Contacts of the strand formed by residues 1583 - 1588 (chain B) in PDB entry 2D4Q
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 PRO1583 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1574B GLN* 3.9 12.8 - - - +
1576B GLY 3.6 7.9 - - - +
1577B THR* 4.4 4.3 - - + +
1581B GLY 4.1 4.7 - - - +
1582B ASN* 1.3 83.4 - - - +
1584B ILE* 1.3 60.6 + - - +
1585B PHE* 4.1 3.9 - - + -
1613B TYR* 3.6 36.6 - - + -
1616B LYS* 6.5 0.2 - - + -
1617B PRO 3.7 15.9 - - - +
1618B TYR* 3.5 9.5 - - + +
1619B GLU 2.9 24.8 + - - +
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Residues in contact with ILE1584 (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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1574B GLN* 3.1 8.8 + - - +
1575B ALA 2.9 31.2 + - - +
1576B GLY* 3.1 7.3 + - - -
1577B THR 3.3 12.8 - - - +
1578B SER* 3.2 30.5 - - - +
1582B ASN 3.8 5.6 - - - +
1583B PRO* 1.3 77.0 - - - +
1585B PHE* 1.3 72.3 + - - +
1586B TYR* 3.6 26.5 - - + +
1619B GLU* 3.5 13.7 - - + +
1621B VAL* 3.8 16.6 - - + +
1698B ILE* 3.5 34.3 - - + -
1702B GLN 5.1 0.9 - - - +
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Residues in contact with PHE1585 (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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1572B PHE* 3.7 27.8 - + + -
1573B TYR 3.4 5.2 - - - +
1574B GLN* 3.5 36.3 - - + -
1583B PRO 4.1 5.8 - - - -
1584B ILE* 1.3 81.4 - - - +
1586B TYR* 1.3 57.7 + - - +
1609B THR* 3.7 19.5 - - + -
1610B LEU* 3.5 33.0 - - + -
1613B TYR* 3.3 34.1 - + - -
1618B TYR* 3.9 21.1 - + + -
1619B GLU 2.9 16.0 + - - +
1620B ILE* 3.3 7.7 - - + +
1621B VAL* 2.7 32.2 + - - +
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Residues in contact with TYR1586 (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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1571B ILE 3.4 1.8 - - - +
1572B PHE* 3.2 11.4 - - - -
1573B TYR* 2.8 70.2 + + + +
1575B ALA* 3.5 23.6 - - + -
1584B ILE* 3.6 11.1 - - + +
1585B PHE* 1.3 76.1 - - - +
1587B TYR* 1.3 58.4 + - - +
1588B VAL* 4.0 3.8 - - + -
1621B VAL* 3.4 41.4 - - + +
1623B ASP* 5.6 1.3 - - + -
1694B LEU* 5.0 1.8 - - + +
1698B ILE* 4.4 7.1 - - - +
1702B GLN 4.5 1.4 + - - -
1703B GLN* 3.6 11.3 - - - +
1704B LYS* 2.9 45.5 + - + -
1705B LEU* 3.7 17.9 - - + -
1706B PRO* 5.0 1.3 - - + -
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Residues in contact with TYR1587 (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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702B OXN 3.4 55.0 - + + +
1571B ILE* 3.3 26.2 - - + -
1572B PHE* 4.1 17.5 - + + -
1585B PHE 4.3 0.2 + - - -
1586B TYR* 1.3 73.4 - - - +
1588B VAL* 1.3 56.9 + - - +
1589B ALA* 3.5 29.5 + - + -
1592B PHE* 3.4 18.7 - - - +
1602B LEU* 4.6 12.5 - - + +
1606B VAL* 5.5 1.8 - - + -
1620B ILE* 4.9 1.5 - - + +
1621B VAL 2.9 11.2 + - - +
1622B VAL* 3.7 9.5 - - + -
1623B ASP* 2.8 32.3 + - - +
1633B PHE* 3.1 36.5 - + - -
1641B TRP* 5.8 0.7 - + - -
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Residues in contact with VAL1588 (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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1570B SER 3.5 22.9 - - - +
1571B ILE* 2.7 21.4 + - - +
1573B TYR* 4.1 11.4 - - + +
1586B TYR* 4.9 2.0 - - + -
1587B TYR* 1.3 75.0 - - - +
1589B ALA* 1.3 64.1 + - - +
1590B ARG* 3.6 30.1 - - + +
1591B ARG* 3.1 42.1 + - + +
1623B ASP* 3.9 7.2 - - + +
1706B PRO* 3.5 28.0 - - + -
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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