Contacts of the strand formed by residues 85 - 94 (chain K) in PDB entry 6R90
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 ASN 85 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58K TYR 5.2 1.6 - - - +
79K ILE 3.7 1.6 - - - +
80K LEU* 3.3 4.0 - - - +
81K THR* 2.7 59.1 + - + +
83K LYS* 3.6 6.7 - - - +
84K TYR* 1.3 72.2 - - - +
86K ALA* 1.3 60.3 + - - +
87K CYS* 5.2 1.9 - - - -
106K GLY 3.9 5.9 - - - +
107K ASN* 3.5 18.0 - - - +
1068K ILE* 3.9 30.4 - - + +
1072K PHE* 3.2 38.1 - - - -
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Residues in contact with ALA 86 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78K PHE* 3.7 15.7 - - + -
79K ILE 3.5 4.7 - - - -
80K LEU* 3.6 15.0 - - + -
84K TYR 3.6 1.4 + - - -
85K ASN* 1.3 74.3 - - - +
87K CYS* 1.3 63.8 + - - +
105K HIS* 3.4 1.2 - - - +
106K GLY 2.9 36.8 + - - +
108K VAL* 3.8 17.7 - - + -
143K ILE* 4.3 3.1 - - + -
152K LEU* 3.3 13.5 - - + -
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Residues in contact with CYS 87 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57K MET* 4.2 19.3 - - - -
77K LEU 3.7 0.7 - - - +
78K PHE* 3.1 7.6 - - - -
79K ILE* 2.9 57.3 + - - -
81K THR* 6.2 0.7 - - - -
85K ASN* 5.2 2.2 - - + -
86K ALA* 1.3 78.8 - - - +
88K ILE* 1.3 63.1 + - - +
89K LEU* 4.3 14.6 - - + -
104K ALA 3.3 14.8 - - - +
105K HIS* 4.3 1.1 - - + -
152K LEU* 3.6 2.7 - - - +
1066K GLY* 3.9 21.5 - - - +
1068K ILE* 5.6 3.8 - - + -
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Residues in contact with ILE 88 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67K PHE* 3.8 17.5 - - + -
76K LEU* 3.8 32.1 - - + -
77K LEU 3.3 3.8 - - - +
78K PHE* 3.9 15.0 - - + -
87K CYS* 1.3 75.7 - - - +
89K LEU* 1.3 66.8 + - - +
103K ARG* 3.2 13.1 + - + -
104K ALA* 2.9 42.7 + - + +
131K ILE* 4.7 2.2 - - + -
145K LEU* 3.9 28.7 - - + -
149K ASN 5.6 0.4 - - - +
152K LEU* 3.9 22.4 - - + -
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Residues in contact with LEU 89 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23K PHE* 4.5 1.7 - - + -
39K LEU* 5.7 2.9 - - + -
57K MET* 5.0 0.9 - - - -
76K LEU* 3.5 10.8 - - - +
77K LEU* 2.8 60.3 + - + +
79K ILE* 4.5 13.9 - - + -
87K CYS* 4.3 15.3 - - + -
88K ILE* 1.3 79.9 - - - +
90K GLU* 1.3 59.6 - - - +
100K ILE* 3.6 21.3 - - + +
101K ILE 3.8 9.4 - - - +
102K THR* 4.2 6.7 - - - +
103K ARG* 4.8 1.3 - - - -
1065K VAL* 3.5 36.6 - - + -
1066K GLY* 4.0 13.0 - - - +
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Residues in contact with GLU 90 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23K PHE* 4.4 2.7 - - - -
72K GLU* 4.9 3.8 - - - +
74K LYS* 3.3 15.3 + - - +
75K ASP 5.4 0.4 - - - +
76K LEU* 3.6 17.7 - - + -
89K LEU* 1.3 75.8 - - - +
91K TYR* 1.3 71.4 + - - +
92K LYS* 2.3 40.3 + - + -
100K ILE* 3.5 8.4 - - - +
101K ILE* 3.2 33.8 + - + +
103K ARG* 2.6 47.5 + - + +
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Residues in contact with TYR 91 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23K PHE* 3.4 49.8 - + + +
24K THR* 3.4 45.8 - - + +
41K ILE* 5.3 6.7 - - + -
52K VAL* 3.8 11.7 - - + +
53K LYS* 5.6 4.9 - - + -
74K LYS* 3.4 23.0 - - - +
75K ASP 5.3 1.0 + - - -
90K GLU* 1.3 76.1 - - - +
92K LYS* 1.3 68.2 + - - +
93K GLN* 3.3 28.9 + - + -
98K ILE* 3.0 47.2 - - + +
100K ILE* 3.5 14.6 - - + -
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Residues in contact with LYS 92 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74K LYS* 3.4 14.5 - - - +
90K GLU* 2.3 39.2 + - + +
91K TYR* 1.3 78.9 - - - +
93K GLN* 1.3 61.4 + - - +
97K SER 4.2 0.2 - - - +
98K ILE* 3.5 4.2 - - - +
99K ASP* 2.8 49.3 + - + +
101K ILE* 4.0 27.8 - - + -
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Residues in contact with GLN 93 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24K THR* 5.6 1.4 - - - -
52K VAL* 5.4 2.2 - - - +
91K TYR* 3.3 32.5 + - + -
92K LYS* 1.3 75.8 - - - +
94K SER* 1.3 66.6 + - - +
95K GLY 3.4 20.1 - - - +
96K GLU* 5.3 1.9 - - - +
97K SER 3.5 4.0 - - - +
98K ILE* 3.5 25.6 - - + +
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Residues in contact with SER 94 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93K GLN* 1.3 76.8 - - - +
95K GLY* 1.3 64.1 + - - +
97K SER* 2.5 43.7 + - - -
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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