Contacts of the strand formed by residues 75 - 79 (chain U) in PDB entry 3SDI
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 GLY 75 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68U PHE 3.3 9.0 - - - -
70U ILE* 4.5 0.2 - - - -
74U ILE* 1.3 77.9 - - - +
76U MET* 1.3 63.2 + - - +
138U PHE* 3.5 2.3 - - - -
139U VAL* 2.9 39.2 + - - +
221U PHE* 3.6 30.5 - - - -
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Residues in contact with MET 76 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48U VAL* 5.9 1.8 - - - -
67U ILE* 3.4 4.5 - - - +
68U PHE* 2.7 44.6 + - + +
70U ILE* 3.8 15.0 - - + -
75U GLY* 1.3 76.5 - - - +
77U VAL* 1.3 68.2 + - - +
78U VAL* 3.7 20.0 - - + -
85U ALA 4.0 0.7 - - - +
88U ALA 3.8 6.5 - - - +
89U ALA* 3.4 44.4 - - + +
92U ALA* 5.0 0.2 - - - -
136U LEU* 4.1 14.6 - - + -
137U THR 3.1 10.3 - - - +
138U PHE* 3.3 39.5 - - + -
139U VAL* 5.3 0.4 - - - -
221U PHE* 4.6 1.8 - - - -
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Residues in contact with VAL 77 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37U SER* 4.1 28.7 - - - +
38U LEU 6.4 0.4 - - - -
48U VAL* 4.5 21.9 - - + +
50U SER* 4.3 11.2 - - - +
66U TYR* 3.4 11.9 - - + +
67U ILE* 4.2 17.3 - - + +
76U MET* 1.3 74.5 - - - +
78U VAL* 1.3 73.9 + - - +
79U ASN* 5.3 1.0 - - - +
135U ILE 3.7 0.5 - - - +
136U LEU* 3.6 3.5 - - - -
137U THR* 2.9 59.1 + - + +
139U VAL* 6.1 0.2 - - - +
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Residues in contact with VAL 78 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35U ILE* 5.8 2.4 - - - +
50U SER* 5.7 0.2 + - - -
66U TYR* 3.0 31.4 + - + +
68U PHE* 3.8 10.8 - - + -
76U MET* 3.7 20.0 - - + -
77U VAL* 1.3 83.0 - - - +
79U ASN* 1.3 71.7 + - - +
80U GLY 3.9 1.8 - - - +
85U ALA* 3.5 33.7 - - + +
134U VAL* 3.6 30.1 - - + -
135U ILE 3.4 4.9 - - - +
136U LEU* 3.7 18.2 - - + -
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Residues in contact with ASN 79 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31U THR* 3.4 22.1 + - - +
34U THR* 5.2 2.6 + - - -
35U ILE* 3.3 36.3 + - - +
37U SER* 2.7 27.5 + - - +
77U VAL* 4.2 1.1 + - - +
78U VAL* 1.3 76.6 + - - +
80U GLY* 1.3 56.4 + - - +
135U ILE* 3.0 34.5 + - + +
137U THR* 5.0 3.5 + - - -
165U THR* 3.0 40.9 + - + +
166U GLY* 4.2 2.5 - - - +
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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