Contacts of the strand formed by residues 142 - 148 (chain o) in PDB entry 6FF7
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 142 (chain o).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141o GLN* 1.3 75.5 - - - +
143o TYR* 1.3 61.6 + - - +
157o GLN* 3.4 4.9 - - - +
158o MET* 2.8 37.5 + - + +
160o LEU* 6.3 0.2 - - - +
173o ARG* 5.5 7.4 - - + -
176o CYS* 4.1 17.0 - - + -
298o GLY 3.2 15.7 - - - +
299o GLU* 4.1 3.8 - - + +
300o TYR 4.6 0.9 - - - +
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Residues in contact with TYR 143 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142o VAL* 1.3 78.2 - - - +
144o MET* 1.3 62.2 - - - +
155o ARG* 5.4 7.0 - - + -
156o ILE 3.2 12.6 - - - +
157o GLN* 4.6 4.5 - - + -
176o CYS* 4.8 1.6 - - - +
297o CYS* 3.2 25.6 - - - +
298o GLY 2.9 15.6 + - - +
299o GLU 6.4 0.7 - - - -
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Residues in contact with MET 144 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143o TYR* 1.3 77.5 - - - +
145o ASP* 1.3 64.5 + - - +
146o ILE* 3.8 3.6 + - + +
155o ARG* 3.4 3.3 - - - -
156o ILE* 2.8 40.7 + - + +
294o ILE* 5.0 10.5 - - + -
296o ASP 3.4 8.3 - - - +
297o CYS* 4.6 5.2 - - + -
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Residues in contact with ASP 145 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143o TYR* 4.3 0.6 - - - +
144o MET* 1.3 73.2 - - - +
146o ILE* 1.3 56.3 + - - +
154o GLY 3.6 8.7 - - - +
155o ARG* 4.4 6.1 - - + +
294o ILE* 3.5 4.5 - - - -
295o ALA* 2.8 37.5 + - + -
296o ASP* 2.8 31.3 + - + +
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Residues in contact with ILE 146 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144o MET* 3.8 4.2 + - + +
145o ASP* 1.3 74.0 - - - +
147o LYS* 1.3 56.2 + - - +
152o PRO* 3.7 3.5 - - - +
153o ALA* 2.8 41.2 + - + +
154o GLY 2.9 16.1 + - - +
156o ILE* 6.0 2.0 - - + +
274o VAL* 5.4 9.2 - - + +
278o ILE* 6.4 1.8 - - + -
292o VAL* 6.6 0.2 - - + -
293o ILE 3.4 7.4 - - - +
294o ILE* 4.9 0.7 - - - +
295o ALA* 4.8 1.6 - - - -
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Residues in contact with LYS 147 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145o ASP 4.2 0.4 + - - -
146o ILE* 1.3 75.5 - - - +
148o ILE* 1.3 60.7 + - - +
149o GLY 4.1 7.7 - - - +
150o ASN 5.6 1.1 - - - -
151o LYS 3.4 13.9 - - - +
152o PRO* 4.2 3.8 - - + -
291o LYS 3.7 1.4 - - - +
292o VAL* 3.5 2.9 - - - +
293o ILE* 2.9 43.8 + - + +
295o ALA* 4.2 15.9 - - + -
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Residues in contact with ILE 148 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146o ILE 4.3 0.6 + - - -
147o LYS* 1.3 72.1 - - - +
149o GLY* 1.3 64.7 + - - +
150o ASN 3.3 0.2 + - - -
151o LYS* 2.8 31.2 + - + +
153o ALA* 4.7 12.9 - - + +
277o GLN* 5.6 9.2 - - + +
278o ILE* 6.3 1.3 - - - -
281o GLN* 6.2 3.6 - - + -
290o GLN* 5.1 5.4 - - + -
291o LYS 3.4 6.3 - - - +
292o VAL* 4.6 5.6 - - + +
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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