Contacts of the strand formed by residues 1512 - 1517 (chain A) in PDB entry 5CZV
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 VAL1512 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1511A GLY* 1.3 71.1 - - - -
1513A LEU* 1.3 58.1 + - - +
1514A VAL* 3.7 19.5 + - + -
1546A ARG* 3.6 41.5 - - + +
1583A MET* 3.9 10.3 - - + -
1584A LEU 3.2 32.5 - - - +
1585A GLU* 4.5 3.8 - - + -
1604A ALA* 3.2 7.8 - - - +
1631A GLY* 3.4 1.4 - - - -
1632A GLU* 2.7 48.9 + - + +
1633A PRO 5.1 5.8 - - - +
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Residues in contact with LEU1513 (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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1511A GLY 4.5 0.2 + - - -
1512A VAL* 1.3 70.5 - - - +
1514A VAL* 1.3 59.0 + - - +
1515A LEU* 3.6 31.6 - - + +
1535A LEU* 5.4 1.8 - - + -
1539A LEU* 4.3 14.4 - - + -
1543A LEU* 3.6 26.7 - - + -
1582A VAL 3.4 3.1 - - - +
1583A MET* 3.5 1.2 - - - -
1584A LEU* 2.7 47.5 + - + +
1586A ILE* 4.6 6.5 - - + +
1604A ALA* 3.5 30.1 - - + +
1607A ALA* 4.4 5.2 - - + -
1608A ALA* 3.9 24.5 - - + +
1611A LEU* 4.5 6.5 - - + -
1630A ARG 3.7 6.1 - - - +
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Residues in contact with VAL1514 (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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1512A VAL* 3.8 26.7 - - + +
1513A LEU* 1.3 75.0 - - - +
1515A LEU* 1.4 64.4 + - - +
1516A THR* 5.3 0.2 - - + -
1581A VAL* 3.6 24.2 - - + -
1582A VAL 3.3 5.2 - - - +
1583A MET* 4.6 15.9 - - + -
1628A ASP* 3.9 1.6 - - - +
1629A VAL* 3.3 6.6 - - - -
1630A ARG* 2.8 71.3 + - + +
1632A GLU* 4.1 17.9 - - + -
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Residues in contact with LEU1515 (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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1513A LEU* 3.6 28.7 - - + +
1514A VAL* 1.4 78.6 - - - +
1516A THR* 1.3 62.8 + - - +
1517A VAL* 3.8 8.1 + - + -
1531A PHE* 5.0 2.2 - - + -
1535A LEU* 4.8 8.5 - - + -
1580A SER 3.5 2.1 - - - +
1581A VAL* 3.6 0.9 - - - -
1582A VAL* 2.8 56.7 + - + +
1584A LEU* 3.4 37.0 - - + -
1611A LEU* 4.7 3.6 - - + -
1626A LEU* 3.7 17.5 - - + -
1628A ASP 3.5 2.7 - - - -
1629A VAL* 3.0 32.5 - - + -
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Residues in contact with THR1516 (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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1515A LEU* 1.3 74.3 - - - +
1517A VAL* 1.3 55.2 + - - +
1518A LEU* 5.6 0.4 - - - -
1558A TYR* 4.5 29.6 - - + -
1580A SER 3.2 10.1 - - - +
1581A VAL* 4.5 10.5 - - + -
1626A LEU* 3.7 4.5 - - - +
1627A ARG* 2.8 33.9 + - - +
1628A ASP* 2.6 54.1 + - - +
1630A ARG* 4.5 12.6 - - - +
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Residues in contact with VAL1517 (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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1515A LEU* 4.4 8.7 - - + +
1516A THR* 1.3 77.2 - - - +
1518A LEU* 1.3 56.5 + - - +
1519A LEU* 2.8 15.6 + - + +
1524A LEU* 3.9 25.1 - - + -
1531A PHE* 3.9 27.8 - - + -
1558A TYR* 6.0 0.2 - - - -
1579A GLY* 4.2 0.2 - - - -
1580A SER* 2.7 36.4 + - - +
1582A VAL* 4.4 6.3 - - + -
1624A TYR* 4.2 6.7 - - + -
1625A PRO* 3.4 31.9 - - + +
1626A LEU* 4.1 14.8 - - + -
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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