Contacts of the strand formed by residues 1146 - 1150 (chain B) in PDB entry 5IY8
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 ILE1146 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A CYS* 3.5 12.8 - - - -
14A PRO* 4.5 7.8 - - - +
1117B HIS* 3.9 24.5 - - + -
1118B VAL 3.3 15.7 - - - +
1119B CYS* 4.5 5.4 - - + -
1127B ILE* 3.9 11.2 - - + -
1135B TYR* 3.5 41.5 - - + -
1136B GLU* 3.7 23.3 - - - +
1137B CYS 4.2 2.5 - - - +
1142B ASN* 3.6 14.4 - - - +
1143B LYS 5.5 1.1 - - - -
1144B THR 2.3 28.4 + - - +
1145B GLN* 1.3 74.5 - - - +
1147B SER* 1.3 70.9 + - - +
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Residues in contact with SER1147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A CYS* 3.8 8.1 - - - -
14A PRO* 3.9 4.5 + - - +
16A ARG* 3.8 24.7 + - - +
1117B HIS* 3.1 7.0 - - - +
1118B VAL* 3.0 35.9 + - - +
1120B ASN* 4.2 12.1 + - - +
1146B ILE* 1.3 76.3 + - - +
1148B LEU* 1.3 61.0 + - - +
1149B VAL* 4.1 5.1 + - - -
1173B SER* 3.7 23.1 + - - -
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Residues in contact with LEU1148 (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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11A SER* 3.7 22.2 - - - +
13A CYS* 3.8 10.5 - - - +
14A PRO 3.3 12.6 + - - +
15A LEU* 3.1 23.4 - - + +
16A ARG 3.0 25.8 + - - +
1115B GLN* 3.8 28.0 - - + -
1116B VAL 3.6 10.8 - - - +
1117B HIS* 3.5 31.0 - - + +
1147B SER* 1.3 73.3 - - - +
1149B VAL* 1.3 67.5 + - - +
1150B ARG* 6.0 0.9 - - + -
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Residues in contact with VAL1149 (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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15A LEU* 4.5 0.9 - - - -
16A ARG* 4.1 18.4 - - + +
17A THR* 5.6 0.2 - - - -
18A ILE* 4.5 30.7 - - + +
1460A LEU* 5.6 1.6 - - + -
1114B TYR 3.8 0.3 - - - +
1115B GLN* 3.3 5.4 - - - +
1116B VAL* 2.8 42.2 + - + +
1118B VAL* 4.5 20.4 - - + -
1147B SER* 4.6 9.2 - - - +
1148B LEU* 1.3 81.8 - - - +
1150B ARG* 1.3 76.7 + - - +
1151B MET* 3.9 15.1 + - + +
1171B MET* 5.2 2.7 - - - -
1173B SER* 5.5 2.7 - - - +
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Residues in contact with ARG1150 (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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15A LEU* 4.7 29.9 - - + +
16A ARG 4.9 1.6 + - - -
1460A LEU* 4.0 7.4 - - - +
1461A GLY 4.8 5.5 - - - -
1462A GLN* 4.9 2.1 + - - +
1108B PHE* 3.8 29.2 - - + -
1114B TYR 3.3 11.4 - - - +
1115B GLN* 4.7 10.4 - - + +
1148B LEU* 6.4 0.2 - - + -
1149B VAL* 1.3 81.0 - - - +
1151B MET* 1.3 61.0 + - - +
63G ARG* 4.4 31.3 - - - +
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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