Contacts of the strand formed by residues 147 - 156 (chain B) in PDB entry 5FN7
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 GLU 147 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146B HIS* 1.3 74.6 - - - +
148B TYR* 1.3 73.0 + - - +
167B ILE* 3.8 29.6 - - + +
168B ILE 3.4 6.7 - - - +
169B LYS* 3.4 29.0 - - + +
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Residues in contact with TYR 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ASN* 3.5 22.2 + - + -
130A MET* 3.7 36.1 - - + -
131A ILE* 3.1 27.9 + - + +
104B ILE* 4.0 12.6 - - + -
128B GLY* 4.5 13.9 - - - +
142B LEU* 5.0 2.2 - - + +
143B GLU 5.1 0.6 + - - -
146B HIS* 3.5 38.3 + + + +
147B GLU* 1.3 82.6 - - - +
149B LYS* 1.3 61.6 + - - +
150B CYS* 3.7 16.7 + - - -
166B LYS 3.7 0.5 - - - +
167B ILE* 3.3 6.6 - - - +
168B ILE* 2.7 42.5 + - - +
170B THR* 4.4 15.0 - - + -
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Residues in contact with LYS 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B GLN 3.6 7.4 - - - +
128B GLY* 4.1 12.9 + - - +
148B TYR* 1.3 71.8 - - - +
150B CYS* 1.3 59.6 + - - +
151B ASP* 2.9 39.5 + - - +
165B SER* 3.1 18.7 + - - +
166B LYS 3.7 3.8 - - - +
167B ILE* 4.2 29.4 - - + -
1174B NAG 5.0 2.4 - - - +
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Residues in contact with CYS 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B LEU* 5.2 2.8 - - - +
104B ILE* 4.6 4.9 - - - -
106B LEU* 3.6 19.5 - - + +
125B PHE* 5.5 1.1 - - + -
126B GLN 3.2 3.8 - - - -
127B CYS* 2.1 47.8 - - - -
148B TYR* 4.5 10.3 - - - -
149B LYS* 1.3 71.2 - - - +
151B ASP* 1.3 62.2 + - - +
152B SER* 4.2 0.4 + - - -
165B SER* 3.4 2.5 - - - -
166B LYS* 2.7 43.6 + - - +
168B ILE* 3.7 20.2 - - + -
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Residues in contact with ASP 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B PHE* 3.3 3.5 - - - +
126B GLN* 2.7 51.3 + - + +
149B LYS* 2.9 27.8 + - - +
150B CYS* 1.3 73.6 - - - +
152B SER* 1.3 62.2 + - - +
164B ALA 3.7 2.5 - - - -
165B SER* 2.3 31.4 + - - -
1174B NAG 3.4 16.0 - - + +
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Residues in contact with SER 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B LEU* 4.3 6.5 - - - -
108B TRP* 2.7 35.6 + - - -
124B ARG 2.7 19.8 + - - -
125B PHE* 3.5 22.2 - - - -
150B CYS 5.3 0.2 - - - -
151B ASP* 1.3 77.0 - - - +
153B GLU* 1.3 59.3 + - - +
163B ASN* 3.2 6.5 - - - +
164B ALA 2.8 35.6 + - - +
1174B NAG 4.3 2.6 - - - +
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Residues in contact with GLU 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B THR 3.9 0.5 - - - +
123B TYR* 3.6 2.9 - - - -
124B ARG* 2.7 70.6 + - + +
152B SER* 1.3 77.9 + - - +
154B ILE* 1.3 65.0 + - - +
155B LEU* 3.4 27.6 - - + +
160B LYS* 3.4 21.0 - - + +
162B THR 3.4 12.8 - - - +
163B ASN* 3.8 9.6 + - + +
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Residues in contact with ILE 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B PHE* 3.6 22.4 - - + -
108B TRP* 3.6 44.0 - - + -
121B ILE* 3.6 21.8 - - + -
122B THR 3.5 10.5 - - - +
123B TYR* 3.9 12.1 - - + -
153B GLU* 1.3 77.4 - - - +
155B LEU* 1.3 63.6 + - - +
160B LYS* 3.5 3.6 - - - -
161B PHE* 3.1 43.8 + - + -
162B THR* 2.9 37.1 + - + +
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Residues in contact with LEU 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B ASN 3.6 0.4 - - - +
121B ILE* 3.3 6.4 - - - +
122B THR* 2.9 53.3 + - - +
124B ARG* 3.8 22.2 - - - -
153B GLU* 3.4 29.2 - - + +
154B ILE* 1.3 75.3 - - - +
156B TYR* 1.4 61.4 + - - +
157B ASN 4.2 0.4 - - - -
158B ASN* 3.9 31.9 - - + +
159B HIS 3.2 7.6 - - - +
160B LYS* 3.6 25.8 - - + +
161B PHE* 3.8 5.1 - - - -
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Residues in contact with TYR 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B TYR* 6.0 0.2 - + - -
59B CYS* 5.7 0.2 - - - -
81B ASP* 3.5 25.6 - - + +
82B VAL 3.7 9.5 + - - -
83B PRO* 3.6 33.7 - - + -
84B PRO* 4.4 2.5 - - + -
116B CYS* 3.7 34.2 - - + +
117B ASP* 4.1 7.0 + - - +
120B ASN* 3.3 23.4 + - + +
121B ILE* 3.7 20.0 - - + -
155B LEU* 1.4 71.5 - - - +
157B ASN* 1.4 92.3 + - - +
159B HIS* 2.8 26.4 + - - +
161B PHE* 3.8 9.6 - - + -
1176B NAG 4.6 5.4 + - - -
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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