Contacts of the strand formed by residues 31 - 44 (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 THR 31 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29J HIS* 4.2 2.3 - - - +
30J ALA* 1.3 81.5 - - - +
39J LEU* 1.3 64.4 + - - +
40J TYR* 3.6 16.8 - - + +
55J GLN* 3.6 28.5 - - + +
56J PHE 3.2 11.4 - - - +
57J GLN* 4.8 2.1 + - - +
80J ARG* 3.9 0.4 + - - -
106J SER* 3.3 9.2 - - - -
107J SER* 3.0 40.5 + - - +
108J PHE 3.1 17.5 + - - -
109J THR* 3.7 0.3 - - - -
110J TRP* 3.3 22.5 + - + -
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Residues in contact with LEU 39 (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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23J CYS* 3.9 15.7 - - - -
25J PRO* 3.7 23.3 - - + -
31J THR* 1.3 76.7 - - - +
40J TYR* 1.3 72.5 + - - +
41J TRP* 4.0 13.5 - - + +
55J GLN* 3.4 0.9 - - - -
56J PHE* 2.6 41.9 + - + +
80J ARG* 3.5 19.7 - - - +
85J VAL 3.5 24.9 - - - +
87J SER* 3.6 31.4 - - - +
105J ALA 3.3 9.6 - - - +
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Residues in contact with TYR 40 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109I GLN* 6.4 1.6 - - - -
110I PHE* 5.6 0.2 - - - -
31J THR* 3.6 9.9 - - + -
39J LEU* 1.3 75.9 - - - +
41J TRP* 1.3 60.8 - - - +
42J TYR* 3.7 12.1 - - + -
52J LEU* 3.7 19.7 - - + -
54J ILE 3.4 5.2 - - - -
55J GLN* 3.4 35.7 - - + +
104J CYS* 3.1 6.9 - - - +
105J ALA* 2.8 44.7 + - + +
107J SER* 2.7 38.3 + - - -
109J THR 3.5 9.9 + - - -
110J TRP* 3.5 12.0 - - + +
117J ASP 4.1 1.6 + - - -
119J GLN* 3.2 46.9 + - + +
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Residues in contact with TRP 41 (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* 3.8 14.6 - - - -
21J PHE* 3.6 44.0 - - + -
22J TRP 3.9 3.8 - - - -
23J CYS* 3.3 30.7 - - + -
39J LEU* 4.0 11.3 - - + +
40J TYR* 1.3 73.2 - - - +
42J TYR* 1.3 56.2 + - - +
52J LEU* 3.5 5.5 - - - +
53J LEU* 2.8 40.5 + - + +
54J ILE* 2.8 37.9 + - + -
56J PHE* 4.2 4.7 - + - -
78J ALA* 4.4 2.2 - - + -
87J SER* 3.0 26.5 + - - -
88J THR 4.3 0.8 - - - -
89J LEU* 3.6 34.0 - - + +
102J TYR* 4.4 7.9 - - + -
103J LEU 3.7 7.4 - - - -
104J CYS* 3.6 20.2 - - + -
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Residues in contact with TYR 42 (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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109I GLN* 5.7 0.2 - - - -
110I PHE* 3.7 16.7 + - - +
112I PHE* 3.9 15.7 - + - -
40J TYR* 3.7 18.3 - - + -
41J TRP* 1.3 76.8 - - - +
43J GLN* 1.3 60.5 + - - +
50J PRO* 3.5 26.9 - - + -
51J LYS 3.4 6.7 - - - -
52J LEU* 3.3 40.2 - - + +
53J LEU* 4.0 5.2 - - - +
102J TYR* 3.3 9.9 - - - +
103J LEU* 2.6 44.3 + - + +
105J ALA* 4.3 4.0 - - + -
119J GLN* 2.5 40.2 + - - -
121J PHE* 3.3 26.0 - + - -
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Residues in contact with GLN 43 (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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42J TYR* 1.3 74.3 - - - +
44J GLN* 1.3 64.2 + - - +
45J ILE* 3.9 24.4 + - + +
49J GLY 4.1 1.0 - - - +
50J PRO* 3.5 1.6 - - - +
51J LYS* 2.9 37.8 + - + +
53J LEU* 3.8 19.4 - - + +
72J PRO* 5.9 2.3 - - - +
76J PHE* 4.3 8.9 - - - -
97J GLU 4.4 2.6 + - - -
98J ASP* 4.0 10.3 + - - +
100J ALA* 3.8 15.0 - - + +
101J VAL 3.6 2.7 - - - -
102J TYR* 2.8 40.6 + - + -
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Residues in contact with GLN 44 (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* 2.8 43.5 + - - +
50I MET* 4.9 0.2 - - - -
99I PHE* 3.5 11.9 - - - -
43J GLN* 1.3 73.0 - - - +
45J ILE* 1.3 65.1 + - - +
46J LEU 3.9 0.5 + - - -
48J GLN 2.9 29.4 + - - +
49J GLY* 3.8 9.8 - - - -
50J PRO* 3.9 17.9 - - + +
100J ALA* 3.3 4.9 - - - +
101J VAL* 2.7 50.4 + - + +
103J LEU* 3.8 14.1 - - + +
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Residues in contact with ILE 45 (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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43J GLN* 3.9 28.6 + - - +
44J GLN* 1.3 82.9 - - - +
46J LEU* 1.3 78.1 + - + +
47J GLY 3.2 0.5 + - - -
48J GLN* 3.1 42.3 + - + +
49J GLY 5.1 0.2 + - - -
97J GLU* 4.3 15.9 - - + +
99J SER 4.5 5.8 - - - +
100J ALA* 4.0 11.7 - - + +
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Residues in contact with LEU 46 (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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44J GLN* 3.9 1.6 + - - -
45J ILE* 1.3 84.4 - - + +
47J GLY* 1.3 65.7 + - - +
48J GLN* 3.7 3.1 + - - +
99J SER 5.3 0.8 + - - -
100J ALA* 5.3 2.2 - - - +
126J ARG* 5.4 10.8 - - - +
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Residues in contact with GLY 47 (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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97I MET* 5.7 7.9 - - - +
99I PHE* 6.1 0.2 - - - -
114I THR* 3.7 19.3 - - - +
45J ILE 3.2 0.6 + - - -
46J LEU* 1.3 79.9 - - - +
48J GLN* 1.3 64.1 + - - +
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Residues in contact with GLN 48 (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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99I PHE* 3.7 10.2 - - - -
114I THR* 4.3 17.1 - - + +
44J GLN* 2.9 23.7 + - - +
45J ILE* 3.1 38.5 + - + +
46J LEU 4.1 6.3 - - - +
47J GLY* 1.3 86.1 + - - +
49J GLY* 1.3 67.3 - - - +
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Residues in contact with GLY 49 (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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99I PHE* 3.3 17.5 - - - -
112I PHE* 4.4 2.5 - - - -
113I GLY 3.7 14.9 + - - -
114I THR* 4.3 2.6 + - - +
43J GLN 4.1 3.3 - - - +
44J GLN* 4.0 5.2 - - - +
45J ILE 5.1 0.3 + - - -
48J GLN* 1.3 83.8 - - - +
50J PRO* 1.3 77.0 - - - +
51J LYS* 3.5 4.7 + - - +
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Residues in contact with PRO 50 (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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50I MET* 3.5 27.6 - - + -
99I PHE* 4.6 1.8 - - + -
110I PHE 5.0 0.7 - - - +
112I PHE* 3.4 44.8 + - + +
42J TYR* 3.5 30.8 - - + -
43J GLN 3.5 7.4 - - - +
44J GLN* 3.9 12.1 - - + +
49J GLY* 1.3 84.5 - - - +
51J LYS* 1.3 58.9 + - - +
103J LEU* 3.9 19.7 - - + -
121J PHE* 4.6 2.7 - - + -
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Residues in contact with LYS 51 (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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109I GLN* 4.2 11.7 - - - +
42J TYR* 3.4 3.4 - - - -
43J GLN* 2.9 36.9 + - + +
49J GLY 4.5 3.8 - - - +
50J PRO* 1.3 74.9 - - - +
52J LEU* 1.3 68.1 + - - +
53J LEU* 3.3 1.9 + - - +
70J GLN* 3.8 36.7 + - + +
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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