Contacts of the strand formed by residues 92 - 98 (chain X) in PDB entry 3F6B
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 92 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51X VAL* 4.0 23.1 - - + -
54X ALA 3.9 14.6 - - - +
55X ASP* 3.9 14.1 - - + -
58X ALA* 3.8 20.9 - - + -
65X ALA* 3.6 9.0 - - + +
67X ILE* 4.0 14.6 - - + -
82X LEU* 4.7 3.8 - - + -
85X ALA* 3.6 28.0 - - + -
90X SER* 3.0 17.2 + - - +
91X PRO* 1.3 80.7 - - - +
93X ILE* 1.3 62.5 + - - +
94X VAL* 3.6 3.3 + - + -
146X ALA* 4.3 0.4 - - - -
152X GLY 3.6 3.3 + - - +
153X PRO* 3.3 7.6 - - + +
154X VAL* 2.9 30.5 + - - +
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Residues in contact with ILE 93 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17X ILE* 3.6 30.1 - - + -
64X PRO* 3.9 18.8 - - + -
65X ALA 2.9 15.7 + - - +
66X PHE* 3.7 24.6 - - + -
67X ILE* 2.9 29.4 + - - +
92X LEU* 1.3 74.5 - - - +
94X VAL* 1.3 59.0 + - - +
95X THR* 4.2 8.5 - - + -
139X MET* 4.3 5.2 - - - -
142X ALA* 4.1 28.0 - - + +
143X ILE* 3.9 17.7 - - + +
146X ALA* 4.0 16.4 - - + -
154X VAL* 3.8 4.0 - - + -
156X LEU* 5.9 0.4 - - + -
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Residues in contact with VAL 94 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51X VAL* 5.4 1.3 - - + -
67X ILE* 3.9 23.3 - - + -
69X LEU* 3.8 28.7 - - + -
75X THR* 5.5 0.4 - - + -
82X LEU* 3.9 33.0 - - + -
92X LEU* 4.4 7.4 - - + +
93X ILE* 1.3 74.7 - - - +
95X THR* 1.3 63.9 + - - +
123X VAL* 5.7 0.4 - - + -
153X PRO* 4.9 2.0 - - + -
154X VAL 2.9 20.8 + - - +
155X TYR* 3.2 25.9 - - + -
156X LEU* 2.9 24.8 + - - +
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Residues in contact with THR 95 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31X PHE* 4.8 1.6 - - - -
66X PHE* 3.6 36.2 - - + -
67X ILE 2.9 21.4 + - - +
68X ASN* 3.0 17.8 + - - -
69X LEU* 2.8 33.8 + - - +
93X ILE* 4.2 5.8 - - + -
94X VAL* 1.3 80.6 - - - +
96X ALA* 1.3 57.3 + - - +
139X MET* 3.9 20.0 - - + -
155X TYR* 5.0 0.2 - - - -
156X LEU* 3.2 17.0 - - + +
158X VAL* 5.7 4.0 - - - -
163X TRP* 6.4 2.2 - - - -
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Residues in contact with ALA 96 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68X ASN* 4.6 2.5 - - - -
69X LEU* 3.2 13.2 - - + +
71X SER* 4.0 11.2 - - - +
75X THR* 3.4 13.7 - - - +
95X THR* 1.3 76.6 - - - +
97X GLY* 1.3 61.4 + - - +
112X ASN* 4.7 2.0 - - - +
155X TYR* 3.4 30.5 - - + +
156X LEU 3.0 6.7 + - - +
157X SER* 3.3 4.0 - - - -
158X VAL* 3.0 25.3 + - - +
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Residues in contact with GLY 97 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27X ASN* 3.1 29.3 + - - -
28X GLU* 2.9 27.9 + - - +
69X LEU 3.3 2.0 + - - -
71X SER* 3.1 20.8 + - - -
96X ALA* 1.3 73.9 - - - +
98X GLN* 1.3 57.7 - - - -
112X ASN* 5.0 1.1 - - - +
157X SER* 5.0 0.7 - - - -
158X VAL* 3.6 8.3 - - - -
163X TRP* 6.2 0.7 - - - -
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Residues in contact with GLN 98 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27X ASN* 3.3 17.2 - - - +
71X SER* 5.1 0.4 - - - -
97X GLY* 1.3 72.1 - - - -
99X GLN* 1.3 89.4 + - - +
104X ILE* 3.6 22.6 - - + +
111X THR* 3.4 8.9 - - - +
112X ASN* 2.8 52.4 + - + +
115X ALA* 4.2 0.8 - - - +
128X GLU* 2.9 26.3 + - - +
157X SER* 3.6 13.4 + - - +
158X VAL 2.9 5.5 + - - -
159X PRO* 3.5 19.3 - - + -
160X TYR* 3.0 15.9 + - - +
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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