Contacts of the strand formed by residues 92 - 96 (chain A) in PDB entry 3F7F
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 THR 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A PRO* 3.6 22.0 - - + -
22A ASN 3.3 4.0 + - - -
23A THR* 3.4 20.3 + - - +
24A VAL 3.1 23.2 + - - +
80A THR* 4.7 10.1 - - - +
81A PHE 2.8 12.6 - - - -
82A TYR* 3.4 18.2 - - + -
87A ALA 4.1 5.2 - - - +
90A GLY 4.5 0.4 - - - +
91A LYS* 1.3 77.1 - - - +
93A ILE* 1.3 60.1 + - - +
94A ASN* 5.0 1.6 + - - -
479A TYR* 2.8 30.9 + - + +
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Residues in contact with ILE 93 (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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24A VAL* 3.5 26.2 - - + +
26A LEU* 4.0 26.7 - - + -
79A LEU 3.6 0.7 - - - +
80A THR* 3.2 3.6 - - - -
81A PHE* 2.6 49.2 + - + +
91A LYS* 4.2 12.8 - - - +
92A THR* 1.3 77.0 - - - +
94A ASN* 1.3 62.6 + - - +
95A ILE* 3.7 9.3 + - + -
133A LEU* 5.6 1.6 - - + -
137A PHE* 3.6 20.0 - - + -
138A LEU* 3.1 44.9 - - + +
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Residues in contact with ASN 94 (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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23A THR* 3.7 22.5 - - - +
24A VAL 2.8 9.1 + - - -
25A ASP* 3.0 26.8 + - - +
26A LEU 2.9 27.9 + - - +
78A LEU* 3.9 20.6 - - + +
79A LEU 3.5 2.9 - - - -
80A THR* 2.9 35.7 + - - +
92A THR* 5.0 1.9 + - - -
93A ILE* 1.3 71.1 - - - +
95A ILE* 1.3 61.0 + - - +
96A HIS* 3.6 2.2 + - - -
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Residues in contact with ILE 95 (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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26A LEU* 3.5 12.1 - - + +
28A VAL* 4.3 9.6 - - + -
78A LEU* 3.6 3.5 - - - -
79A LEU* 2.6 41.0 + - + +
81A PHE* 3.5 18.8 - - + -
93A ILE* 4.5 11.9 - - + -
94A ASN* 1.3 72.6 - - - +
96A HIS* 1.3 70.1 + - - +
97A LEU* 3.9 9.0 + - + +
131A LEU* 3.6 30.5 - - + -
133A LEU* 3.3 41.1 - - + -
149A TRP* 4.3 7.0 - - + -
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Residues in contact with HIS 96 (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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25A ASP* 3.1 25.6 + - + -
26A LEU 2.8 21.0 + - - +
27A TYR* 3.6 46.3 + + + -
28A VAL* 3.4 28.4 + - - +
77A THR 3.9 1.1 + - - -
78A LEU* 3.5 26.3 - - + +
94A ASN* 3.8 9.0 - - + -
95A ILE* 1.3 75.3 - - - +
97A LEU* 1.3 63.3 + - - +
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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