Contacts of the strand formed by residues 97 - 104 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9D PRO 5.6 2.7 - - - +
42D TYR 4.0 0.2 - - - +
43D LYS* 3.4 2.6 - - - -
44D GLN* 2.6 44.1 + - + +
96D ALA* 1.3 73.9 - - - +
98D TYR* 1.3 59.4 + - - +
99D PHE* 4.0 21.5 + - + -
114D THR 4.8 3.8 - - - +
115D GLY* 3.9 22.4 - - - +
116D THR 3.7 6.5 - - - -
117D SER* 3.6 35.4 - - - +
47E GLY* 5.7 8.7 - - - +
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Residues in contact with TYR 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D GLN* 3.3 5.2 + - - -
21D LEU* 3.5 29.4 - - + -
41D TRP* 3.9 8.7 - + + -
42D TYR 3.4 5.6 - - - -
43D LYS* 3.3 37.1 - - + +
53D VAL* 5.1 2.9 - - + -
72D TYR* 4.1 9.8 + + - -
85D LEU* 3.7 19.7 - - + -
87D ILE* 3.7 20.5 - - + +
94D ASP* 3.3 34.6 + - - +
96D ALA* 3.2 28.9 - - + -
97D MET* 1.3 77.4 - - - +
99D PHE* 1.3 62.2 + - - +
115D GLY* 3.2 4.0 - - - -
116D THR 2.8 35.4 + - - -
118D LEU* 3.9 10.8 - - + -
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Residues in contact with PHE 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D GLN* 3.6 1.1 - - - -
40D PHE 3.8 0.3 - - - +
41D TRP* 3.3 8.8 - - - -
42D TYR* 2.7 45.7 + - + +
44D GLN* 3.3 24.2 - - + -
50D MET* 3.3 20.4 - - + -
97D MET* 4.0 26.5 - - + -
98D TYR* 1.3 75.0 - - - +
100D CYS* 1.3 61.6 + - - +
112D PHE* 3.8 21.1 - + + -
113D GLY 3.2 17.9 - - - -
114D THR 3.5 16.2 - - - -
115D GLY* 3.6 8.7 - - - -
44E GLN* 3.5 16.2 - - - -
47E GLY 6.1 0.2 - - - -
48E GLN 3.6 4.5 - - - -
49E GLY* 3.2 27.4 - - - -
50E PRO* 4.5 0.9 - - + -
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Residues in contact with CYS 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ILE* 3.8 11.1 - - + +
6D GLN* 3.1 19.0 + - - +
23D CYS* 2.0 52.7 - - + -
39D LEU* 4.2 12.1 - - - -
40D PHE 3.6 3.8 - - - -
41D TRP* 3.7 19.1 - - + -
83D ALA 4.2 0.7 - - - -
99D PHE* 1.3 73.1 - - - +
101D ALA* 1.3 60.6 + - - +
111D TYR 3.6 1.2 - - - +
112D PHE* 3.4 1.3 - - - -
113D GLY 2.7 27.5 + - - -
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Residues in contact with ALA 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D ILE* 4.2 3.1 - - - -
39D LEU* 3.4 4.5 - - - +
40D PHE* 2.7 51.0 + - + +
42D TYR* 4.7 0.2 - - + -
100D CYS* 1.3 76.2 - - - +
102D MET* 1.3 60.7 + - - +
110D PHE* 4.4 12.3 - - + -
111D TYR 3.0 12.1 - - - +
112D PHE* 3.7 35.9 - - + -
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Residues in contact with MET 102 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3D LYS 3.5 34.5 - - - +
4D ILE* 3.7 12.5 - - + +
25D TYR* 3.7 14.1 - - + -
26D ASP 3.6 18.4 - - - +
27D THR* 3.8 17.9 - - - -
32D TYR* 4.6 4.0 - - + -
33D GLY 3.5 12.6 - - - +
39D LEU* 3.9 19.1 - - + -
101D ALA* 1.3 73.8 - - - +
103D ARG* 1.3 60.9 + - - +
104D GLU* 3.7 30.3 - - + +
110D PHE* 3.5 3.9 - - - -
111D TYR* 2.8 45.8 + - + +
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Residues in contact with ARG 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ARG* 5.8 3.4 - - - +
31D SER* 4.6 2.0 + - - -
32D TYR* 3.2 28.8 + - - +
33D GLY* 2.7 40.2 + - - +
40D PHE* 3.6 23.6 - - + -
55D TYR* 5.0 1.6 + - - -
101D ALA 4.2 0.6 + - - -
102D MET* 1.3 73.1 - - - +
104D GLU* 1.3 62.4 + - - +
105D ASP* 2.4 45.8 + - - +
109D GLN 4.5 6.5 - - - +
110D PHE* 3.5 26.9 - - + +
110E TRP 3.8 21.8 - - - +
111E THR* 5.1 4.4 + - - +
113E GLY* 3.3 32.4 + - - +
117E ASP* 3.5 10.2 + - + +
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Residues in contact with GLU 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ARG* 5.6 0.3 + - - -
3D LYS 5.6 2.1 + - - -
26D ASP 4.2 2.3 - - - +
27D THR* 2.8 50.7 + - - +
29D ASP* 3.4 15.1 - - - +
32D TYR* 3.7 9.4 - - + -
102D MET* 3.7 16.8 - - - +
103D ARG* 1.3 78.1 - - - +
105D ASP* 1.3 56.3 + - - +
106D THR* 3.0 5.5 - - - +
107D GLY* 2.5 42.8 + - - +
109D GLN 5.0 1.8 + - - -
111D TYR* 3.7 29.9 + - + -
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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