Contacts of the strand formed by residues 1583 - 1588 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1574A GLN* 4.0 14.1 - - - +
1576A GLY 3.6 8.7 - - - +
1577A THR* 4.5 3.3 - - - +
1582A ASN* 1.3 89.5 - - + +
1584A ILE* 1.3 60.4 + - - +
1585A PHE* 3.9 10.1 - - + -
1613A TYR* 3.6 35.0 - - + -
1616A LYS* 6.1 4.7 - - + -
1617A PRO 3.7 8.7 - - - +
1618A TYR* 3.9 16.1 - - + +
1619A GLU* 3.0 25.6 + - - +
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Residues in contact with ILE1584 (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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1574A GLN* 3.5 5.2 - - - +
1575A ALA 3.0 35.8 + - - +
1576A GLY 3.2 6.8 + - - +
1577A THR 3.6 8.5 - - - +
1578A SER* 3.5 33.0 - - - +
1582A ASN 3.8 0.9 - - - +
1583A PRO* 1.3 78.5 - - - +
1585A PHE* 1.3 66.6 + - - +
1586A TYR* 3.9 15.0 - - + -
1619A GLU* 3.5 14.4 - - + +
1621A VAL* 3.7 28.9 - - + -
1657A TYR* 5.9 2.2 - - + -
1698A ILE* 3.4 37.7 - - + -
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Residues in contact with PHE1585 (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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1572A PHE* 3.4 30.7 - + + -
1573A TYR 3.5 2.5 - - - +
1574A GLN* 3.6 38.1 - - + -
1583A PRO* 3.9 14.8 - - + -
1584A ILE* 1.3 74.5 - - - +
1586A TYR* 1.3 58.4 + - - +
1609A THR* 3.6 22.4 - - - -
1610A LEU* 3.8 25.1 - - + -
1613A TYR* 3.9 26.9 - + + -
1618A TYR* 3.9 23.1 - + + -
1619A GLU 2.8 21.3 + - - +
1620A ILE* 3.3 7.2 - - + +
1621A VAL* 2.8 32.9 + - - +
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Residues in contact with TYR1586 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1571A ILE 3.4 2.1 - - - +
1572A PHE* 3.2 9.7 - - - -
1573A TYR* 2.8 77.6 + + + +
1575A ALA* 3.4 26.5 + - + -
1584A ILE* 3.9 6.1 - - + -
1585A PHE* 1.3 76.9 - - - +
1587A TYR* 1.3 59.9 + - - +
1588A VAL* 4.0 2.9 - - + -
1621A VAL* 3.4 36.5 - - + +
1623A ASP* 5.9 2.0 - - + -
1694A LEU* 4.3 2.0 - - + +
1698A ILE* 3.5 21.3 - - - +
1702A GLN 5.0 0.2 + - - -
1703A GLN* 3.9 0.3 - - - -
1704A LYS* 2.9 45.3 + - + +
1705A LEU* 3.8 16.2 - - + -
1706A PRO* 5.0 1.3 - - + -
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Residues in contact with TYR1587 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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701A OXN 3.8 41.0 - + + +
1571A ILE* 3.4 28.3 - - + -
1572A PHE* 4.0 18.8 - + + -
1585A PHE 4.0 0.4 + - - -
1586A TYR* 1.3 73.3 - - - +
1588A VAL* 1.3 59.3 + - - +
1589A ALA* 3.5 30.9 + - + -
1592A PHE* 3.4 19.2 - - - +
1602A LEU* 3.9 13.1 - - + +
1606A VAL* 5.4 2.5 - - + -
1620A ILE* 4.7 3.8 - - + +
1621A VAL 2.8 12.7 + - - +
1622A VAL* 3.6 18.2 - - + -
1623A ASP* 2.9 27.7 + - - +
1631A ASN 5.3 0.3 + - - -
1633A PHE* 3.2 34.9 - + - -
1641A TRP* 5.8 0.2 - + - -
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Residues in contact with VAL1588 (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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1570A SER 4.0 5.2 - - - +
1571A ILE* 2.8 22.5 + - - +
1573A TYR* 3.9 20.9 - - + +
1586A TYR* 4.7 2.7 - - + +
1587A TYR* 1.3 76.5 - - - +
1589A ALA* 1.3 58.6 + - - +
1590A ARG* 4.1 20.9 - - + +
1591A ARG* 3.0 55.8 + - - +
1592A PHE 4.0 2.3 + - - -
1623A ASP* 4.1 12.1 - - + +
1706A PRO* 3.5 29.8 - - + -
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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