Contacts of the strand formed by residues 97 - 104 (chain I) in PDB entry 3FFC
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 97 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9I PRO 5.4 2.9 - - - +
42I TYR 4.0 0.2 - - - +
43I LYS* 3.5 2.3 - - - -
44I GLN* 2.7 47.8 + - + +
96I ALA* 1.3 72.4 - - - +
98I TYR* 1.3 60.4 + - - +
99I PHE* 3.9 22.1 + - + -
114I THR 4.9 4.0 - - - +
115I GLY* 3.7 22.9 - - - +
116I THR 3.6 7.4 - - - -
117I SER* 3.4 39.5 - - - +
47J GLY* 5.7 7.9 - - - +
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Residues in contact with TYR 98 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I GLN* 3.3 5.0 + - - -
21I LEU* 3.8 13.0 - - + -
41I TRP* 4.0 15.5 - + + -
42I TYR 3.5 3.8 - - - -
43I LYS* 3.6 33.7 - - + +
53I VAL* 5.2 1.1 - - + -
72I TYR* 4.9 7.5 - + - -
85I LEU* 4.1 20.0 - - + -
87I ILE* 3.7 18.3 - - + +
94I ASP* 3.2 38.6 + - - +
96I ALA* 3.3 29.3 - - + +
97I MET* 1.3 76.6 - - - +
99I PHE* 1.3 62.3 + - - +
115I GLY* 3.2 4.0 - - - -
116I THR 2.7 45.6 + - - +
118I LEU* 3.7 18.4 - - + -
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Residues in contact with PHE 99 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6I GLN* 3.5 0.9 - - - -
40I PHE 3.8 0.5 - - - +
41I TRP* 3.3 9.1 - - - -
42I TYR* 2.7 45.0 + - + +
44I GLN* 3.2 25.4 - - + -
50I MET* 4.0 16.4 - - + -
97I MET* 3.9 27.1 - - + -
98I TYR* 1.3 73.2 - - - +
100I CYS* 1.3 60.7 + - - +
112I PHE* 3.9 22.0 - + + -
113I GLY 3.2 18.6 - - - +
114I THR 3.5 20.9 - - - -
115I GLY* 3.6 9.2 - - - -
44J GLN* 3.5 17.7 - - - -
47J GLY 6.1 0.2 - - - -
48J GLN 3.7 3.8 - - - -
49J GLY* 3.3 24.7 - - - -
50J PRO* 4.6 0.7 - - + -
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Residues in contact with CYS 100 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I ILE* 3.7 9.9 - - + +
6I GLN* 2.8 21.8 + - - +
23I CYS* 2.0 49.4 - - + -
39I LEU* 4.3 9.9 - - - -
40I PHE 3.6 2.2 - - - -
41I TRP* 3.5 25.8 - - + -
83I ALA 4.0 0.9 - - - -
99I PHE* 1.3 73.5 - - - +
101I ALA* 1.3 61.3 + - - +
111I TYR 3.6 1.2 - - - +
112I PHE* 3.4 1.7 - - - -
113I GLY 2.7 31.4 + - - -
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Residues in contact with ALA 101 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I ILE* 4.2 3.8 - - - -
39I LEU* 3.4 4.4 - - - +
40I PHE* 2.7 55.1 + - + +
42I TYR* 4.5 0.4 - - + -
100I CYS* 1.3 76.4 - - - +
102I MET* 1.3 59.3 + - - +
110I PHE* 4.3 7.6 - - + -
111I TYR 3.0 11.4 - - - +
112I PHE* 3.7 35.7 - - + -
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Residues in contact with MET 102 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3I LYS 4.1 18.8 - - - +
4I ILE* 3.6 17.4 - - + +
25I TYR* 4.3 16.4 - - - -
26I ASP 4.1 4.9 - - - +
27I THR* 3.8 26.2 - - - -
32I TYR* 4.6 6.1 - - + -
33I GLY 3.4 11.9 - - - +
39I LEU* 4.0 9.2 - - + -
40I PHE* 4.9 0.7 - - - -
101I ALA* 1.3 74.2 - - - +
103I ARG* 1.3 66.5 + - - +
104I GLU* 3.4 34.1 - - + +
110I PHE* 3.5 4.0 - - - -
111I TYR* 2.9 60.9 + - + +
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Residues in contact with ARG 103 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31I SER* 4.5 2.2 + - - -
32I TYR* 3.3 30.3 + - - +
33I GLY* 2.7 42.5 + - - +
40I PHE* 3.7 11.5 - - + -
55I TYR* 4.7 1.8 + - - -
102I MET* 1.3 73.2 - - - +
104I GLU* 1.3 62.5 + - - +
105I ASP* 2.4 42.8 + - - +
109I GLN 4.5 5.6 - - - +
110I PHE* 3.5 30.1 - - + -
110J TRP 3.9 15.1 + - - +
111J THR* 4.9 4.4 + - - +
113J GLY* 3.5 29.3 + - - +
117J ASP* 3.3 31.4 + - - +
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Residues in contact with GLU 104 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26I ASP 4.1 1.4 - - - +
27I THR* 3.0 47.9 + - - +
29I ASP* 3.5 13.5 - - - +
32I TYR* 3.8 9.9 - - + -
102I MET* 3.4 22.3 + - + +
103I ARG* 1.3 79.2 - - - +
105I ASP* 1.3 55.8 + - - +
106I THR* 3.0 16.6 - - - +
107I GLY* 2.4 49.2 + - - +
109I GLN 5.1 2.2 + - - -
111I TYR* 4.1 11.7 + - + -
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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