Contacts of the strand formed by residues 78 - 90 (chain C) in PDB entry 5FJV
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 MET 78 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71C ASP 4.4 0.2 - - - +
72C VAL* 4.2 3.2 - - - +
73C ASP* 3.3 30.9 + - + +
76C ASN* 2.7 32.8 + - + +
77C GLN* 1.3 76.8 - - - +
79C MET* 1.3 65.2 + - - +
80C THR* 5.3 3.8 - - - +
124C ASN* 4.2 16.4 - - - +
126C ASP* 4.5 6.1 - - - +
154C LYS* 4.3 24.9 - - - -
155C SER 3.1 17.7 - - - +
156C SER* 4.3 3.8 - - - +
157C CYS* 4.9 1.6 - - - -
70D ILE* 4.3 17.7 - - + +
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Residues in contact with MET 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C LEU* 4.8 13.2 - - + -
71C ASP 3.8 6.7 - - - +
72C VAL* 5.0 4.0 - - + +
78C MET* 1.3 76.2 - - - +
80C THR* 1.3 67.5 + - - +
81C THR* 3.7 26.5 + - + -
153C TYR 3.5 1.4 - - - +
154C LYS* 3.3 3.7 - - - -
155C SER* 2.6 64.7 + - - +
157C CYS* 4.4 9.0 - - + -
171C CYS* 3.5 34.3 - - + +
173C MET* 4.3 16.2 - - + -
207C ILE* 6.3 1.8 - - - -
233C PHE* 4.9 11.4 - - + -
235C ILE* 5.0 10.8 - - + -
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Residues in contact with THR 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B ASP* 3.6 20.5 + - - +
69C LEU* 3.8 3.8 - - - +
70C ILE* 2.9 56.4 + - + -
71C ASP* 3.0 31.4 + - - +
78C MET* 5.3 4.0 - - - +
79C MET* 1.3 75.0 - - - +
81C THR* 1.3 64.5 + - - +
152C ILE* 4.0 5.6 - - + -
153C TYR 3.2 7.9 - - - +
154C LYS* 3.8 17.2 - - + +
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Residues in contact with THR 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C ILE* 3.9 22.0 - - + -
68C GLN 3.7 4.5 - - - +
69C LEU* 5.0 3.6 - - + -
70C ILE* 3.7 5.5 - - - +
79C MET* 3.7 32.3 + - + +
80C THR* 1.3 80.0 - - - +
82C ASN* 1.3 61.2 + - - +
83C VAL* 3.4 17.1 + - - +
151C ALA 3.6 0.9 - - - +
152C ILE* 3.5 4.7 - - - -
153C TYR* 2.8 48.7 + - - +
173C MET* 3.6 13.0 - - - +
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Residues in contact with ASN 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B TYR 3.3 10.9 + - - +
123B ASN* 2.3 38.7 + - - +
129B PHE* 4.0 10.9 - - - -
66C ILE 4.0 0.2 - - - -
67C ALA* 3.0 27.9 + - - +
68C GLN* 2.9 23.7 + - + +
70C ILE* 3.7 16.5 - - + +
81C THR* 1.3 71.1 - - - +
83C VAL* 1.3 67.1 + - - +
84C TRP* 3.8 17.5 + - - -
151C ALA 3.3 6.1 - - - +
152C ILE* 3.7 13.7 - - - +
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Residues in contact with VAL 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C LEU* 3.8 16.4 - - + -
65C SER 3.3 11.9 - - - +
66C ILE* 4.9 5.4 - - + -
81C THR* 3.4 32.5 - - + +
82C ASN* 1.3 78.4 - - - +
84C TRP* 1.3 70.2 + - - +
85C LEU* 3.5 27.4 - - + -
150C PRO* 3.4 0.3 - - - +
151C ALA* 2.9 35.7 + - + -
153C TYR* 3.6 20.9 - - + -
173C MET* 4.9 5.6 - - - -
175C PHE* 4.9 1.3 - - + -
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Residues in contact with TRP 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B TYR* 4.0 15.4 + + - -
174B LYS* 5.2 0.9 - - - -
178B TRP* 3.3 37.6 - + - -
219B TYR* 4.2 5.2 - + - -
221B CYS* 4.7 4.9 - - - -
300B EPJ 3.4 31.0 - - + -
64C LEU* 4.1 0.7 - - - -
65C SER* 2.8 39.7 + - - -
67C ALA* 3.6 25.5 - - + +
82C ASN* 3.8 9.6 + - - -
83C VAL* 1.3 85.8 - - - +
85C LEU* 1.3 63.1 + - - +
86C LYS* 3.3 5.2 + - + -
148C VAL* 4.2 17.7 - - + +
149C PRO 3.5 4.7 - - - +
150C PRO* 4.1 3.8 - - + +
199C TYR* 3.0 64.6 - + + -
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Residues in contact with LEU 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C PHE* 3.7 30.1 - - + -
63C GLY 3.9 3.6 - - - -
64C LEU* 5.2 2.9 - - + +
83C VAL* 3.5 27.4 - - + -
84C TRP* 1.3 69.5 - - - +
86C LYS* 1.3 64.8 + - - +
87C GLN* 3.3 17.0 + - - +
119C ILE* 4.1 15.7 - - + +
131C VAL* 6.2 4.9 - - + -
147C TRP 3.3 12.8 - - - +
148C VAL* 3.5 2.5 - - - -
149C PRO* 3.0 28.0 + - + +
151C ALA* 4.3 8.3 - - + -
153C TYR* 3.8 20.2 - - + +
175C PHE* 4.0 21.3 - - + -
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Residues in contact with LYS 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B CYS* 4.0 11.2 - - + +
61C ARG 3.4 2.6 - - - +
62C PHE* 3.3 7.6 - - - -
63C GLY* 2.9 56.2 + - - +
64C LEU 4.0 2.7 + - - +
65C SER* 3.2 24.3 + - - +
84C TRP* 4.1 4.7 - - + +
85C LEU* 1.3 68.9 - - - +
87C GLN* 1.3 60.2 + - - +
147C TRP 4.0 2.5 - - - -
148C VAL* 4.3 20.0 - - + -
190C MET* 3.6 29.1 - - + +
191C GLU 4.6 1.8 + - - -
192C GLN* 6.2 0.2 - - - +
194C VAL* 3.1 49.2 + - + +
196C LEU* 5.9 0.4 - - - +
199C TYR* 3.9 3.1 - - - +
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Residues in contact with GLN 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C VAL* 4.2 5.2 - - + -
61C ARG 3.2 5.8 - - - +
62C PHE* 3.8 16.8 - - + -
85C LEU* 3.4 28.8 + - - +
86C LYS* 1.3 79.8 - - - +
88C GLU* 1.3 63.4 + - - +
89C TRP* 3.5 16.4 - - + -
117C PRO* 3.5 16.9 - - - +
119C ILE* 3.3 29.3 - - + +
146C HIS* 3.4 2.6 - - - +
147C TRP* 2.8 58.0 + - - +
148C VAL* 4.6 1.8 - - - +
149C PRO* 3.9 7.9 - - - +
190C MET* 4.1 1.6 - - - -
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Residues in contact with GLU 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C ILE 4.2 0.2 - - - +
61C ARG* 2.7 81.4 + - + +
87C GLN* 1.3 75.8 - - - +
89C TRP* 1.3 62.1 + - - +
144C THR* 6.4 0.7 - - - -
145C VAL 2.9 15.0 - - - +
146C HIS* 2.6 41.0 + - + +
190C MET* 3.2 16.3 - - + +
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Residues in contact with TRP 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C PRO* 4.8 6.2 - - + +
58C VAL* 4.7 4.7 - - + -
59C ILE 3.6 18.6 - - - +
60C VAL* 3.6 22.9 - - + -
87C GLN* 3.5 25.8 - - + -
88C GLU* 1.3 82.0 - - - +
90C SER* 1.3 71.5 + - - +
91C ASP* 4.4 3.5 - - - +
114C ILE* 4.1 2.2 - - + +
115C TRP* 3.8 40.0 + + - -
116C ILE* 3.8 9.4 - - + -
117C PRO* 3.5 22.9 - - + -
144C THR* 3.3 7.5 - - - -
145C VAL* 2.7 58.3 + - + +
147C TRP* 3.6 31.2 - + + -
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Residues in contact with SER 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C PRO* 3.7 13.3 - - - +
58C VAL* 5.1 5.8 - - - +
59C ILE 4.6 2.6 + - - -
89C TRP* 1.3 84.0 - - - +
91C ASP* 1.3 60.5 + - - +
92C TYR* 4.6 4.5 + - - +
142C THR 6.0 0.4 - - - -
143C GLY 3.6 6.3 - - - -
144C THR* 4.2 12.8 - - - +
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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