Contacts of the strand formed by residues 62 - 68 (chain T) in PDB entry 3FKS
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 LYS 62 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54T LEU* 4.0 33.2 - - + +
55T VAL 3.2 16.4 - - - +
56T GLU* 4.4 20.4 - - + +
57T PHE* 4.2 4.4 - - - -
60T GLY 3.7 8.9 + - - +
61T VAL* 1.3 83.1 - - - +
63T GLY* 1.3 58.2 + - - +
77T LEU* 4.2 1.6 - - - -
78T PHE* 3.2 28.3 + - + +
113T LEU* 4.2 28.4 - - + +
115T ASN* 4.8 13.5 + - - +
128T ARG* 5.8 3.6 - - - +
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Residues in contact with GLY 63 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54T LEU* 3.2 23.7 - - - +
55T VAL* 3.1 30.5 + - - +
57T PHE* 4.1 3.1 - - - -
62T LYS* 1.3 75.7 - - - +
64T MET* 1.3 60.4 + - - -
75T ILE* 3.9 5.8 - - - -
76T VAL 3.2 14.1 - - - -
78T PHE* 3.7 6.7 - - - -
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Residues in contact with MET 64 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52T GLU* 4.0 22.0 - - + +
53T GLU 3.7 2.9 - - - +
54T LEU* 5.6 0.2 - - + -
63T GLY* 1.3 74.3 - - - +
65T ALA* 1.3 63.4 + - - +
66T LEU* 2.9 37.7 + - + -
75T ILE* 3.3 6.1 - - - +
76T VAL* 2.8 50.1 + - + +
78T PHE* 3.5 24.0 - - + -
97T VAL* 3.7 32.3 - - + -
132T GLN* 6.5 0.7 - - - -
246T TYR* 5.1 15.3 - - + +
247T LEU* 5.3 7.6 - - - -
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Residues in contact with ALA 65 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49T ILE* 4.1 15.5 - - + -
50T GLN 3.7 20.6 - - - +
51T ALA* 3.8 1.8 - - - -
52T GLU* 2.8 28.9 + - - -
53T GLU 3.1 17.9 + - - +
55T VAL* 5.2 3.2 - - + +
63T GLY 4.4 0.2 - - - -
64T MET* 1.3 68.8 - - - +
66T LEU* 1.3 64.8 + - - +
68T LEU* 4.5 2.6 - - + +
73T VAL* 4.2 15.9 - - + -
74T GLY 4.2 0.9 - - - -
75T ILE* 4.1 13.3 - - + +
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Residues in contact with LEU 66 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51T ALA* 5.0 2.4 - - - +
52T GLU* 4.8 8.5 + - + +
64T MET* 2.9 29.9 + - + -
65T ALA* 1.3 75.8 - - - +
67T ASN* 1.3 75.4 + - + +
68T LEU* 3.6 10.9 - - - +
74T GLY 3.2 12.3 + - - +
76T VAL* 3.8 18.4 - - + -
287T LEU* 3.9 28.5 - - + -
289T ARG* 4.4 18.4 - - - +
16X VAL* 4.0 3.1 - - - +
18X GLY* 5.0 10.3 + - - +
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Residues in contact with ASN 67 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66T LEU* 1.3 98.2 - - + +
68T LEU* 1.3 62.4 + - - +
69T GLU* 3.4 22.2 - - - +
73T VAL* 3.4 8.3 - - - +
74T GLY* 3.0 53.3 + - - -
287T LEU* 5.2 7.9 - - - +
16X VAL 3.7 4.5 - - - -
17X ILE* 3.4 32.1 - - + +
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Residues in contact with LEU 68 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49T ILE* 3.8 18.2 - - + +
50T GLN 4.4 5.2 - - - +
51T ALA* 4.0 21.1 - - + -
65T ALA 4.5 3.1 - - - +
66T LEU 3.6 13.0 - - - +
67T ASN* 1.3 78.7 - - - +
69T GLU* 1.3 62.7 + - - +
72T GLN 4.6 1.6 - - - -
73T VAL* 4.7 9.9 - - + -
15X ALA* 3.0 10.0 - - - +
16X VAL* 2.9 52.0 + - + +
17X ILE* 3.9 1.9 - - - +
70X LEU 3.6 23.6 - - - +
72X ARG* 3.8 33.9 - - + +
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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