Contacts of the strand formed by residues 83 - 93 (chain B) in PDB entry 5FLM
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 83 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67B LEU 3.4 11.2 - - - +
68B GLN* 4.7 9.5 + - + +
81B PRO 4.7 4.0 - - - +
82B PRO* 1.3 76.0 - - - +
84B TYR* 1.3 75.6 + - - +
85B LEU* 5.2 10.0 - - + +
131B THR 4.2 1.3 - - - -
132B VAL* 3.2 2.1 - - - -
133B ILE* 2.9 68.8 + - + +
135B GLU* 5.3 5.4 + - - +
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Residues in contact with TYR 84 (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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65B ILE* 3.5 2.4 - - - +
67B LEU* 2.9 56.3 + - + +
68B GLN 5.1 2.7 - - - -
82B PRO* 4.3 25.1 - - + +
83B ARG* 1.3 82.4 - - - +
85B LEU* 1.3 61.9 + - - +
86B LEU* 5.4 3.8 - - + -
130B LYS* 4.8 9.6 - - + -
131B THR 3.4 2.0 - - - -
132B VAL* 3.4 31.6 - - + -
423B ILE* 3.4 54.3 - - + -
426B GLY* 4.5 11.7 + - - -
427B LYS 5.1 0.2 + - - -
428B ASP* 4.5 16.2 + - - -
429B PHE* 4.9 12.3 - - + -
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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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64B PRO* 6.0 3.1 - - + -
65B ILE 3.0 7.4 - - - +
66B ASP* 3.1 37.7 - - + +
67B LEU 4.3 3.4 - - - +
83B ARG* 5.2 11.4 - - + +
84B TYR* 1.3 79.1 - - - +
86B LEU* 1.3 65.8 + - - +
129B THR 3.9 0.7 - - - +
130B LYS* 3.5 5.2 - - - +
131B THR* 2.9 53.2 + - + +
133B ILE* 4.8 14.6 - - + -
139B GLN* 5.5 2.2 - - - +
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Residues in contact with LEU 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B PRO* 3.5 7.7 - - - +
65B ILE* 2.9 69.1 + - + +
67B LEU* 6.3 2.9 - - + -
84B TYR* 5.4 4.3 - - + -
85B LEU* 1.3 85.2 - - - +
87B LYS* 1.3 61.2 + - - +
88B PHE* 5.1 7.2 - - + -
128B ILE* 4.4 8.3 - - + -
129B THR 3.6 2.5 - - - +
130B LYS* 3.7 24.7 - - + -
415B VAL* 4.1 15.0 - - + -
419B ALA* 6.0 1.1 - - + -
429B PHE* 4.4 9.6 - - + -
431B LEU* 3.6 34.1 - - + -
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Residues in contact with LYS 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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64B PRO* 5.0 18.6 - - + -
86B LEU* 1.3 75.1 - - - +
88B PHE* 1.3 77.7 + - - +
89B GLU* 5.6 2.7 - - - +
128B ILE* 3.5 4.9 - - - +
129B THR* 2.9 48.8 + - - +
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Residues in contact with PHE 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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56B GLN* 5.3 1.2 + - - -
59B VAL* 3.7 37.7 - - + +
60B GLU* 5.2 7.6 - - - +
62B ALA* 5.7 3.4 - - + -
63B PRO 5.8 3.6 - - - -
64B PRO* 6.3 1.1 - - + -
65B ILE* 4.4 15.3 - - + -
86B LEU* 5.1 6.7 - - + -
87B LYS* 1.3 88.5 - - - +
89B GLU* 1.3 64.9 + - - +
90B GLN 3.6 0.7 - - - -
126B VAL* 3.5 22.9 - - + -
127B ASP 3.4 2.2 - - - -
128B ILE* 3.6 34.3 - - + -
149B ILE* 5.3 7.4 - - + -
408B PHE* 4.5 13.9 - + - -
411B LEU* 6.1 3.1 - - + -
412B LEU* 3.6 33.0 - - + -
415B VAL* 6.3 2.2 - - + -
435B ILE* 5.6 2.7 - - + -
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Residues in contact with GLU 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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56B GLN* 4.1 8.5 + - - -
87B LYS* 3.9 5.2 + - - +
88B PHE* 1.3 74.8 - - - +
90B GLN* 1.3 72.7 + - + +
127B ASP* 2.9 39.6 + - + +
129B THR* 4.5 19.4 - - + +
143B GLN* 4.9 5.5 - - - +
145B GLN* 3.9 7.0 - - - +
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Residues in contact with GLN 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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56B GLN* 3.7 19.3 - - - +
59B VAL* 5.7 1.0 - - - +
88B PHE 3.6 1.2 - - - -
89B GLU* 1.3 94.4 - - + +
91B ILE* 1.3 72.6 + - - +
92B TYR* 3.0 42.8 + - + +
125B TYR 4.1 0.2 - - - +
126B VAL* 3.3 7.7 - - - +
127B ASP* 3.0 29.2 + - - +
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Residues in contact with ILE 91 (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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51B ILE 5.9 2.0 - - - +
55B VAL* 3.5 24.7 - - + -
56B GLN* 3.2 34.9 - - + +
59B VAL* 3.8 14.6 - - + -
90B GLN* 1.3 80.4 + - - +
92B TYR* 1.3 76.5 + - - +
93B LEU* 5.9 0.4 - - + -
124B LEU* 3.4 34.3 - - + -
125B TYR 3.3 11.0 - - - +
126B VAL* 3.6 18.4 - - + -
149B ILE* 4.6 0.2 - - + -
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Residues in contact with TYR 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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90B GLN* 3.0 48.1 + - + +
91B ILE* 1.3 83.4 - - - +
93B LEU* 1.3 64.6 + - - +
123B PRO 4.0 1.2 - - - +
124B LEU* 4.0 4.2 - - - +
125B TYR* 2.8 42.3 + - + +
127B ASP* 3.9 26.6 + - - -
145B GLN* 5.0 4.8 + - - -
146B LYS* 3.2 39.5 - - + +
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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
----------------------------------------------------------
51B ILE* 3.5 48.2 - - + -
55B VAL* 6.4 0.4 - - + -
91B ILE* 5.9 0.2 - - + -
92B TYR* 1.3 75.4 - - - +
94B SER* 1.3 61.7 + - - +
122B ALA* 4.0 17.9 - - + +
123B PRO 3.2 21.8 - - - +
124B LEU* 3.5 27.6 - - + -
125B TYR* 6.1 0.4 - - - -
152B ILE* 5.0 11.9 - - + -
154B ILE* 5.3 4.3 - - + -
160B TYR* 4.6 22.9 - - + -
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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