Contacts of the strand formed by residues 33 - 36 (chain M) 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 LEU 33 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2M VAL* 4.8 0.2 - - + -
13M ILE* 3.8 33.9 - - + +
14M ALA* 4.2 2.2 - - - +
15M ALA* 4.0 20.2 - - + -
31M GLU* 2.8 30.5 + - - +
32M ARG* 1.3 87.5 - - - +
34M ILE* 1.3 63.5 - - - +
35M PRO* 3.4 9.6 - - - +
41M VAL* 3.9 8.3 - - + -
42M VAL 3.7 0.7 - - - -
43M GLY* 4.0 14.4 - - - -
187M SER* 3.7 35.0 - - - +
188M LEU 3.8 3.8 - - - +
189M ALA* 3.8 13.9 - - + +
199M PHE* 3.7 12.0 - - + -
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Residues in contact with ILE 34 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31M GLU 5.2 3.4 - - - +
32M ARG 4.6 5.2 - - - +
33M LEU* 1.3 77.8 - - - +
35M PRO* 1.3 71.5 - - + +
36M VAL* 3.6 5.7 + - + +
41M VAL* 3.3 3.1 - - - +
42M VAL* 2.7 43.5 + - + +
44M ILE* 3.4 38.4 - - + -
51M MET* 4.6 8.3 - - + -
55M GLU* 3.7 39.3 - - + +
58M LEU* 4.0 23.6 - - + -
59M LYS* 6.3 2.9 - - - -
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Residues in contact with PRO 35 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31M GLU* 5.9 0.2 - - + -
33M LEU 3.4 11.9 - - - +
34M ILE* 1.3 90.0 - - + +
36M VAL* 1.3 62.1 + - - +
37M GLY 4.1 4.5 - - - +
40M THR 3.3 9.6 - - - +
41M VAL* 4.2 6.5 - - + -
197M LEU* 4.2 21.3 - - + -
199M PHE* 4.0 20.2 - - + -
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Residues in contact with VAL 36 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34M ILE* 3.8 12.3 - - + +
35M PRO* 1.3 78.3 - - - +
37M GLY* 1.3 66.2 + - - +
39M ASN* 3.5 4.2 + - - -
40M THR* 2.8 32.1 + - + +
42M VAL* 4.1 9.9 - - + -
58M LEU* 3.9 36.3 - - + +
61M LEU* 6.1 0.7 - - + -
62M VAL* 3.7 26.2 - - + -
78M LEU* 4.5 4.7 - - + -
83M ILE* 3.7 30.1 - - + +
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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