Contacts of the strand formed by residues 1194 - 1200 (chain B) in PDB entry 5M64
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 ILE1194 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A PHE* 5.1 5.6 - - + -
17A GLY 4.0 3.8 - - - +
18A ILE* 4.7 0.4 - - + -
19A LEU* 4.3 0.9 - - - -
89A LEU* 4.6 5.2 - - + -
90A PHE* 3.6 30.5 - - + -
1622A LEU* 5.2 9.2 - - + +
1623A THR* 6.5 0.4 - - - -
1626A VAL* 3.6 42.0 - - + -
1189B LEU* 2.8 46.4 + - + +
1190B SER* 3.2 12.4 - - - -
1192B MET* 3.6 28.9 - - + +
1193B GLY* 1.3 80.0 - - - +
1195B ARG* 1.3 70.3 + - - +
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Residues in contact with ARG1195 (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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16A PHE* 3.5 8.5 + - - +
17A GLY* 2.9 46.9 + - - +
18A ILE 3.8 13.2 - - - +
19A LEU* 4.0 15.9 - - + -
23A GLU* 4.0 18.8 - - - -
1107B CYS 2.6 30.7 + - - -
1109B SER* 4.5 2.0 + - - -
1130B ARG* 3.1 34.6 - - - +
1190B SER* 5.3 3.4 - - - +
1193B GLY 3.8 1.6 + - - -
1194B ILE* 1.3 79.7 - - - +
1196B LEU* 1.3 69.9 + - - +
1197B ARG* 3.0 51.0 - - - +
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Residues in contact with LEU1196 (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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14A VAL* 3.6 24.9 - - + -
15A ASP 4.4 0.4 - - - -
16A PHE* 3.6 22.7 - - + -
1610A PHE* 5.7 1.8 - - + -
1108B GLY 3.3 12.7 - - - +
1109B SER* 4.4 4.2 + - - -
1110B ILE* 4.9 2.9 - - + -
1186B ASP* 4.6 16.8 - - + +
1189B LEU* 3.6 30.7 - - + +
1190B SER* 5.9 1.2 - - - -
1195B ARG* 1.3 88.0 + - - +
1197B ARG* 1.3 78.0 + - - +
1198B TYR* 3.5 44.9 - - + +
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Residues in contact with ARG1197 (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 ASP* 2.8 54.5 + - + +
16A PHE 5.1 1.3 - - - +
348A LYS* 5.4 10.9 - - - +
1105B ARG 5.7 2.7 - - - +
1106B GLU 4.5 9.3 + - - -
1107B CYS 3.8 3.6 + - - -
1108B GLY* 3.3 15.5 - - - +
1130B ARG* 3.6 17.6 - - - +
1195B ARG* 3.0 46.9 - - - +
1196B LEU* 1.3 78.7 - - - +
1198B TYR* 1.3 72.0 - - - +
1199B ASN* 5.5 0.5 + - - -
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Residues in contact with TYR1198 (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 ILE* 4.4 28.3 - - + -
13A SER 4.1 4.5 - - - +
14A VAL* 3.5 35.4 - - + -
1610A PHE* 5.2 8.4 - + - -
1642A VAL* 5.8 1.0 - - - +
1643A VAL* 3.7 18.1 - - + +
1103B VAL* 5.3 8.3 - - + -
1105B ARG 5.1 2.6 - - - +
1108B GLY* 3.5 18.3 + - - +
1110B ILE* 3.6 25.6 - - + -
1178B ILE* 5.8 3.6 - - + -
1182B LEU* 3.3 46.6 - - + +
1185B LEU* 5.5 4.3 - - - +
1186B ASP* 5.7 0.5 - - - +
1196B LEU* 3.5 19.4 - - + +
1197B ARG* 1.3 89.9 - - - +
1199B ASN* 1.3 66.3 + - - +
1200B VAL* 5.8 0.2 - - - -
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Residues in contact with ASN1199 (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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10A GLU 4.0 1.4 - - - +
11A ILE* 3.8 13.9 - - - +
12A THR 4.4 0.2 + - - -
13A SER* 2.5 47.4 + - - +
14A VAL* 5.0 0.8 - - - +
15A ASP 5.4 0.2 - - - +
1631A ARG* 3.5 25.3 - - - +
1103B VAL* 6.3 0.2 - - - -
1105B ARG* 5.8 3.1 - - - +
1197B ARG 5.5 0.2 + - - -
1198B TYR* 1.3 77.7 - - - +
1200B VAL* 1.3 70.0 + - - +
1201B GLU* 3.9 14.1 - - - +
1203B LYS 5.3 3.4 - - - +
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Residues in contact with VAL1200 (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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9A SER* 4.5 9.4 - - - +
10A GLU 3.8 4.9 - - - +
11A ILE* 3.7 20.6 - - + -
1103B VAL* 4.1 22.4 - - + -
1104B CYS 5.5 0.4 - - - +
1105B ARG* 3.8 47.3 - - + +
1174B THR* 4.9 2.5 - - + -
1176B VAL* 4.3 13.5 - - + -
1199B ASN* 1.3 77.4 - - - +
1201B GLU* 1.3 70.4 + - - +
1202B PRO 4.5 3.6 - - - +
1203B LYS 2.9 28.8 - - - +
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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