Contacts of the strand formed by residues 58 - 71 (chain V) in PDB entry 6GYK
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 SER 58 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5U GLU* 4.8 9.5 + - - -
275U THR 3.2 24.8 + - - -
276U PHE* 3.6 6.7 - - - -
277U GLN* 2.9 24.9 + - - +
278U LYS 3.4 4.9 + - - -
56V THR 3.9 0.2 - - - -
57V GLN* 1.3 81.1 + - - +
59V LYS* 1.3 62.3 + - - +
60V LEU* 5.0 1.8 - - - -
87V VAL* 4.7 12.9 - - - +
88V GLU* 3.3 18.9 + - - +
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Residues in contact with LYS 59 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278U LYS* 3.3 31.5 - - + +
279U ALA* 4.0 16.2 - - - +
280U GLN* 4.1 14.9 - - - +
57V GLN 5.1 1.1 - - - +
58V SER* 1.3 75.6 - - - +
60V LEU* 1.3 85.2 + - - +
61V THR* 4.5 6.3 + - - +
86V THR 3.4 2.1 - - - +
88V GLU* 2.8 45.5 + - - +
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Residues in contact with LEU 60 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244U MET* 4.8 6.7 - - + -
267U VAL* 3.7 20.2 - - + -
269U ILE* 6.2 0.2 - - + -
274U TYR* 4.9 14.8 - - + -
275U THR 6.0 0.2 - - - +
276U PHE* 3.6 37.2 - - + -
278U LYS 3.3 5.5 + - - -
279U ALA* 4.3 11.4 - - + -
280U GLN 3.5 12.9 + - - -
58V SER* 5.0 2.2 - - - -
59V LYS* 1.3 87.9 - - - +
61V THR* 1.3 70.4 + - - +
62V VAL* 4.3 4.0 - - + -
85V VAL* 4.2 16.8 - - + -
86V THR 3.0 7.2 - - - +
87V VAL* 3.7 41.1 - - + -
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Residues in contact with THR 61 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280U GLN* 3.7 16.0 - - + +
282U GLU* 5.9 0.4 - - - +
59V LYS* 4.5 8.3 + - - +
60V LEU* 1.3 83.5 + - - +
62V VAL* 1.3 60.5 + - - +
63V LYS* 3.7 33.4 - - + +
84V GLN 3.0 8.3 - - - +
85V VAL* 3.1 0.5 - - - -
86V THR* 2.9 50.7 + - - +
88V GLU 5.7 0.7 + - - -
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Residues in contact with VAL 62 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244U MET* 4.1 25.4 - - + -
279U ALA* 6.1 2.2 - - + -
280U GLN 3.2 9.4 + - - +
281U VAL* 3.6 24.0 - - + +
282U GLU 3.0 24.9 + - - -
60V LEU* 5.1 3.1 - - + -
61V THR* 1.3 77.7 - - - +
63V LYS* 1.3 65.9 + - - +
64V GLY 4.3 0.9 - - - +
80V VAL* 5.1 6.3 - - + -
83V CYS* 3.8 29.8 - - + -
84V GLN 3.2 3.6 - - - +
85V VAL* 3.8 20.9 - - + -
111V LEU* 4.1 8.7 - - + -
113V ILE* 5.2 3.6 - - + -
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Residues in contact with LYS 63 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282U GLU* 3.4 44.7 + - + +
61V THR* 3.7 27.0 - - + +
62V VAL* 1.3 81.2 - - - +
64V GLY* 1.3 57.7 + - - +
82V ASN 4.2 0.9 - - - +
83V CYS* 3.3 2.1 - - - -
84V GLN* 2.9 43.2 + - + +
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Residues in contact with GLY 64 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282U GLU 3.7 5.0 + - - +
283U ALA* 3.4 5.2 - - - +
284U GLU* 3.2 22.2 + - - +
62V VAL* 4.3 0.8 - - - +
63V LYS* 1.3 74.6 - - - +
65V ASN* 1.3 67.1 + - - +
80V VAL* 3.8 6.2 - - - +
82V ASN 3.5 14.8 - - - -
83V CYS* 3.6 11.2 - - - +
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Residues in contact with ASN 65 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284U GLU* 3.5 15.5 - - - +
286U VAL* 6.0 5.4 - - + -
64V GLY* 1.3 74.6 - - - +
66V LEU* 1.3 63.4 + - - +
67V ASP* 3.1 0.9 + - - -
80V VAL* 3.2 3.5 - - - +
81V LYS* 2.9 50.0 + - + +
82V ASN* 4.8 11.2 + - - +
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Residues in contact with LEU 66 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107O ARG* 4.1 5.4 + - - -
258U TRP* 3.5 42.6 - - + -
283U ALA* 3.6 15.2 - - + +
284U GLU 2.5 27.4 + - - +
285U TRP* 3.8 16.7 - - + +
286U VAL* 4.5 2.1 + - - +
64V GLY 3.8 0.4 + - - -
65V ASN* 1.3 68.8 - - - +
67V ASP* 1.3 60.5 + - - +
68V THR 3.4 21.1 - - - +
69V TYR* 3.5 29.8 - - + -
78V PHE* 3.8 17.5 - - + -
79V ILE 3.9 6.5 - - - +
80V VAL* 4.1 14.1 - - + -
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Residues in contact with ASP 67 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91O ASN* 5.0 3.5 - - - +
107O ARG* 3.1 26.6 + - - +
285U TRP* 4.9 6.2 + - - -
65V ASN 3.1 3.4 + - - +
66V LEU* 1.3 75.4 - - - +
68V THR* 1.3 67.2 + - - +
79V ILE* 2.8 24.7 + - - +
81V LYS* 3.3 48.3 + - + -
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Residues in contact with THR 68 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90O ARG* 4.0 32.3 - - + +
91O ASN* 4.5 5.6 - - - +
66V LEU* 3.4 10.9 - - - +
67V ASP* 1.3 91.9 + - - +
69V TYR* 1.3 68.2 + - - +
77V THR 4.5 0.4 - - - +
78V PHE* 3.4 1.7 - - - -
79V ILE* 2.9 53.0 + - + +
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Residues in contact with TYR 69 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90O ARG 2.9 21.6 - - - +
91O ASN* 2.1 47.9 + - - -
92O ALA 3.6 16.5 - - - +
93O GLU* 3.5 23.1 - - + -
103O ILE 5.1 0.2 + - - -
105O ARG* 3.6 26.7 + - - +
258U TRP* 3.5 28.2 + + + -
285U TRP* 3.4 18.4 - + - -
66V LEU* 3.5 21.5 - - + -
68V THR* 1.3 79.4 - - - +
70V GLY* 1.3 58.7 + - - +
76V TRP* 5.0 1.3 - + + -
77V THR 3.3 7.4 - - - -
78V PHE* 3.7 25.8 - - + -
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Residues in contact with GLY 70 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86O ALA 5.7 2.7 - - - -
90O ARG 4.8 1.8 - - - -
92O ALA 4.0 9.9 - - - -
69V TYR* 1.3 76.9 - - - +
71V PHE* 1.3 61.3 + - - -
75V VAL 4.1 0.4 - - - -
76V TRP* 3.2 13.0 - - - -
77V THR* 2.9 38.6 + - - -
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Residues in contact with PHE 71 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86O ALA* 4.2 17.7 + - - +
92O ALA 4.7 3.2 + - - -
93O GLU* 5.6 1.1 - - - -
94O TYR* 3.3 39.0 + - - +
95O ASN* 4.5 14.1 - - + -
96O PRO* 6.1 1.1 - - + -
248U TYR* 3.4 24.5 - - - -
70V GLY* 1.3 77.1 - - - +
72V CYS* 1.3 65.0 + - - +
73V ASP 5.2 0.7 - - - -
74V ASP* 3.5 29.2 - - - -
75V VAL 3.0 25.6 - - - -
76V TRP* 3.3 47.8 - + + -
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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