Contacts of the strand formed by residues 1127 - 1140 (chain B) in PDB entry 5YS0
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 GLN1127 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1102A ASP* 5.3 2.3 - - - +
1098B PHE* 4.1 15.0 - - - -
1116B THR* 3.9 21.9 - - + +
1117B LYS 2.9 17.5 - - - +
1118B LYS* 4.3 8.3 - - + +
1119B LEU* 3.5 6.5 - - - +
1125B PRO* 3.2 19.7 + - - +
1126B LYS* 1.3 85.1 + - + +
1128B THR* 1.3 67.5 + - - +
1155B ASP* 4.5 5.2 - - - +
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Residues in contact with THR1128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1116B THR* 3.9 4.7 - - - -
1117B LYS* 2.6 50.4 + - + +
1119B LEU* 3.7 26.5 - - + -
1127B GLN* 1.3 80.4 - - - +
1129B LYS* 1.3 74.9 + - - +
1130B CYS* 4.1 1.7 - - - -
1153B SER* 3.7 13.6 - - - +
1155B ASP* 3.8 21.4 + - - +
1156B VAL* 4.3 11.2 - - + -
1301B ERG 4.1 15.0 - - + -
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Residues in contact with LYS1129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1115B TYR 3.5 7.2 - - - +
1116B THR* 4.2 14.4 - - + +
1128B THR* 1.3 87.2 + - - +
1130B CYS* 1.3 60.0 - - - +
1131B ILE* 5.4 7.2 - - + -
1152B ARG 3.5 0.6 - - - +
1153B SER* 3.4 16.3 - - - -
1154B PRO* 3.7 18.0 - - + +
1155B ASP* 2.7 44.7 + - - +
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Residues in contact with CYS1130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1113B ILE 3.9 0.5 - - - +
1114B THR* 3.3 7.6 - - - -
1115B TYR* 2.7 60.2 + - + +
1117B LYS* 4.2 6.7 - - - -
1128B THR* 4.1 11.2 - - - -
1129B LYS* 1.3 79.1 - - - +
1131B ILE* 1.3 64.9 + - - +
1132B VAL* 3.9 2.2 - - + +
1151B VAL* 4.2 9.2 - - + -
1152B ARG 3.2 5.4 - - - +
1153B SER* 4.0 9.4 - - - -
1301B ERG 3.6 29.2 - - - -
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Residues in contact with ILE1131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1112B GLU* 3.3 31.4 - - - +
1113B ILE 3.9 1.6 - - - -
1114B THR* 4.4 10.3 - - + -
1129B LYS* 5.4 7.0 - - + -
1130B CYS* 1.3 77.2 - - - +
1132B VAL* 1.3 61.3 + - - +
1133B THR* 3.9 3.7 + - - +
1150B ILE 3.5 4.9 - - - +
1152B ARG* 2.9 44.3 + - + +
1154B PRO* 4.9 19.3 - - + -
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Residues in contact with VAL1132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1111B ARG 3.9 0.5 - - - +
1112B GLU* 3.6 7.8 - - - +
1113B ILE* 2.8 55.5 + - + +
1115B TYR* 3.9 28.3 - - + +
1130B CYS* 4.3 2.9 - - + -
1131B ILE* 1.3 75.3 - - - +
1133B THR* 1.3 63.8 + - - +
1134B GLU* 4.5 4.3 - - + +
1149B GLN* 3.5 39.0 - - + +
1150B ILE 3.6 3.1 - - - +
1151B VAL* 3.8 27.8 - - + -
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Residues in contact with THR1133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1110B ALA* 5.5 4.3 - - + -
1111B ARG 3.9 5.4 - - - +
1112B GLU* 3.9 13.4 + - + +
1131B ILE* 3.9 4.0 + - - +
1132B VAL* 1.3 72.2 - - - +
1134B GLU* 1.3 60.8 + - - +
1135B THR* 4.5 17.1 + - + -
1148B LYS 3.5 1.7 - - - +
1149B GLN* 3.3 2.8 - - - -
1150B ILE* 2.9 54.9 + - + +
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Residues in contact with GLU1134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1081B TYR* 3.4 18.5 + - - -
1088B ILE* 5.5 4.2 - - - +
1106B PHE* 3.5 8.3 - - + -
1110B ALA* 3.2 3.6 - - - +
1111B ARG* 2.8 83.0 + - + +
1113B ILE* 3.9 12.3 - - + +
1132B VAL* 3.9 1.5 - - + -
1133B THR* 1.3 72.7 - - - +
1135B THR* 1.3 59.8 + - - +
1147B VAL* 3.7 18.6 - - + +
1148B LYS 3.2 7.2 - - - +
1149B GLN* 3.3 37.8 + - + -
1168B PHE* 5.6 0.5 - - - -
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Residues in contact with THR1135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1106B PHE* 4.2 2.2 - - - -
1109B ASN 3.0 6.7 - - - +
1110B ALA* 3.7 20.6 - - + -
1133B THR* 4.1 14.0 + - + -
1134B GLU* 1.3 79.0 - - - +
1136B ILE* 1.3 65.5 + - - +
1137B GLU* 2.7 28.3 + - - +
1147B VAL* 3.5 4.3 - - - +
1148B LYS* 2.9 39.8 + - - +
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Residues in contact with ILE1136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1077B PHE* 3.7 31.4 - - + -
1106B PHE* 3.8 40.6 - - + -
1109B ASN* 2.8 42.7 + - - +
1135B THR* 1.3 70.7 - - - +
1137B GLU* 1.3 64.1 + - - +
1138B HIS 3.8 16.8 - - - +
1139B MET* 3.8 21.1 - - + -
1145B PHE* 5.4 0.4 - - + -
1146B MET 3.8 13.2 - - - +
1147B VAL* 4.7 9.0 - - + +
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Residues in contact with GLU1137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1135B THR* 2.7 25.8 + - - +
1136B ILE* 1.3 75.2 - - - +
1138B HIS* 1.3 80.1 + - + +
1139B MET 4.3 0.4 + - - -
1146B MET* 3.3 36.8 + - + -
1148B LYS* 3.9 27.5 - - + +
1167B ARG* 5.1 2.0 - - - +
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Residues in contact with HIS1138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1136B ILE* 3.8 4.3 - - - +
1137B GLU* 1.3 105.1 + - + +
1139B MET* 1.3 60.6 + - - +
1140B ASP 3.9 1.1 - - - -
1144B PHE* 3.5 42.1 - + + -
1145B PHE* 3.1 9.0 - - - +
1146B MET* 3.0 47.3 + - + +
1169B PHE* 5.2 3.6 - + - -
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Residues in contact with MET1139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1077B PHE* 3.7 35.0 - - + -
1109B ASN* 4.9 8.3 - - - +
1136B ILE* 3.8 24.0 - - + -
1137B GLU 4.3 0.2 - - - -
1138B HIS* 1.3 70.7 - - - +
1140B ASP* 1.3 59.6 + - - +
1141B LEU* 3.6 39.0 + - + -
1145B PHE* 4.5 7.0 - - - -
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Residues in contact with ASP1140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1138B HIS 4.0 0.2 + - - -
1139B MET* 1.3 74.8 - - - +
1141B LEU* 1.3 52.3 + - - +
1142B ASN* 2.6 40.2 + - - +
1143B SER* 2.4 42.8 + - - -
1144B PHE* 2.8 48.2 + - + +
1145B PHE* 4.5 0.2 - - - +
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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
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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