Contacts of the strand formed by residues 1297 - 1301 (chain A) in PDB entry 5EIX
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 LEU1297 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1252A VAL 3.4 4.3 - - - +
1253A VAL* 4.3 0.4 - - - -
1254A ILE* 2.9 58.1 + - + +
1257A LEU* 4.3 23.6 - - + -
1263A GLY* 4.3 11.7 - - - +
1266A VAL* 4.0 23.8 - - + -
1267A LEU* 3.7 29.8 - - + -
1286A ARG 3.8 1.8 - - - -
1287A ASP* 3.4 26.5 - - - +
1289A SER* 5.3 1.1 - - - -
1295A THR* 5.3 2.2 - - - -
1296A ARG* 1.3 79.3 - - - +
1298A VAL* 1.3 61.8 + - - +
1299A ILE* 3.8 3.1 + - + +
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Residues in contact with VAL1298 (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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1251A ALA* 4.3 7.4 - - + -
1252A VAL 3.3 7.6 - - - +
1253A VAL* 4.0 20.6 - - + -
1284A ASP 4.0 0.3 - - - +
1285A LEU* 3.6 5.4 - - - +
1286A ARG* 2.9 69.9 + - + +
1288A GLU* 3.3 39.5 - - + +
1296A ARG* 4.5 6.3 - - + +
1297A LEU* 1.3 73.1 - - - +
1299A ILE* 1.3 65.8 + - - +
1300A VAL* 3.9 11.8 - - + +
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Residues in contact with ILE1299 (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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1251A ALA* 4.3 0.2 - - - -
1252A VAL* 2.6 45.1 + - + +
1254A ILE* 4.4 19.1 - - + -
1270A ILE* 5.8 5.2 - - + -
1282A VAL* 4.4 18.6 - - + -
1284A ASP 3.8 4.3 - - - +
1285A LEU* 5.2 10.3 - - + -
1297A LEU* 4.5 6.7 - - + +
1298A VAL* 1.3 76.9 - - - +
1300A VAL* 1.3 61.3 + - - +
1301A PRO* 3.6 5.5 - - - +
1308A MET* 4.1 21.6 - - + +
1311A VAL* 5.5 1.3 - - + -
1312A MET* 4.5 11.2 - - + -
1315A LEU* 3.7 29.8 - - + -
1321A LEU* 5.5 0.2 - - + -
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Residues in contact with VAL1300 (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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1251A ALA* 4.0 9.9 - - + -
1282A VAL* 3.6 2.5 - - - -
1283A ASP* 2.6 39.5 + - + +
1284A ASP* 2.9 35.8 + - + +
1286A ARG* 3.5 33.7 - - - +
1298A VAL* 3.9 10.3 - - + -
1299A ILE* 1.3 74.8 - - - +
1301A PRO* 1.3 69.2 - - + +
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Residues in contact with PRO1301 (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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1250A GLY 3.3 28.0 - - - +
1251A ALA* 3.9 3.1 - - + -
1281A MET 3.6 7.4 - - - +
1282A VAL* 4.2 2.5 - - - -
1283A ASP* 3.6 4.9 - - - +
1299A ILE 3.6 7.6 - - - +
1300A VAL* 1.3 96.9 - - + +
1302A ARG* 1.3 61.7 + - - +
1303A SER 3.4 11.4 + - - +
1304A ASN* 5.5 3.1 - - - -
1306A VAL* 3.6 22.0 - - + -
1308A MET* 3.5 25.6 - - + -
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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