Contacts of the strand formed by residues 1110 - 1118 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1105A LYS 4.3 0.5 - - - +
1106A PHE* 3.7 4.6 - - - -
1107A VAL* 3.1 35.0 + - - +
1108A ASN* 3.9 5.6 - - + +
1109A ASN* 1.3 81.5 - - - +
1111A ARG* 1.3 62.5 + - - +
1133A THR* 5.8 3.1 - - + -
1134A GLU 3.4 6.5 - - - -
1135A THR* 3.6 15.9 - - + -
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Residues in contact with ARG1111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1080A LEU 3.1 26.5 + - - -
1081A TYR* 3.8 1.4 - - - +
1082A GLY 4.6 5.9 + - - -
1085A THR* 4.2 9.3 - - - +
1088A ILE* 4.0 17.2 - - - +
1103A ILE* 4.0 13.0 - - - +
1104A PRO* 2.9 32.5 + - + +
1105A LYS* 3.9 13.5 - - - +
1106A PHE* 3.1 36.3 - - + -
1110A ALA* 1.3 78.1 - - - +
1112A GLU* 1.3 60.9 + - - +
1113A ILE* 4.1 13.2 - - + +
1132A VAL 3.9 0.2 - - - +
1133A THR* 3.9 5.2 - - - +
1134A GLU* 2.4 67.9 + - + +
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Residues in contact with GLU1112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1101A CYS* 4.4 2.6 - - - -
1104A PRO* 3.1 29.0 - - + +
1111A ARG* 1.3 74.1 - - - +
1113A ILE* 1.3 67.8 + - - +
1114A THR* 4.6 7.9 - - + +
1131A ILE* 4.0 24.3 - - + +
1132A VAL 3.4 11.4 - - - +
1133A THR* 4.9 8.8 + - + +
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Residues in contact with ILE1113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088A ILE* 5.3 0.2 - - + -
1092A ILE* 3.7 22.4 - - + -
1101A CYS* 3.8 4.3 - - - -
1103A ILE* 3.7 41.1 - - + -
1104A PRO* 4.3 3.4 - - + -
1111A ARG* 4.1 11.7 - - + +
1112A GLU* 1.3 80.4 - - - +
1114A THR* 1.3 67.8 + - - +
1115A TYR* 3.8 26.5 - - + -
1130A CYS 3.7 0.9 - - - +
1132A VAL* 2.8 48.7 + - + +
1134A GLU* 4.0 22.9 - - + +
1149A GLN* 6.3 0.4 - - - +
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Residues in contact with THR1114 (chain A).
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 4.3 1.7 + - - -
1100A VAL* 3.5 0.7 - - - +
1101A CYS* 2.9 49.5 + - - +
1112A GLU* 4.6 10.8 - - + +
1113A ILE* 1.3 80.5 - - - +
1115A TYR* 1.3 67.3 + - - +
1130A CYS 3.3 10.1 - - - +
1131A ILE* 4.1 25.6 - - + -
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Residues in contact with TYR1115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092A ILE* 3.8 20.0 - - + -
1097A ASN* 3.7 36.1 + - + -
1098A PHE 3.6 9.0 - - - +
1099A ASN 3.5 10.3 - - - -
1100A VAL* 3.8 15.7 - - + -
1113A ILE* 3.8 22.7 - - + -
1114A THR* 1.3 81.3 - - - +
1116A THR* 1.3 63.2 + - - +
1117A LYS* 4.2 5.5 + - - -
1129A LYS* 3.5 3.4 - - - +
1130A CYS* 2.7 56.5 + - + +
1132A VAL* 3.7 22.5 - - + +
1149A GLN* 6.2 0.2 - - - -
1301A ERG 4.0 23.4 + - - +
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Residues in contact with THR1116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1097A ASN* 3.2 4.7 - - - +
1098A PHE* 2.9 61.6 + - + -
1099A ASN* 4.1 11.6 + - - +
1115A TYR* 1.3 76.4 + - - +
1117A LYS* 1.3 60.6 + - - +
1127A GLN* 3.7 28.9 - - - +
1128A THR 3.4 22.7 - - - +
1129A LYS* 4.0 14.9 - - + +
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Residues in contact with LYS1117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1095A GLN* 3.3 17.1 + - - +
1096A ASN* 4.4 2.0 - - + +
1097A ASN* 2.9 33.2 + - - +
1115A TYR* 4.2 8.1 + - + -
1116A THR* 1.3 72.8 - - - +
1118A LYS* 1.3 72.8 + - - +
1119A LEU* 3.7 11.0 + - + +
1127A GLN* 3.2 6.5 - - - +
1128A THR* 2.8 40.8 + - + +
1130A CYS* 4.1 9.4 - - - -
1209A SER* 5.7 0.2 - - - -
1301A ERG 3.4 72.9 - - + +
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Residues in contact with LYS1118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1096A ASN* 3.0 42.7 + - - +
1098A PHE* 3.8 21.5 - - + -
1116A THR 4.0 0.8 + - - -
1117A LYS* 1.3 80.6 - - - +
1119A LEU* 1.3 61.2 + - - +
1120A ASN 4.3 0.2 + - - -
1126A LYS* 4.0 11.9 - - - +
1127A GLN* 4.3 7.0 - - + -
1102B ASP* 3.1 31.1 + - - +
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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