Contacts of the strand formed by residues 45 - 50 (chain B) in PDB entry 1SMK
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 PHE 45 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B GLY* 1.3 82.8 - - - -
46B LYS* 1.3 62.1 + - - +
47B VAL* 3.9 1.4 + - + +
69B LEU* 2.7 36.2 + - + +
70B VAL* 3.4 5.9 - - - -
71B SER* 2.8 26.5 + - - -
72B VAL 3.4 2.1 + - - +
114B ASP* 3.6 16.8 - - + +
283B LEU* 3.5 45.3 - - + -
286B LEU* 3.6 28.7 - - + -
287B ARG* 3.5 33.7 - - + -
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Residues in contact with LYS 46 (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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44B GLY 5.0 2.7 - - - +
45B PHE* 1.3 74.8 - - - +
47B VAL* 1.3 62.1 + - - +
71B SER* 4.0 6.3 - - - +
72B VAL* 3.5 27.6 - - + -
112B GLY* 3.2 33.2 + - - +
113B MET* 3.9 18.2 - - + -
114B ASP* 2.8 39.8 + - - +
115B LEU 3.0 8.0 + - - -
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Residues in contact with VAL 47 (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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45B PHE 4.3 2.2 - - - +
46B LYS* 1.3 81.0 - - - +
48B ALA* 1.3 59.9 + - - +
49B ILE* 4.5 0.2 - - + -
64B MET* 4.0 10.5 - - + -
70B VAL* 4.0 24.9 - - + -
72B VAL 2.8 12.9 + - - +
73B LEU* 3.1 19.3 - - + +
74B HIS 2.7 30.7 + - - -
113B MET* 3.7 3.9 - - - +
115B LEU* 3.3 21.1 - - + +
117B ILE* 3.6 31.6 - - + -
283B LEU* 4.3 12.3 - - + -
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Residues in contact with ALA 48 (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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47B VAL* 1.3 75.6 - - - +
49B ILE* 1.3 63.0 + - - +
50B LEU* 4.1 4.9 - - + -
74B HIS* 3.2 16.6 - - + +
109B ALA* 3.9 7.4 - - + +
110B LEU* 4.8 6.1 - - + -
113B MET* 3.4 29.1 - - + -
115B LEU 2.9 8.7 + - - +
116B ILE* 3.3 14.3 - - + +
117B ILE 2.9 25.1 + - - +
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Residues in contact with ILE 49 (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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48B ALA* 1.3 76.1 - - - +
50B LEU* 1.3 62.4 + - - +
52B ALA* 3.8 20.3 - - + +
57B GLY 4.7 1.8 - - - +
60B LEU* 3.9 17.5 - - + -
61B ALA* 3.6 29.4 - - - -
64B MET* 3.8 21.5 - - + -
73B LEU* 3.9 17.9 - - + -
74B HIS 2.8 11.3 + - - +
75B LEU* 4.0 7.7 - - + -
76B TYR* 3.0 28.1 + - - +
117B ILE* 3.4 17.3 - - + +
119B PRO* 4.1 18.6 - - + -
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Residues in contact with LEU 50 (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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48B ALA* 4.8 5.8 - - + -
49B ILE* 1.3 72.1 - - - +
51B GLY* 1.3 58.4 + - - +
76B TYR* 4.0 19.5 - - + -
106B LEU* 3.9 15.7 - - + -
109B ALA* 5.4 0.9 - - + -
110B LEU* 3.7 24.0 - - + -
116B ILE* 3.5 28.5 - - + -
117B ILE 2.9 11.4 + - - +
118B VAL* 3.6 15.5 - - + -
119B PRO* 3.0 21.6 - - - +
120B ALA* 3.0 13.1 + - - +
144B LEU* 3.9 33.7 - - + -
148B ILE* 3.8 14.4 - - + -
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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