Contacts of the strand formed by residues 89 - 99 (chain C) in PDB entry 4FPR
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 89 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135B MET* 4.1 26.5 - - + +
136B LYS* 3.9 8.8 - - + +
30C GLU* 3.4 20.9 - - - +
31C ILE 3.8 1.6 - - - -
32C ARG* 3.1 29.6 - - + +
76C CYS* 3.6 0.7 - - - -
77C ALA* 3.2 32.9 + - + +
87C VAL* 3.5 16.9 + - + +
88C VAL* 1.3 74.4 - - - +
90C CYS* 1.3 62.9 + - - +
123C THR* 3.5 31.0 - - + +
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Residues in contact with CYS 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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136B LYS* 5.1 0.2 - - - -
30C GLU* 3.2 9.0 - - - +
31C ILE* 2.8 48.3 + - + +
33C TYR* 3.6 28.7 - - + +
39C PRO* 4.9 0.9 - - - -
44C ALA* 4.0 5.2 - - + +
74C VAL* 3.9 10.8 - - + -
75C GLN 3.3 3.8 - - - +
76C CYS* 2.0 46.0 - - - -
88C VAL* 4.2 4.0 - - - -
89C LEU* 1.3 77.0 - - - +
91C THR* 1.3 61.1 + - - +
92C CYS* 3.8 1.0 + - + -
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Residues in contact with THR 91 (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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136B LYS* 2.8 41.2 + - - +
28C SER* 4.6 7.2 - - - +
29C GLY 3.5 8.5 - - - +
30C GLU* 4.7 4.0 + - - +
73C LYS 4.1 0.2 - - - +
74C VAL* 3.2 7.4 - - - +
75C GLN* 2.8 36.8 + - + +
89C LEU 4.2 0.6 + - - -
90C CYS* 1.3 70.6 - - - +
92C CYS* 1.3 69.0 + - - +
93C LYS* 5.0 4.2 - - + +
122C GLU* 3.8 23.3 + - - +
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Residues in contact with CYS 92 (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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27C ILE 3.9 0.3 - - - +
28C SER* 3.3 5.0 - - - -
29C GLY 2.8 36.2 + - - +
31C ILE* 4.4 12.8 - - + -
48C CYS* 2.0 57.7 - - + -
51C VAL* 4.2 4.7 - - - -
73C LYS 3.8 1.3 - - - -
74C VAL* 4.4 2.7 - - + -
90C CYS* 3.8 1.5 + - + +
91C THR* 1.3 74.9 - - - +
93C LYS* 1.3 59.2 - - - +
94C ILE* 3.3 24.0 - - - -
119C PHE* 4.2 12.0 - - + -
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Residues in contact with LYS 93 (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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26C SER* 3.6 30.4 - - - +
27C ILE 3.5 4.3 - - - +
28C SER* 3.5 19.1 - - - +
71C THR 3.8 0.9 - - - +
72C ALA* 3.6 1.9 - - - -
73C LYS* 3.1 48.4 + - + +
91C THR* 5.2 5.6 - - + +
92C CYS* 1.3 76.4 - - - +
94C ILE* 1.3 64.6 + - - +
95C THR* 4.0 7.0 + - - +
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Residues in contact with ILE 94 (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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26C SER* 3.1 5.0 + - - -
27C ILE* 2.9 40.9 + - + +
48C CYS* 3.9 3.6 - - - -
51C VAL* 3.5 23.8 - - + -
52C THR* 3.5 23.3 - - + +
55C LEU* 4.2 8.3 - - + -
70C MET* 4.0 36.6 - - + -
71C THR 3.5 5.4 - - - +
72C ALA* 4.4 2.7 - - + -
92C CYS* 3.3 33.7 - - - -
93C LYS* 1.3 75.6 - - - +
95C THR* 1.3 65.6 + - - +
96C ALA 4.1 0.5 + - - -
119C PHE* 4.3 8.1 - - + -
131C TRP* 4.2 3.8 - - + -
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Residues in contact with THR 95 (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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24C GLU* 3.7 26.9 + - + +
25C ALA 3.3 10.1 - - - +
26C SER* 2.6 16.6 + - - +
70C MET* 3.3 3.8 - - - -
71C THR* 2.9 35.1 + - - -
73C LYS* 6.0 3.3 - - - +
93C LYS* 4.0 10.1 + - - +
94C ILE* 1.3 75.5 - - - +
96C ALA* 1.3 62.3 + - - +
97C HIS* 3.5 29.1 - - + +
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Residues in contact with ALA 96 (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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23C ARG 3.9 1.4 - - - +
24C GLU* 3.5 4.9 - - - +
25C ALA 2.5 38.1 + - - +
66C TRP 3.6 22.4 - - - +
69C ASP 3.7 4.0 - - - -
70C MET* 4.1 8.7 - - + -
94C ILE 4.1 1.0 + - - -
95C THR* 1.3 72.5 - - - +
97C HIS* 1.3 61.0 + - - +
98C ARG 3.6 0.9 - - - -
99C TYR* 4.3 11.9 - - + -
131C TRP* 3.7 28.3 - - + -
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Residues in contact with HIS 97 (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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23C ARG 3.5 2.0 - - - +
24C GLU* 4.5 10.3 + - - +
69C ASP* 2.9 43.6 + - + +
70C MET* 4.2 0.7 - - - -
71C THR* 2.7 28.3 + - - -
95C THR* 3.5 28.0 + - + +
96C ALA* 1.3 74.5 - - - +
98C ARG* 1.3 63.2 + - + +
99C TYR 3.7 0.7 - - - -
140C ARG* 2.8 40.5 + - - +
41D LYS* 3.4 44.4 - - + +
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Residues in contact with ARG 98 (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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22C CYS* 3.5 14.7 - - + -
66C TRP 4.2 5.0 + - - -
67C GLY* 3.6 23.1 + - - -
68C ILE 5.8 0.4 - - - +
69C ASP* 4.4 18.0 + - + +
97C HIS* 1.3 88.9 - - + +
99C TYR* 1.3 61.9 + - - +
100C ARG* 3.8 3.1 + - - +
140C ARG* 4.3 8.8 - - + +
141C GLY* 2.9 46.2 + - - +
142C CYS 3.9 13.2 - - - +
143C ASP 3.3 24.1 + - - -
144C HIS* 3.1 45.7 + - - +
145C HIS 5.2 0.8 - - - +
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Residues in contact with TYR 99 (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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22C CYS* 3.0 18.6 - - - +
23C ARG 3.0 28.0 + - - +
25C ALA* 3.5 26.7 - - + -
65C ALA 4.2 0.2 - - - -
66C TRP* 3.4 46.7 + + + -
96C ALA* 4.2 8.5 - - + +
98C ARG* 1.3 74.9 - - - +
100C ARG* 1.3 74.7 + - - +
101C GLU* 3.4 20.8 + - + -
103C VAL 5.5 1.3 + - - -
105C LYS* 4.5 22.5 - - - +
106C ILE 5.0 0.2 + - - -
131C TRP* 3.7 35.4 - + + +
133C VAL* 3.8 19.5 - - + +
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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