Contacts of the strand formed by residues 101 - 105 (chain A) in PDB entry 3SF8
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 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A ASP 3.3 17.4 + - - +
69A VAL* 3.3 16.8 - - + -
70A VAL 3.1 14.0 + - - -
95A GLN* 3.0 18.7 + - - +
100A GLY* 1.3 72.3 - - - -
102A ILE* 1.3 61.5 - - - +
103A ALA 4.9 0.2 - - - +
148A LYS* 4.0 20.6 - - - -
151A LEU* 3.4 40.3 - - + +
153A LEU* 4.1 20.0 - - + -
168A ILE* 4.5 6.7 - - + -
171A ALA* 3.9 15.3 - - + -
172A LEU* 3.7 26.5 - - + -
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Residues in contact with ILE 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A VAL* 3.5 8.3 - - + +
72A LEU* 4.9 2.5 - - + -
92A LEU* 3.7 37.9 - - + +
95A GLN* 3.6 13.2 - - + -
96A GLU* 4.0 15.9 - - + +
100A GLY 4.2 2.2 - - - +
101A LEU* 1.3 79.2 - - - +
103A ALA* 1.3 67.5 + - - +
112A LEU* 3.7 28.2 - - + +
117A ILE* 3.7 25.6 - - + -
151A LEU 2.9 12.0 + - - +
152A ILE* 3.6 11.8 - - + +
153A LEU* 2.9 27.0 + - - +
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Residues in contact with ALA 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A VAL* 3.9 14.6 - - + -
70A VAL 2.9 7.7 + - - +
71A VAL* 3.2 5.1 - - + -
72A LEU* 2.8 25.3 + - - +
101A LEU* 5.0 0.7 - - + -
102A ILE* 1.3 75.6 - - - +
104A ALA* 1.3 60.8 + - - +
153A LEU* 3.1 12.1 - - + +
164A PHE* 3.6 22.4 - - + -
168A ILE* 3.8 22.0 - - + -
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Residues in contact with ALA 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A LEU* 3.4 18.6 - - + -
103A ALA* 1.3 75.7 - - - +
105A ILE* 1.3 60.5 + - - +
108A GLY 3.8 6.5 - - - +
109A PRO* 3.4 33.8 - - + +
112A LEU* 4.2 15.9 - - + -
153A LEU 2.9 7.6 + - - +
154A THR* 3.2 24.4 - - - -
155A SER 3.3 1.6 + - - -
164A PHE* 3.6 3.9 - - - -
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Residues in contact with ILE 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A GLU* 3.9 24.5 - - + +
72A LEU 3.1 11.9 + - - +
73A PRO* 3.9 6.7 - - + -
74A GLY 3.3 11.1 + - - -
104A ALA* 1.3 75.6 - - - +
106A CSO 1.3 68.5 + - + +
108A GLY 2.9 21.0 + - - -
109A PRO* 3.6 2.7 - - - -
155A SER* 3.6 12.6 - - - +
157A GLY* 3.5 28.0 - - - +
160A THR* 3.7 9.6 - - - +
161A SER* 3.7 24.2 - - - +
164A PHE* 3.8 36.3 - - + -
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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