Contacts of the strand formed by residues 86 - 97 (chain B) in PDB entry 5FL6
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 ARG 86 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A PRO* 6.0 5.2 - - + +
196A GLU* 3.4 36.6 + - - +
45B LEU* 5.8 4.0 - - - +
81B ALA* 3.3 2.1 - - - -
82B LEU* 3.0 59.5 + - + +
83B GLY* 2.9 18.6 + - - +
84B PRO* 3.7 13.5 - - - +
85B GLY* 1.3 76.3 - - - +
87B GLU* 1.3 59.3 + - - +
88B TYR* 3.6 15.4 + - + +
194B GLN* 5.0 10.5 + - - -
209B ILE* 3.8 26.7 - - - +
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Residues in contact with GLU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B GLU* 4.9 3.0 - - + +
80B MET 3.3 5.6 - - - +
81B ALA* 4.2 12.6 - - + -
85B GLY* 3.5 11.6 + - - +
86B ARG* 1.3 83.5 - - - +
88B TYR* 1.3 72.3 + - - +
124B SER* 3.6 4.7 + - - -
125B THR* 3.1 42.4 + - + +
50C LEU 4.1 4.7 - - - +
51C LEU* 3.8 22.0 - - + +
52C GLY* 2.9 33.4 + - - -
53C PHE* 4.9 0.5 + - - +
54C GLN* 3.7 23.8 + - - +
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Residues in contact with TYR 88 (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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137A PRO* 4.7 6.1 - - + +
79B GLU* 3.4 7.1 - - - +
80B MET* 2.8 50.3 + - + +
82B LEU* 3.8 17.0 - - + -
86B ARG* 3.6 26.7 + - + -
87B GLU* 1.3 88.2 - - - +
89B ARG* 1.3 60.8 + - - +
122B HIS* 3.7 16.8 - - + -
123B LEU 3.3 8.3 - - - -
124B SER* 3.3 31.4 - - - -
125B THR* 4.2 6.5 - - - +
138B GLY* 2.6 38.2 + - - -
141B ALA* 3.6 28.5 - - + -
209B ILE* 3.9 9.9 - - - +
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Residues in contact with ARG 89 (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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76B PRO* 5.8 10.9 - - + +
77B GLY 5.6 5.8 - - - +
78B LEU 3.1 12.6 - - - +
79B GLU* 5.2 4.5 - - + -
88B TYR* 1.3 73.7 - - - +
90B ALA* 1.3 65.2 + - - +
91B LEU* 3.4 24.8 + - + +
122B HIS* 3.3 3.1 - - - -
123B LEU* 2.9 67.7 + - + +
124B SER 5.8 0.4 + - - -
125B THR* 4.5 11.0 - - + +
127B PHE 5.2 1.8 + - - -
128B ALA* 3.6 14.5 + - - +
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Residues in contact with ALA 90 (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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53B PHE* 4.3 3.4 - - + -
74B LEU* 3.7 21.8 - - + +
75B PRO 4.1 15.2 - - - +
76B PRO* 5.7 0.3 - - - +
78B LEU* 2.9 33.6 + - + +
89B ARG* 1.3 76.4 + - - +
91B LEU* 1.3 62.7 + - - +
120B VAL* 4.4 3.1 - - + -
121B VAL 3.7 3.8 - - - +
122B HIS* 3.5 26.5 - - + +
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Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B THR* 4.0 5.5 - - - +
74B LEU* 3.0 28.6 + - - +
89B ARG* 3.4 41.3 - - - +
90B ALA* 1.3 76.5 - - - +
92B GLN* 1.3 67.8 + - + +
121B VAL* 2.8 25.5 + - + +
122B HIS 4.5 3.8 - - - -
123B LEU* 4.0 21.3 - - + +
130B VAL* 3.5 31.2 - - + -
140B LEU* 4.9 2.5 - - + -
269B Y0R 5.4 5.2 - - - +
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Residues in contact with GLN 92 (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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71B GLN* 3.4 26.6 + - + +
72B LEU 3.2 15.7 - - - +
73B THR* 4.5 2.5 - - + -
74B LEU* 3.7 11.9 - - - +
91B LEU* 1.3 88.1 - - + +
93B LEU* 1.3 66.7 + - - +
94B HIS* 2.7 23.9 + - - -
120B VAL* 3.6 0.9 - - - -
121B VAL* 2.9 43.0 + - + +
269B Y0R 3.4 20.6 + - - +
1261B GOL 2.7 26.7 + - - -
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Residues in contact with LEU 93 (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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71B GLN* 3.4 1.2 - - - -
72B LEU* 2.9 64.7 + - + -
74B LEU* 4.1 5.1 - - + +
92B GLN* 1.3 78.6 - - - +
94B HIS* 1.3 68.5 + - - +
95B LEU* 5.4 3.1 - - + -
118B ILE* 4.1 17.9 - - + -
119B HIS 3.1 13.7 - - - +
120B VAL* 4.1 13.9 - - + -
160B LEU* 4.3 16.8 - - + -
181B ILE* 3.7 22.9 - - + -
184B LEU* 3.6 23.8 - - + -
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Residues in contact with HIS 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B SER* 3.4 6.5 - - - +
70B VAL 3.2 19.1 - - - +
71B GLN* 4.1 2.0 - - - -
92B GLN* 2.7 24.4 + - - +
93B LEU* 1.3 77.7 - - - +
95B LEU* 1.3 65.7 + - - +
96B HIS* 3.3 10.5 - + - -
118B ILE* 3.6 5.2 - - - +
119B HIS* 2.9 34.6 + - + -
121B VAL* 3.6 13.9 - - + -
269B Y0R 3.2 17.3 + - - -
1260B ZN 2.1 36.5 - - - -
1261B GOL 3.6 35.3 - - - +
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Residues in contact with LEU 95 (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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69B SER* 2.6 25.9 + - - -
70B VAL* 3.6 14.9 + - + +
93B LEU* 5.4 3.4 - - + -
94B HIS* 1.3 78.6 - - - +
96B HIS* 1.3 71.2 + - - +
97B TRP* 3.4 21.3 - - + -
117B GLU 3.3 4.7 - - - +
118B ILE* 3.5 39.3 - - + -
147B LEU* 4.2 9.0 - - + -
157B TYR* 4.2 17.0 - - + -
160B LEU* 5.0 17.0 - - + -
161B LEU* 5.3 5.4 - - + -
227B LEU* 3.9 27.6 - - + -
242B ASN* 3.4 4.7 + - - -
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Residues in contact with HIS 96 (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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11B TYR* 3.8 12.3 - - - -
68B HIS 5.4 0.7 - - - -
69B SER* 5.4 0.2 - - - -
94B HIS* 3.3 9.8 - + - -
95B LEU* 1.3 80.1 + - - +
97B TRP* 1.3 62.8 + - - +
104B GLY 3.6 8.5 - - - +
106B GLU* 3.3 30.4 + - + -
116B ALA* 3.2 7.3 - - - +
117B GLU* 2.9 36.8 + - + +
119B HIS* 3.2 20.4 + + - -
200B THR* 4.1 1.3 - - - -
201B THR* 5.1 0.2 - - + -
242B ASN* 2.7 31.3 + - - +
269B Y0R 3.8 4.7 - - - -
1260B ZN 2.1 35.6 - - - -
1261B GOL 4.6 8.1 - - - -
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Residues in contact with TRP 97 (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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69B SER* 3.9 6.7 - - - -
70B VAL* 3.8 20.4 - - + -
95B LEU* 3.4 35.7 - - + -
96B HIS* 1.3 76.4 - - - +
98B GLY* 1.3 68.8 + - - +
104B GLY* 3.5 13.5 + - - +
115B PRO 3.9 5.6 - - - +
116B ALA* 4.0 4.3 - - + -
227B LEU* 3.6 47.1 - - + -
228B SER* 3.4 28.0 - - - +
231B LEU* 3.9 17.3 - - + -
239B LEU* 2.8 44.4 + - + -
240B GLN* 3.8 1.0 - - - +
241B LEU* 3.2 13.0 + - - -
242B ASN* 2.9 36.1 + - - +
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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