Contacts of the strand formed by residues 63 - 67 (chain D) in PDB entry 1SBB
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 ASN 63 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D ILE* 4.0 8.7 - - + -
51D TYR 3.3 6.7 - - - +
52D SER* 3.8 14.9 + - - -
54D LYS* 5.1 1.4 - - - -
61D TYR* 4.1 1.4 - - - +
62D ASP* 1.3 97.3 - - - +
64D VAL* 1.3 64.7 + - - +
95D PHE* 4.2 2.0 - - + -
106D GLN* 3.3 14.8 + - - +
107D THR* 2.8 57.3 + - + +
108D ASP 4.3 2.2 + - - +
109D LYS 5.2 0.8 + - - -
110D ARG 3.3 3.4 + - - +
111D LYS* 3.2 5.4 - - - +
112D THR 3.0 24.6 + - - +
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Residues in contact with VAL 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D VAL* 4.1 9.9 - - + -
49D LEU 3.5 2.4 - - - +
50D ILE* 3.4 4.0 - - - -
51D TYR* 2.8 33.3 + - + +
53D ILE* 3.7 35.2 - - + -
61D TYR* 3.9 12.1 - - + -
63D ASN* 1.3 78.1 - - - +
65D ARG* 1.3 71.3 + - - +
66D VAL* 3.8 6.6 + - + +
112D THR* 3.4 28.9 - - + +
114D MET* 3.9 25.6 - - + -
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Residues in contact with ARG 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A GLN* 5.8 0.2 - - - +
44D PHE* 3.6 18.0 - - - -
45D LEU* 4.0 5.3 - - - +
47D PHE* 3.5 15.2 - - - -
48D ASP* 2.9 39.1 + - + +
49D LEU 3.7 3.1 - - - +
50D ILE* 3.6 15.5 - - + -
63D ASN 4.2 0.2 - - - -
64D VAL* 1.3 76.0 - - - +
66D VAL* 1.3 61.4 + - - +
67D GLU* 3.0 32.0 + - + +
89D TYR* 5.5 3.2 + - - -
94D TYR 3.4 17.6 + - - -
95D PHE* 3.3 39.6 - - + -
112D THR 3.0 6.9 + - - -
113D CYS* 3.5 15.6 - - + +
114D MET 3.0 26.9 + - - +
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Residues in contact with VAL 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D ASP* 3.1 4.7 - - - -
49D LEU 2.9 31.6 + - - +
51D TYR* 3.5 32.5 - - + -
64D VAL* 4.1 9.0 - - + +
65D ARG* 1.3 77.1 - - - +
67D GLU* 1.3 60.4 + - - +
68D PHE* 3.9 10.0 - - + -
84D VAL* 4.3 10.3 - - + -
114D MET* 3.6 18.6 - - + -
116D GLY 3.0 36.6 - - - +
118D VAL* 3.8 13.9 - - + -
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Residues in contact with GLU 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A LYS* 3.9 8.7 - - - +
141A GLN* 3.7 21.6 + - - +
47D PHE* 3.3 40.0 - - + -
48D ASP* 3.8 5.6 - - + +
65D ARG* 3.0 35.7 + - + +
66D VAL* 1.3 73.7 - - - +
68D PHE* 1.3 62.4 + - - +
89D TYR* 5.5 1.9 + - - +
114D MET 3.1 9.6 + - - +
115D TYR* 3.5 40.2 + - + +
116D GLY 3.2 23.0 + - - -
215D MET* 4.8 1.6 - - - +
218D ASN* 4.2 0.3 - - - +
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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