Contacts of the strand formed by residues 128 - 134 (chain D) in PDB entry 3F7F
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 PHE 128 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120D ASN* 3.8 30.5 - - + -
121D VAL 4.1 1.8 - - - -
122D ILE* 3.4 33.9 - - + -
126D GLY 5.2 0.4 - - - +
127D SER* 1.3 74.0 - - - +
129D LEU* 1.3 62.0 + - - +
130D THR* 3.5 6.5 + - - -
151D HIS 3.6 5.7 - - - +
153D GLN* 2.7 29.0 + - - +
155D PRO* 3.8 18.6 - - + -
158D PHE* 5.9 4.7 - + + -
166D LEU* 3.9 17.3 - - + -
174D SER* 5.2 4.3 - - - -
186D LEU* 4.0 22.4 - - + -
194D TYR* 3.3 45.8 - + - -
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Residues in contact with LEU 129 (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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28D VAL* 4.0 16.8 - - + -
97D LEU* 3.8 29.4 - - + -
98D PRO* 4.6 0.4 - - + -
119D VAL 4.3 0.2 - - - -
120D ASN* 3.4 6.2 - - - +
121D VAL* 3.0 45.1 + - + +
123D LEU* 4.4 17.3 - - + -
127D SER 3.8 1.2 - - - -
128D PHE* 1.3 76.3 - - - +
130D THR* 1.3 69.6 + - - +
131D LEU* 4.2 9.4 - - + -
150D PHE* 3.8 35.0 - - + -
151D HIS 3.8 6.5 - - - +
152D LEU* 3.8 24.3 - - + +
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Residues in contact with THR 130 (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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118D LEU* 4.0 20.6 - - + -
119D VAL 3.4 1.8 - - - -
120D ASN* 3.2 20.3 + - - +
128D PHE* 3.5 11.4 + - - -
129D LEU* 1.3 80.9 + - - +
131D LEU* 1.3 62.0 + - - +
132D GLN* 4.9 5.2 - - + +
149D TRP 3.4 0.2 - - - +
150D PHE* 2.8 27.8 - - - -
151D HIS* 3.0 31.0 + - + +
153D GLN* 4.4 7.4 + - - -
192D VAL* 5.2 4.0 + - + -
194D TYR* 4.5 10.7 - - + +
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Residues in contact with LEU 131 (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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28D VAL* 4.3 8.3 - - + -
79D LEU* 4.4 6.7 - - + -
95D ILE* 3.6 36.3 - - + -
97D LEU* 4.9 6.5 - - + -
117D LEU 3.3 2.3 - - - +
118D LEU* 3.4 7.6 - - - +
119D VAL* 2.6 68.9 + - + +
121D VAL* 5.7 2.0 - - + -
129D LEU* 4.6 10.8 - - + -
130D THR* 1.3 73.5 - - - +
132D GLN* 1.3 62.1 + - - +
133D LEU* 4.0 4.9 - - + -
149D TRP* 3.0 34.8 - - + +
150D PHE* 3.6 17.9 - - + -
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Residues in contact with GLN 132 (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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116D GLN* 3.0 30.6 + - - +
117D LEU 3.7 2.9 - - - -
118D LEU* 3.5 26.6 - - + +
130D THR* 4.9 3.9 - - + +
131D LEU* 1.3 71.7 - - - +
133D LEU* 1.3 61.7 + - - +
134D PRO* 3.5 8.2 - - - +
148D GLU 4.4 4.9 + - - +
149D TRP* 2.6 38.1 + - - +
151D HIS* 3.2 32.0 + - + +
191D GLY 4.7 11.5 + - - -
192D VAL* 5.1 1.6 - - - +
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Residues in contact with LEU 133 (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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26D LEU* 4.4 9.9 - - + -
81D PHE* 3.8 23.8 - - + -
93D ILE* 5.6 2.0 - - + -
95D ILE* 3.3 35.9 - - + -
116D GLN* 3.4 2.5 - - - -
117D LEU* 2.7 50.1 + - + +
119D VAL* 4.7 5.4 - - + -
131D LEU* 4.8 4.3 - - + -
132D GLN* 1.3 81.3 - - - +
134D PRO* 1.3 68.8 - - + +
135D LEU* 3.3 0.7 + - - -
137D PHE* 5.0 5.6 - - + -
138D LEU* 4.5 19.2 - - + +
145D LEU* 4.1 19.5 - - + -
149D TRP* 4.6 8.1 - - + -
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Residues in contact with PRO 134 (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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115D GLN 4.0 0.4 - - - +
116D GLN* 3.6 24.7 - - + +
132D GLN 3.5 8.7 - - - +
133D LEU* 1.3 83.9 - - + +
135D LEU* 1.3 66.9 + - - +
136D SER* 2.9 16.9 + - - +
137D PHE* 2.9 20.8 + - + +
138D LEU* 3.3 9.9 + - - +
145D LEU* 4.0 29.4 - - + -
146D ASN 5.8 1.3 - - - +
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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