Contacts of the strand formed by residues 1553 - 1558 (chain A) in PDB entry 2LVM
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 PHE1553 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1500A TYR* 5.5 0.9 - - - -
1545A THR* 4.2 8.7 - - + -
1546A ALA 3.6 4.5 - - - -
1547A LEU* 3.7 18.2 - - + -
1552A TYR* 1.3 73.5 - - - +
1554A SER* 1.3 76.6 + - - +
1555A ALA* 6.1 1.6 - - + -
15B ALA* 3.9 28.8 - - + +
16B LYS* 3.1 29.8 - - - +
17B ARG* 3.9 3.4 - - - -
18B HIS* 2.9 50.9 - + + +
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Residues in contact with SER1554 (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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1545A THR* 3.3 9.1 - - - +
1546A ALA* 2.8 36.6 + - - +
1552A TYR* 5.4 1.0 - - - +
1553A PHE* 1.3 86.2 + - - +
1555A ALA* 1.3 61.6 + - - +
1574A LYS* 3.0 39.6 + - - -
1581A TYR* 5.7 4.2 + - - -
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Residues in contact with ALA1555 (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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1543A GLU* 5.2 9.6 - - + -
1544A VAL 3.3 14.4 - - - +
1545A THR* 4.0 12.3 - - - +
1546A ALA* 4.6 1.6 - - - +
1553A PHE* 6.1 1.6 - - + -
1554A SER* 1.3 73.9 - - - +
1556A GLY* 1.3 57.6 + - - +
1572A ILE* 5.3 0.7 - - - -
1574A LYS* 3.4 21.3 - - - +
1589A SER* 5.5 0.9 - - - +
1592A GLN* 6.3 0.4 - - - +
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Residues in contact with GLY1556 (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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1543A GLU* 3.4 9.2 - - - +
1544A VAL 2.9 29.4 + - - -
1555A ALA* 1.3 74.4 - - - +
1557A VAL* 1.3 62.8 + - - +
1572A ILE* 3.8 11.9 - - - +
1573A GLU 3.5 13.0 - - - -
1574A LYS* 4.3 5.6 - - - -
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Residues in contact with VAL1557 (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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1541A ASP* 3.5 27.1 - - - +
1542A THR 3.4 2.2 - - - +
1543A GLU* 3.6 27.8 - - + +
1544A VAL* 4.6 0.2 - - - -
1556A GLY* 1.3 78.3 - - - +
1558A VAL* 1.3 75.9 - - - +
1559A LYS* 3.4 19.5 + - + -
1572A ILE* 3.3 5.5 - - - +
1573A GLU* 2.8 42.8 + - + +
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Residues in contact with VAL1558 (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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1538A ILE* 3.7 35.0 - - + +
1539A PRO 3.9 8.3 - - - +
1540A LEU* 3.7 20.4 - - + -
1541A ASP 2.8 26.7 + - - -
1542A THR 3.0 8.3 + - - +
1544A VAL* 3.8 9.6 - - + -
1557A VAL* 1.3 77.1 - - - +
1559A LYS* 1.3 62.5 + - - +
1560A GLY 3.7 18.6 - - - +
1561A HIS* 4.7 0.4 - - + -
1570A TYR* 3.8 17.7 - - + -
1571A SER 3.7 4.7 - - - -
1572A ILE* 3.6 19.1 - - + -
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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