Contacts of the strand formed by residues 46 - 53 (chain B) in PDB entry 1SID
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 VAL 46 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ASP 3.3 13.7 - - - +
45B SER* 1.3 72.2 - - - +
47B THR* 1.3 79.5 + - - +
48B GLU* 6.2 0.4 - - + -
123B VAL* 6.3 0.4 - - + -
309B THR* 4.6 12.1 - - + -
310B LEU 3.0 28.0 - - - +
311B ARG* 4.3 7.9 - - + +
352F ARG 3.6 0.2 - - - +
353F VAL* 3.0 6.3 - - - -
354F TYR* 2.8 48.2 + - + +
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Residues in contact with THR 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 3.6 33.8 - - + +
41B THR* 4.9 1.0 - - - +
45B SER 4.1 1.7 + - - -
46B VAL* 1.3 85.1 - - - +
48B GLU* 1.3 65.8 + - - +
49B ILE* 3.9 17.5 - - + -
105B LEU* 6.2 0.9 - - + -
120B TRP* 3.8 22.6 - - + -
308B ILE 3.5 1.7 - - - +
309B THR* 3.6 2.9 - - - -
310B LEU* 3.4 39.4 + - + +
351F VAL* 4.0 2.5 - - + -
352F ARG 3.2 9.2 - - - +
353F VAL* 3.7 12.1 - - + +
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Residues in contact with GLU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B VAL* 4.3 1.3 + - + -
47B THR* 1.3 72.0 - - - +
49B ILE* 1.3 63.3 + - - +
50B GLU* 4.0 3.4 - - - +
307B LYS* 3.1 38.1 + - + -
308B ILE 3.5 2.7 - - - +
309B THR* 3.7 26.2 - - + +
266C GLU* 4.5 9.2 - - - +
350F GLU 3.4 0.9 - - - +
351F VAL* 2.9 28.1 - - - +
352F ARG* 2.8 41.3 + - + +
354F TYR* 3.9 24.0 + - + -
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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
----------------------------------------------------------
34B MET* 4.3 16.4 - - + -
37B LEU* 4.8 0.9 - - + -
47B THR* 3.9 18.2 - - + -
48B GLU* 1.3 77.1 - - - +
50B GLU* 1.3 72.3 + - - +
51B ALA* 4.6 2.7 - - + -
103B LEU* 4.1 23.8 - - + -
105B LEU* 4.7 20.4 - - + -
278B LEU* 4.9 7.9 - - + -
306B PHE 3.2 3.8 - - - +
307B LYS* 4.3 0.9 - - - -
308B ILE* 2.9 46.3 + - + +
310B LEU* 4.5 16.2 - - + -
348F VAL* 4.3 4.3 - - + -
350F GLU 3.4 2.0 - - - -
351F VAL* 3.7 19.1 - - + -
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Residues in contact with GLU 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B GLU* 4.0 2.8 - - - +
49B ILE* 1.3 74.2 - - - +
51B ALA* 1.3 63.8 + - - +
305B TYR* 2.9 34.1 - - + +
306B PHE 2.9 7.0 - - - +
307B LYS* 3.7 23.3 - - + -
233C LYS* 2.4 50.6 - - - +
348F VAL* 3.6 5.5 - - - +
349F GLU* 3.0 21.3 + - + -
350F GLU* 2.8 44.4 + - - +
352F ARG* 3.6 15.5 + - - -
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Residues in contact with ALA 51 (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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49B ILE* 4.6 7.4 - - + +
50B GLU* 1.3 77.4 - - - +
52B PHE* 1.3 71.2 + - - +
103B LEU* 4.7 3.4 - - + -
280B LEU* 4.9 7.6 - - + -
305B TYR* 3.5 4.9 - - - -
306B PHE* 2.7 32.4 + - + +
308B ILE* 5.9 0.2 - - + -
341F MET* 4.0 12.1 - - - -
347F GLN 3.0 18.2 - - - +
348F VAL* 3.7 10.3 - - + -
349F GLU* 3.6 6.6 - - - +
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Residues in contact with PHE 52 (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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51B ALA* 1.3 85.9 - - - +
53B LEU* 1.3 75.1 + - - +
54B ASN* 3.9 10.1 - - - -
304B ARG 2.9 21.3 - - - +
305B TYR* 3.9 3.6 - - + -
306B PHE* 3.8 5.2 - - - -
208C LEU* 3.0 37.2 - - + -
210C PRO* 4.0 17.0 - - + -
341F MET* 3.6 1.0 - - - +
346F THR 4.9 1.1 - - - -
347F GLN* 2.8 93.9 + - + +
348F VAL 5.1 0.2 - - - -
349F GLU* 3.5 26.5 - - + -
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Residues in contact with LEU 53 (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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52B PHE* 1.3 87.6 - - - +
54B ASN* 1.3 64.1 + - - +
99B SER* 4.9 2.5 - - - -
100B MET* 4.3 9.4 - - - -
101B ALA* 4.2 18.6 - - + -
280B LEU* 3.6 38.1 - - + +
281B SER* 3.9 2.0 - - - +
282B CYS* 3.6 31.9 - - - -
303B PRO* 3.5 3.5 - - - +
304B ARG 2.9 29.8 + - - +
306B PHE* 3.6 20.4 - - + -
339F GLN* 3.5 19.7 - - - +
341F MET* 4.3 6.1 - - + -
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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