Contacts of the strand formed by residues 1110 - 1118 (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 ALA1110 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1106B PHE* 3.5 2.9 - - - -
1107B VAL* 3.0 34.6 + - - +
1108B ASN* 3.1 6.3 - - + +
1109B ASN* 1.3 79.7 - - - +
1111B ARG* 1.3 60.0 - - - +
1133B THR* 5.5 4.5 - - + -
1134B GLU 3.2 6.1 - - - -
1135B THR* 3.7 18.2 - - + -
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Residues in contact with ARG1111 (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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1080B LEU 2.9 27.7 + - - -
1081B TYR* 3.8 7.3 - - - +
1082B GLY 4.3 6.7 + - - -
1085B THR* 3.7 19.4 - - - +
1088B ILE* 4.0 13.1 - - - +
1103B ILE* 4.1 8.8 - - - +
1104B PRO* 3.1 30.6 + - + +
1105B LYS* 3.7 17.1 - - - +
1106B PHE* 3.6 31.9 - - + +
1110B ALA* 1.3 76.4 - - - +
1112B GLU* 1.3 61.1 - - - +
1113B ILE* 3.8 15.2 + - + +
1132B VAL 3.9 1.0 - - - +
1133B THR* 3.9 3.4 - - - +
1134B GLU* 2.8 61.0 + - + +
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Residues in contact with GLU1112 (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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1101B CYS* 4.0 4.3 - - - -
1104B PRO* 3.0 28.2 - - + +
1111B ARG* 1.3 75.6 - - - +
1113B ILE* 1.3 61.2 + - - +
1114B THR* 4.0 14.4 - - + +
1131B ILE* 3.3 29.6 - - - +
1132B VAL 3.6 5.2 - - - +
1133B THR* 3.9 17.2 + - - +
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Residues in contact with ILE1113 (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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1088B ILE* 5.8 1.1 - - + -
1092B ILE* 3.7 31.9 - - + -
1100B VAL* 4.9 0.2 - - + -
1101B CYS* 3.9 2.9 - - - -
1103B ILE* 4.1 17.0 - - + -
1104B PRO* 4.1 13.7 - - + -
1111B ARG* 3.8 32.5 - - + +
1112B GLU* 1.3 78.1 - - - +
1114B THR* 1.3 66.3 + - - +
1115B TYR* 3.8 19.1 - - + -
1130B CYS 3.9 0.3 - - - +
1132B VAL* 2.8 48.0 + - + +
1134B GLU* 3.9 19.1 - - + +
1149B GLN* 5.9 1.1 - - - +
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Residues in contact with THR1114 (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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1099A ASN* 5.2 0.7 + - - -
1099B ASN 3.6 3.0 + - - +
1100B VAL* 3.5 1.2 - - - +
1101B CYS* 3.1 40.8 + - - +
1112B GLU* 4.0 24.2 - - + +
1113B ILE* 1.3 80.3 - - - +
1115B TYR* 1.3 68.3 + - - +
1130B CYS 3.3 11.2 - - - +
1131B ILE* 4.4 11.9 - - + -
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Residues in contact with TYR1115 (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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1092B ILE* 3.7 22.8 - - + +
1095B GLN* 5.4 2.4 + - - -
1097B ASN* 3.3 40.7 + - + -
1098B PHE 3.6 9.4 - - - +
1099B ASN 3.7 9.0 - - - -
1100B VAL* 3.9 14.6 - - + -
1113B ILE* 3.8 18.6 - - + -
1114B THR* 1.3 81.5 - - - +
1116B THR* 1.3 62.9 + - - +
1117B LYS* 4.3 3.5 - - - -
1129B LYS* 3.5 3.1 - - - +
1130B CYS* 2.7 57.4 + - + +
1132B VAL* 3.9 21.2 - - + +
1149B GLN* 5.6 0.7 + - - -
1301B ERG 4.5 21.7 + - - +
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Residues in contact with THR1116 (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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1097B ASN* 3.3 3.8 - - - -
1098B PHE* 3.0 68.6 + - + -
1099B ASN* 4.1 11.1 - - - +
1115B TYR* 1.3 76.9 - - - +
1117B LYS* 1.3 61.5 + - - +
1127B GLN* 3.9 23.3 - - + +
1128B THR 3.3 17.5 - - - +
1129B LYS* 4.4 13.0 - - + +
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Residues in contact with LYS1117 (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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1095B GLN* 2.9 32.7 + - - +
1096B ASN* 3.7 3.0 - - + +
1097B ASN* 3.2 20.4 + - - +
1115B TYR* 4.1 5.3 + - - -
1116B THR* 1.3 73.0 - - - +
1118B LYS* 1.3 75.0 + - - +
1119B LEU* 3.6 12.4 + - + +
1127B GLN* 2.9 7.5 - - - +
1128B THR* 2.6 47.1 + - + +
1130B CYS* 4.2 9.4 - - - -
1209B SER* 4.2 5.7 + - - -
1212B GLN* 5.7 1.0 - - - +
1301B ERG 3.7 56.1 - - + +
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Residues in contact with LYS1118 (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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1085A THR* 5.8 1.2 + - - -
1089A LYS* 6.0 1.4 - - - +
1102A ASP* 2.5 45.9 + - - +
1096B ASN* 2.9 49.1 + - + +
1098B PHE* 3.9 20.6 - - + -
1117B LYS* 1.3 75.4 - - - +
1119B LEU* 1.3 62.4 + - - +
1120B ASN* 4.1 1.2 + - - +
1126B LYS* 3.7 28.5 - - - +
1127B GLN* 4.2 4.5 - - + +
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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