Contacts of the strand formed by residues 81 - 89 (chain B) in PDB entry 3FFN
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 81 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B GLY 3.7 22.0 - - - +
37B LYS 3.7 18.6 - - - +
39B PRO* 4.5 11.7 - - + -
73B THR* 3.9 18.4 - - + -
74B VAL 3.5 1.6 - - - -
75B GLN* 4.1 24.0 - - + +
76B LEU* 4.8 0.9 - - - -
79B GLY 4.3 6.7 - - - +
80B ASN* 1.3 82.1 - - - +
82B GLN* 1.3 55.6 + - - +
83B TYR* 3.8 17.7 - - - +
115B ARG* 2.6 36.5 + - - +
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Residues in contact with GLN 82 (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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72B LYS 3.6 1.0 - - - +
73B THR* 3.4 5.5 - - - -
74B VAL* 2.7 57.0 + - - +
76B LEU* 3.2 24.2 - - + +
81B LEU* 1.3 73.7 - - - +
83B TYR* 1.3 68.1 + - - +
84B ASP* 3.7 7.7 + - - +
115B ARG* 4.2 7.2 - - - +
117B VAL* 6.3 0.2 - - + -
381B SER 4.3 2.3 - - - +
382B TYR* 3.2 38.6 - - + -
383B LEU* 2.8 46.9 + - - -
385B SER* 5.2 0.8 - - - +
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Residues in contact with TYR 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B GLY* 2.7 30.1 + - - -
71B LEU* 3.9 18.4 - - + -
72B LYS 3.5 0.7 - - - -
73B THR* 3.4 36.8 - - + -
81B LEU* 3.8 26.9 - - + +
82B GLN* 1.3 80.0 - - - +
84B ASP* 1.3 66.1 + - - +
85B LEU 4.0 0.2 - - - -
112B LEU* 3.8 37.7 - - + +
115B ARG* 4.4 27.0 + - - +
116B ALA* 3.4 17.0 - - + -
117B VAL* 2.9 26.9 + - - +
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Residues in contact with ASP 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ILE 3.4 4.2 - - - +
71B LEU* 3.5 3.7 - - - +
72B LYS* 2.8 43.8 + - + +
74B VAL* 5.3 2.3 - - - +
82B GLN* 3.7 11.4 + - - +
83B TYR* 1.3 76.4 - - - +
85B LEU* 1.3 59.5 - - - +
86B HIS* 3.7 9.0 + - + +
117B VAL* 3.4 6.9 - - - +
119B HIS* 3.1 21.5 + - - +
129B THR* 4.7 2.2 - - - +
133B TYR* 3.6 23.5 + - - +
382B TYR* 2.6 37.9 + - - -
385B SER* 5.7 1.8 - - - -
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Residues in contact with LEU 85 (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 VAL* 4.1 15.7 - - + -
70B ILE 3.4 1.3 - - - +
71B LEU* 3.7 26.2 - - + -
83B TYR 4.0 0.8 - - - -
84B ASP* 1.3 71.4 - - - +
86B HIS* 1.3 60.6 + - - +
105B THR* 3.3 41.3 - - + +
108B LEU* 3.6 29.6 - - + -
109B ASP* 3.5 27.6 - - + +
112B LEU* 4.8 1.6 - - + -
116B ALA* 4.2 9.4 - - + +
117B VAL 2.7 12.9 + - - +
118B GLN* 3.2 5.2 - - + +
119B HIS* 2.8 26.3 + - - -
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Residues in contact with HIS 86 (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 VAL* 3.4 5.4 - - - +
70B ILE* 2.7 49.0 + - + +
84B ASP* 3.7 13.6 - - - +
85B LEU* 1.3 79.5 - - - +
87B TYR* 1.3 59.6 + - - +
105B THR* 4.7 2.7 - - - -
119B HIS* 3.2 29.6 - + - +
121B GLU* 2.8 36.3 + - + -
127B SER* 4.2 0.7 - - - -
129B THR* 3.6 21.1 - - + -
130B PHE* 3.7 19.6 - + + -
133B TYR* 2.8 36.6 + + - -
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Residues in contact with TYR 87 (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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68B TYR 3.3 12.3 - - - +
69B VAL* 4.4 1.8 - - + -
86B HIS* 1.3 74.7 - - - +
88B TRP* 1.3 55.0 + - - +
89B LEU* 3.8 21.5 - - + +
98B SER* 4.1 2.2 - - - -
101B ALA* 3.6 24.2 - - + +
102B ALA* 3.7 23.6 - - + +
105B THR* 3.4 30.5 - - + +
119B HIS 2.8 16.3 + - - +
120B ARG* 3.2 45.3 + - + +
121B GLU* 2.8 33.6 + - - +
332B LEU* 3.5 34.8 + - + +
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Residues in contact with TRP 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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62B PHE* 3.6 27.1 - + + -
63B PHE 3.5 21.1 - - - -
64B THR* 4.7 1.1 - - - -
66B ASP 4.0 2.5 - - - -
67B ALA* 3.2 5.2 - - - +
68B TYR* 3.0 44.5 + + + +
70B ILE* 4.0 18.8 - - + -
87B TYR* 1.3 73.2 - - - +
89B LEU* 1.3 61.1 + - - +
90B GLY* 3.3 28.3 - - - -
121B GLU* 3.2 20.9 - - + -
123B GLN* 3.6 25.0 - - + +
126B GLU* 2.8 25.4 + - - -
130B PHE* 3.8 23.3 - + + -
140B TYR* 3.5 28.8 - + - -
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Residues in contact with LEU 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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66B ASP 4.4 2.2 - - - -
67B ALA* 4.0 8.7 - - + -
87B TYR* 3.8 26.2 - - + +
88B TRP* 1.3 78.4 - - - +
90B GLY* 1.3 66.9 + - - +
93B CYS* 4.4 6.3 - - + -
98B SER* 3.3 39.9 - - - -
120B ARG* 3.7 36.6 - - + +
121B GLU 2.9 14.9 + - - +
122B VAL* 3.8 11.3 - - + +
123B GLN 3.0 24.1 + - - -
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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