9.4 + - + -
1308D GLN* 3.8 36.3 - - + +
1311D ALA* 5.1 8.5 - - + -
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Residues in contact with ILE1132 (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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1004D TYR* 6.1 0.9 - - + -
1090D GLY 5.3 2.4 - - - +
1093D VAL* 4.4 15.0 - - + -
1094D ALA* 4.2 25.9 - - + +
1097D LEU* 3.6 26.9 - - + -
1128D ASP* 2.9 30.4 + - + +
1129D CYS* 3.9 6.7 - - - +
1131D THR* 1.3 78.5 - - + +
1133D ASP* 1.3 64.6 + - - +
1136D ILE* 3.2 35.8 - - + +
1137D PRO* 3.8 2.1 - - - +
1308D GLN 5.7 0.2 - - - +
1311D ALA* 6.0 2.0 - - + -
1312D VAL* 4.1 30.1 - - + +
1315D ILE* 5.1 5.4 - - + -
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Residues in contact with ASP1133 (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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495D ARG* 5.1 2.6 + - - -
526D ARG* 3.0 31.8 + - - -
529D GLU* 4.2 4.0 - - - +
533D LEU* 3.7 32.2 - - + +
536D PHE* 5.9 2.4 - - - -
1091D LEU* 6.1 0.7 - - - +
1094D ALA* 3.1 29.0 - - - +
1129D CYS* 2.9 26.8 + - - +
1130D ASN* 3.9 6.2 - - - +
1132D ILE* 1.3 80.0 - - - +
1134D GLN* 1.3 68.5 + - + +
1137D PRO* 4.0 12.2 - - - +
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Residues in contact with GLN1134 (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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485D GLN* 5.0 5.2 - - - +
488D THR* 4.7 14.3 - - - +
489D LEU* 4.3 11.3 - - - +
529D GLU* 5.4 1.2 + - - -
533D LEU* 4.8 9.7 - - + +
536D PHE* 6.0 4.9 - - + -
598D ARG* 3.2 47.3 + - - +
602D LYS* 2.4 43.1 + - - +
1130D ASN* 2.9 19.9 + - - +
1133D ASP* 1.3 90.2 - - + +
1135D HIS* 1.3 64.7 + - - +
1136D ILE 3.8 0.2 - - - -
1137D PRO* 3.9 5.3 - - - +
1138D SER* 4.0 6.1 + - - -
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Residues in contact with HIS1135 (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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427D GLN* 5.5 5.8 - - - -
430D TRP* 4.9 20.6 + + - -
598D ARG* 3.6 32.1 + - - -
599D SER* 5.9 0.2 + - - -
602D LYS* 5.3 5.6 - - - -
1130D ASN* 4.1 5.3 + - + -
1131D THR* 2.7 42.4 + - + +
1134D GLN* 1.3 77.2 - - + +
1136D ILE* 1.3 61.3 + - - +
1137D PRO* 3.4 1.8 - - - -
1138D SER* 3.5 4.2 + - - -
1139D THR* 3.2 31.0 + - - -
1304D ASP* 5.8 1.3 - - - -
1308D GLN* 3.4 19.1 - - - +
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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