Contacts of the strand formed by residues 1298 - 1302 (chain A) in PDB entry 4Z4Q
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 ILE1298 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1254A ILE 3.6 1.9 - - - +
1255A VAL* 3.3 4.9 - - - +
1256A ILE* 2.9 59.1 + - + +
1259A ILE* 4.7 2.5 - - + -
1265A LYS* 4.2 13.5 - - + -
1268A LEU* 4.4 19.1 - - + -
1269A VAL* 3.7 32.5 - - + -
1272A ILE* 5.0 5.2 - - + -
1287A VAL* 4.5 14.8 - - + -
1288A ARG 3.5 10.3 - - - +
1289A ASP* 4.4 7.9 - - - +
1291A SER* 4.8 0.4 - - - +
1296A LEU* 4.2 11.9 - - + -
1297A ARG* 1.3 80.5 - - - +
1299A ALA* 1.3 62.5 + - - +
1300A ILE* 3.9 3.8 + - + -
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Residues in contact with ALA1299 (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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1253A GLN* 4.7 9.2 - - - +
1254A ILE 3.8 2.9 - - - -
1255A VAL* 4.6 10.8 - - - -
1286A GLU 3.8 1.0 - - - +
1287A VAL* 3.6 3.8 - - - +
1288A ARG* 2.9 48.9 + - - +
1290A GLU* 4.7 5.5 - - - +
1297A ARG* 4.2 1.4 - - - +
1298A ILE* 1.3 71.9 - - - +
1300A ILE* 1.3 63.0 + - - +
1301A GLU 3.8 1.1 + - - -
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Residues in contact with ILE1300 (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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1253A GLN* 3.5 3.9 - - - -
1254A ILE* 2.8 53.2 + - + +
1256A ILE* 4.4 12.3 - - + -
1272A ILE* 4.1 24.0 - - + -
1284A ILE* 3.8 31.2 - - + -
1286A GLU 3.6 3.6 - - - +
1287A VAL* 4.5 5.6 - - + -
1298A ILE* 4.7 11.7 - - + +
1299A ALA* 1.3 73.3 - - - +
1301A GLU* 1.3 63.2 + - - +
1302A LEU* 3.5 14.7 + - + +
1311A VAL* 5.4 0.2 - - + -
1315A LEU* 3.5 28.7 - - + -
1321A LEU* 5.7 0.7 - - + -
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Residues in contact with GLU1301 (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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1247A LEU* 5.4 8.1 - - + -
1251A LYS* 4.5 17.5 - - + +
1252A GLU 4.2 6.5 - - - +
1253A GLN* 4.3 12.1 + - + +
1284A ILE* 3.8 3.6 - - - +
1285A ALA* 2.8 36.9 + - + +
1286A GLU* 3.0 29.9 + - + +
1288A ARG* 2.8 34.5 + - - +
1299A ALA 3.8 2.8 + - - -
1300A ILE* 1.3 71.6 - - - +
1302A LEU* 1.3 62.8 + - - +
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Residues in contact with LEU1302 (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 LYS* 3.9 18.6 - - - +
1252A GLU* 3.1 24.9 + - + +
1254A ILE* 3.9 19.7 - - + -
1283A GLY 3.3 20.9 - - - +
1284A ILE* 4.1 9.2 - - + -
1285A ALA* 3.6 9.9 - - - +
1300A ILE* 4.0 12.1 - - + +
1301A GLU* 1.3 79.5 - - - +
1303A LYS* 1.3 68.4 + - - +
1306A ALA* 4.6 7.2 - - + +
1308A THR* 3.5 39.7 - - + -
1311A VAL* 4.1 24.9 - - + -
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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