Contacts of the strand formed by residues 66 - 75 (chain J) in PDB entry 1FSK
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 TYR 66 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55J LYS* 4.0 36.6 - - + +
56J ILE 3.1 14.1 - - - +
57J SER* 4.5 3.4 - - - +
58J PHE* 4.0 7.6 - - - -
64J PHE* 3.7 2.1 - - - +
65J LYS* 1.3 97.7 - - + +
67J VAL* 1.3 76.1 + - - +
68J LYS* 3.7 27.1 - - + -
87J GLU* 3.0 21.3 + - - +
88J GLY* 3.7 36.7 + - - -
89J GLY* 3.7 5.1 + - - -
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Residues in contact with VAL 67 (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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54J LYS 3.6 0.3 - - - +
55J LYS* 3.7 0.2 - - - -
56J ILE* 2.8 53.5 + - + +
58J PHE* 3.8 19.5 - - + -
66J TYR* 1.3 81.3 - - - +
68J LYS* 1.3 67.0 + - - +
69J ASP* 3.7 10.8 - - - +
85J VAL* 3.3 27.8 - - + -
87J GLU 3.3 6.3 - - - +
88J GLY 3.3 18.2 - - - +
89J GLY* 5.1 1.1 - - - +
90J PRO* 4.7 6.1 - - + -
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Residues in contact with LYS 68 (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 ILE* 4.6 19.9 - - + +
53J ILE* 4.8 8.7 - - + -
54J LYS 3.0 11.9 - - - +
55J LYS* 4.0 27.2 - - + +
66J TYR* 3.7 23.1 - - + -
67J VAL* 1.3 75.7 - - - +
69J ASP* 1.3 61.3 + - - +
85J VAL* 3.7 0.3 - - - +
86J ILE* 2.8 41.7 + - + +
87J GLU* 2.9 51.3 + - + +
31L SER* 5.1 8.7 + - - +
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Residues in contact with ASP 69 (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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53J ILE* 3.7 6.2 - - - +
54J LYS* 3.1 33.3 + - + +
56J ILE* 3.7 25.1 - - + +
67J VAL* 3.7 20.8 - - - +
68J LYS* 1.3 81.9 - - - +
70J ARG* 1.3 64.4 + - - +
83J TYR* 3.3 34.1 - - + -
84J SER 2.9 10.8 - - - +
85J VAL* 4.0 8.3 - - - +
86J ILE* 4.4 1.6 - - - +
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Residues in contact with ARG 70 (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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51J GLY 4.5 1.3 - - - +
52J THR 3.5 4.9 - - - -
53J ILE* 4.0 13.2 - - + -
69J ASP* 1.3 79.5 - - - +
71J VAL* 1.3 71.0 + - - +
72J ASP* 2.6 34.2 + - - +
83J TYR* 4.0 3.1 - - - -
84J SER* 2.9 25.6 + - - +
86J ILE* 3.9 25.4 - - + +
97J LYS* 3.8 14.3 - - - +
33L TRP* 4.7 5.3 - - + +
52L PHE* 3.4 37.3 - - - +
54L SER* 4.3 2.8 + - - -
55L ASP* 2.8 45.0 + - - +
57L TYR* 3.6 21.8 - - - +
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Residues in contact with VAL 71 (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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48J GLY 4.9 3.1 - - - +
49J GLY 4.1 3.6 - - - +
50J PRO* 4.0 12.8 - - + -
51J GLY* 3.0 30.5 + - - +
52J THR* 3.0 21.4 + - - +
54J LYS* 4.0 26.9 - - + +
69J ASP* 4.3 0.8 - - - +
70J ARG* 1.3 74.7 - - - +
72J ASP* 1.3 61.0 + - - +
73J GLU 4.4 0.4 - - - +
74J VAL* 3.5 32.1 - - + -
81J TYR* 4.0 21.5 - - + +
82J ASN 4.0 3.6 - - - +
83J TYR* 4.1 4.9 - - - +
33L TRP* 5.3 0.5 - - - -
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Residues in contact with ASP 72 (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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50J PRO* 5.4 0.4 - - - -
51J GLY* 5.0 2.7 - - - -
70J ARG* 2.6 38.3 + - - +
71J VAL* 1.3 74.1 - - - +
73J GLU* 1.3 66.3 + - + +
82J ASN* 3.0 20.4 + - + +
83J TYR* 3.1 13.9 + - - -
84J SER* 2.3 28.8 + - - -
94K TYR* 4.2 18.6 + - - -
33L TRP* 5.2 3.4 - - - -
57L TYR* 3.8 33.7 + - + +
59L ASN* 5.2 0.5 + - - -
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Residues in contact with GLU 73 (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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50J PRO* 5.3 4.3 - - - -
71J VAL* 3.9 0.4 - - - +
72J ASP* 1.3 83.9 - - + +
74J VAL* 1.3 81.3 + - - +
75J ASP* 3.6 28.5 + - - +
80J LYS* 4.1 10.7 - - - +
81J TYR* 3.6 0.3 - - - -
82J ASN* 2.9 52.8 + - + +
94K TYR* 5.6 4.5 - - + -
57L TYR* 4.8 6.5 - - - +
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Residues in contact with VAL 74 (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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19J PHE* 4.5 6.3 - - + -
24J LEU* 4.4 14.1 - - + -
49J GLY 5.7 0.2 - - - -
50J PRO* 4.6 20.7 - - + +
71J VAL* 3.5 25.6 - - + -
73J GLU* 1.3 89.0 - - - +
75J ASP* 1.3 62.7 + - - +
76J HIS* 3.3 41.2 + - + +
80J LYS 3.7 3.4 - - - +
81J TYR* 3.7 13.5 - - + -
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Residues in contact with ASP 75 (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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19J PHE* 3.8 4.0 - - - -
73J GLU* 3.6 16.5 + - - +
74J VAL* 1.3 70.9 - - - +
76J HIS* 1.3 64.2 + - - +
77J THR* 2.9 13.7 + - - -
78J ASN* 2.7 43.1 + - - +
79J PHE* 3.2 14.9 + - - -
80J LYS* 2.8 36.0 + - + +
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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