Contacts of the strand formed by residues 90 - 98 (chain C) in PDB entry 5NXR
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 GLY 90 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85C LYS* 3.3 13.7 - - - +
86C PHE* 2.9 30.3 + - - +
88C ASP* 3.6 2.2 - - - +
89C PHE* 1.3 80.2 - - - +
91C SER* 1.3 60.1 + - - -
136C TYR* 3.9 4.3 - - - -
137C ARG 3.1 14.8 - - - -
138C ASN* 3.8 8.1 - - - +
139C ASN 5.4 1.1 - - - -
439C LDA 4.4 3.0 + - - -
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Residues in contact with SER 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C PHE* 4.3 14.6 - - - -
84C LEU 3.2 11.7 - - - -
85C LYS* 3.8 22.5 + - - -
90C GLY* 1.3 74.8 - - - -
92C ILE* 1.3 60.6 + - - +
93C ASP* 5.1 4.0 + - - -
135C THR 3.7 0.7 + - - +
136C TYR* 3.1 10.6 - - - -
137C ARG* 2.9 49.6 + - - +
439C LDA 5.3 2.0 - - - -
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Residues in contact with ILE 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C PHE* 3.8 1.4 - - - -
83C GLY* 3.1 2.3 - - - -
84C LEU* 2.8 41.3 + - + +
91C SER* 1.3 74.5 - - - +
93C ASP* 1.3 63.2 + - - +
134C LEU* 3.9 22.4 - - + -
135C THR 3.3 18.2 - - - +
136C TYR* 3.7 24.5 - - + -
406C LDA 3.8 45.0 - - + +
408C LDA 3.9 13.9 - - + -
439C LDA 4.5 12.8 - - + -
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Residues in contact with ASP 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C PHE* 3.7 21.1 - - + -
81C TYR* 4.2 7.6 - - + +
82C ALA 3.3 13.2 - - - +
83C GLY* 3.9 0.7 - - - -
91C SER* 5.1 4.3 + - - -
92C ILE* 1.3 76.4 - - - +
94C TYR* 1.3 64.4 + - - +
97C ASN* 3.3 34.1 + - - +
133C LEU 4.6 1.0 - - - +
134C LEU* 3.4 7.4 - - - +
135C THR* 2.9 55.5 + - - +
137C ARG* 5.1 7.1 + - - +
406C LDA 5.1 2.0 - - - -
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Residues in contact with TYR 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B VAL* 3.6 25.8 - - + +
20B ARG 3.4 31.1 + - - -
21B HIS* 3.2 18.4 - + + -
36B ASP* 3.3 17.0 + - - -
38B SER* 4.0 7.0 - - - -
348B LEU* 5.7 0.2 - - + -
81C TYR* 3.3 7.0 - - - +
82C ALA 2.9 30.7 + - - +
93C ASP* 1.3 77.4 - - - +
95C GLY* 1.3 64.9 + - - +
132C ASN* 2.9 37.0 + - - -
133C LEU 3.2 26.9 - - - -
134C LEU* 4.0 15.0 - - + -
406C LDA 4.6 5.1 - - + +
407C LDA 3.6 37.9 - - + -
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Residues in contact with GLY 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B VAL* 4.1 6.1 - - - -
36B ASP* 4.3 5.6 - - - -
38B SER* 4.6 2.2 - - - -
66B THR 5.8 0.2 - - - -
80C ALA 3.5 7.2 - - - -
81C TYR* 4.2 0.2 - - - -
93C ASP* 4.7 0.4 + - - -
94C TYR* 1.3 91.9 - - - +
96C ARG* 1.3 61.0 + - - -
97C ASN* 3.9 1.8 + - - +
130C ASN 3.9 0.5 - - - +
131C ARG 3.6 0.7 - - - -
132C ASN 3.0 26.6 + - - -
133C LEU* 3.0 16.5 + - - +
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Residues in contact with ARG 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B SER* 6.0 0.4 - - - -
66B THR* 4.3 16.2 - - - +
68B LYS 3.9 14.7 + - - -
70B GLU* 3.1 33.9 + - - +
77C ASN* 3.1 23.1 + - - -
78C ARG 2.9 22.5 + - - +
79C LEU* 3.6 2.9 - - - +
80C ALA* 2.7 42.2 + - + +
81C TYR* 3.4 8.9 - - - +
95C GLY* 1.3 71.2 - - - -
97C ASN* 1.3 64.0 + - - +
122C THR* 3.4 2.8 - - - +
123C ASP* 2.7 32.1 + - - -
129C ARG* 3.4 17.2 + - - +
130C ASN* 3.1 16.4 - - - +
131C ARG* 3.5 19.8 - - - +
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Residues in contact with ASN 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C LEU* 3.9 8.7 - - - +
81C TYR* 3.1 40.8 - - + -
93C ASP* 3.3 30.9 + - - +
95C GLY 3.9 2.7 + - - -
96C ARG* 1.3 72.6 - - - +
98C TYR* 1.3 88.9 + - - +
129C ARG* 3.2 4.2 - - - -
130C ASN 2.8 34.2 + - - +
133C LEU* 3.3 14.8 - - + +
135C THR* 5.3 3.5 + - - +
137C ARG* 6.2 0.9 - - - +
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Residues in contact with TYR 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C ARG* 6.1 0.2 - - - -
61C GLU* 5.1 0.8 + - - -
78C ARG* 3.3 14.6 + - - -
79C LEU* 3.9 22.2 - - + -
97C ASN* 1.3 93.2 + - - +
99C GLY* 1.3 68.3 + - - +
102C TYR* 3.5 45.2 + + + -
103C ASP* 4.8 5.8 - - - +
128C SER* 3.8 4.3 - - - -
129C ARG* 3.1 52.5 + - + -
133C LEU* 4.0 1.4 - - - +
135C THR* 4.7 1.0 + - - +
137C ARG* 4.2 12.2 + - - +
153C GLN* 3.2 12.8 - - - +
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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