Contacts of the strand formed by residues 100 - 107 (chain J) 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 ALA 100 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43J GLN* 3.8 24.9 - - + +
44J GLN 3.3 17.7 - - - +
45J ILE* 4.0 8.1 - - + +
46J LEU 5.3 1.8 - - - +
98J ASP 3.0 10.7 + - - +
99J SER* 1.3 76.8 - - - +
101J VAL* 1.3 66.2 + - - +
102J TYR* 3.8 3.3 - - + -
125J THR 3.8 0.3 - - - +
126J ARG* 3.9 4.0 - - - +
127J LEU* 2.9 32.6 + - - +
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Residues in contact with VAL 101 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44I GLN* 6.0 0.2 - - - +
48I GLY 5.3 3.8 - - - +
43J GLN* 3.6 1.9 - - - -
44J GLN* 2.7 53.0 + - + +
100J ALA* 1.3 76.4 - - - +
102J TYR* 1.3 64.2 + - - +
103J LEU* 3.8 29.5 + - + -
123J PRO 5.1 1.3 - - - +
124J GLY* 4.0 2.9 - - - -
125J THR 3.2 17.3 - - - +
126J ARG* 3.9 31.0 - - + -
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Residues in contact with TYR 102 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6J GLN* 3.0 22.1 + - - -
21J PHE* 3.6 28.0 - + + -
41J TRP* 4.6 4.7 - - + -
42J TYR 3.3 13.0 - - - +
43J GLN* 2.8 37.0 + - + -
53J LEU* 3.9 3.4 - - + -
76J PHE* 3.6 23.8 - + - -
89J LEU* 3.9 23.1 - - + -
91J ILE* 4.0 6.5 - - + -
98J ASP* 2.6 36.1 + - - +
100J ALA 3.8 14.6 - - - -
101J VAL* 1.3 73.2 - - - +
103J LEU* 1.3 61.0 + - - +
125J THR 2.8 27.6 + - - +
127J LEU* 3.9 14.8 - - + -
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Residues in contact with LEU 103 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44I GLN* 5.0 0.2 - - - +
48I GLY 4.0 17.7 - - - +
50I MET* 3.8 25.8 - - + +
6J GLN* 3.6 3.4 - - - -
41J TRP* 3.6 3.4 - - - -
42J TYR* 2.6 42.1 + - + +
44J GLN* 3.8 25.1 - - + +
50J PRO* 3.9 21.3 - - + -
101J VAL* 3.8 14.3 + - + +
102J TYR* 1.3 74.6 - - - +
104J CYS* 1.3 57.0 + - - +
121J PHE* 3.7 17.0 - - + -
122J GLY 4.0 12.6 - - - +
124J GLY* 3.7 20.2 - - - -
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Residues in contact with CYS 104 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J VAL* 3.3 17.5 - - - -
6J GLN* 3.0 17.4 + - - +
23J CYS* 2.0 54.1 - - + -
39J LEU* 4.8 0.4 - - + -
40J TYR 3.1 12.8 - - - +
41J TRP* 3.6 15.9 - - + -
42J TYR* 5.2 0.2 - - - -
103J LEU* 1.3 75.9 - - - +
105J ALA* 1.3 61.1 + - - +
121J PHE* 3.4 4.8 - - - +
122J GLY 2.9 25.5 + - - -
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Residues in contact with ALA 105 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J VAL* 4.6 2.9 - - - -
23J CYS* 5.5 0.2 - - - -
39J LEU* 3.3 6.5 - - - +
40J TYR* 2.8 45.9 + - + -
42J TYR* 4.3 3.4 - - + -
104J CYS* 1.3 79.5 - - - +
106J SER* 1.3 61.2 + - - +
119J GLN* 4.1 11.4 - - + +
120J TYR 3.1 16.8 - - - +
121J PHE* 3.8 23.1 - - + -
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Residues in contact with SER 106 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4J VAL* 3.4 8.9 - - - +
25J PRO* 3.4 26.2 - - - -
26J ILE* 2.9 17.5 + - - +
29J HIS* 2.9 28.9 - - - -
31J THR 3.3 12.6 - - - -
39J LEU* 4.8 0.2 - - - -
40J TYR* 4.3 2.9 - - - -
105J ALA* 1.3 74.8 - - - +
107J SER* 1.3 61.1 + - - +
120J TYR* 2.9 34.1 + - - +
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Residues in contact with SER 107 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29J HIS* 3.3 19.1 - - - +
31J THR* 3.0 34.2 + - - +
40J TYR* 2.7 32.9 + - - -
106J SER* 1.3 74.0 - - - +
108J PHE* 1.3 60.2 + - - +
109J THR 2.9 15.8 + - - -
116J THR 4.0 1.1 - - - -
117J ASP 3.9 3.6 - - - -
118J THR 3.3 22.4 - - - -
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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