Contacts of the strand formed by residues 87 - 95 (chain D) in PDB entry 6NQN
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 87 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65D ASN* 2.7 33.7 + - - -
66D ARG 3.0 18.9 + - - -
67D VAL 3.9 0.2 + - - -
78D TYR* 5.4 1.3 - + + -
79D PHE* 3.6 34.0 - + + -
82D SER* 4.0 10.1 - - - +
83D PHE* 3.9 26.9 - + - -
86D GLY* 1.3 75.6 - - - +
88D SER* 1.3 71.6 + - - +
89D TRP* 3.9 21.5 - + - -
107D ILE* 3.0 48.1 + - + +
177D TYR* 4.0 8.5 - + + -
178D LYS 3.3 15.0 - - - +
179D ALA* 3.6 10.5 - - - -
180D LYS* 3.8 8.2 - - - +
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Residues in contact with SER 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D TYR* 1.3 81.2 - - - +
89D TRP* 1.3 66.0 + - - +
90D GLU* 5.3 2.4 + - - +
105D ASN 3.2 13.0 - - - -
106D ASP* 3.6 19.3 - - - -
178D LYS* 2.8 51.6 + - - +
180D LYS* 4.3 5.1 + - - -
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Residues in contact with TRP 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D VAL* 3.7 39.3 - - + -
63D KZ4 2.7 28.5 + - - -
87D TYR* 3.9 22.0 - + - -
88D SER* 1.3 76.0 - - - +
90D GLU* 1.3 75.3 + - - +
91D ARG* 3.4 53.4 - - + -
103D ALA* 3.7 17.7 - - + -
104D THR* 3.2 7.2 - - - -
105D ASN* 2.9 55.4 + - + +
107D ILE* 4.2 4.3 - - + -
175D THR* 4.2 2.2 - - + -
176D THR 3.1 14.1 - - - +
177D TYR* 3.7 21.3 - + + -
178D LYS* 4.8 0.7 - - - +
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Residues in contact with GLU 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D SER* 5.3 3.8 + - - +
89D TRP* 1.3 79.0 - - - +
91D ARG* 1.3 63.2 + - - +
103D ALA 3.4 7.9 - - - +
104D THR* 4.2 15.3 - - + -
174D LYS 3.9 0.2 - - - +
175D THR* 3.2 5.0 - - - +
176D THR* 2.9 40.6 + - - +
178D LYS* 2.9 40.0 + - + +
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Residues in contact with ARG 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D THR* 2.8 41.0 + - - -
60D VAL* 4.2 2.4 - - - +
63D KZ4 2.8 25.9 + - - +
66D ARG* 3.4 14.4 - - - +
89D TRP* 3.4 37.9 - - + +
90D GLU* 1.3 77.5 - - - +
92D SER* 1.3 71.2 + - - +
93D MET* 3.7 25.9 - - + +
101D CYS 3.7 0.7 - - - +
102D ASN* 3.3 5.3 - - - +
103D ALA 2.7 39.1 + - - +
173D PHE* 4.0 14.3 - - - -
174D LYS 3.2 10.3 - - - +
175D THR* 2.8 27.6 + - - +
177D TYR* 4.9 0.4 - - - -
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Residues in contact with SER 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D ARG* 1.3 75.3 - - - +
93D MET* 1.3 63.0 + - - +
94D ASN* 4.0 4.6 + - - +
100D ILE* 3.7 14.0 - - - +
101D CYS 3.3 3.4 - - - -
102D ASN* 2.9 19.8 + - - -
172D ASP 3.6 2.3 - - - +
173D PHE* 3.6 3.1 - - - -
174D LYS* 3.0 41.0 + - - +
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Residues in contact with MET 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D ILE 4.6 8.7 - - - +
59D THR* 4.0 17.5 - - - -
60D VAL* 3.8 14.1 - - + -
91D ARG* 3.7 25.6 - - + +
92D SER* 1.3 74.7 - - - +
94D ASN* 1.3 60.5 + - - +
95D TYR* 3.7 15.1 - - + -
100D ILE* 3.4 4.0 - - - -
101D CYS* 2.7 57.8 + - + +
103D ALA* 3.8 28.5 - - + -
120D PHE* 4.3 1.6 - - + -
139D TRP* 6.1 0.2 - - - -
171D CYS* 3.7 13.9 - - - -
172D ASP 3.6 4.5 - - - -
173D PHE* 3.6 23.6 - - + -
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Residues in contact with ASN 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D SER* 5.2 3.6 - - - +
93D MET* 1.3 69.8 - - - +
95D TYR* 1.3 72.8 + - - +
96D GLU* 4.9 0.2 - - - -
98D GLY* 4.8 2.6 - - - -
99D GLY 4.0 1.6 - - - -
100D ILE* 3.6 29.2 - - + +
171D CYS* 3.5 3.0 - - - -
172D ASP* 2.9 45.3 + - + +
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Residues in contact with TYR 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D ILE* 3.5 26.1 + - + +
93D MET* 3.7 17.8 - - + +
94D ASN* 1.3 83.5 - - - +
96D GLU* 1.3 61.4 + - - +
97D ASP* 3.2 3.6 - - - +
98D GLY* 3.0 18.7 + - - -
99D GLY 2.8 23.1 + - - +
101D CYS* 4.0 9.1 - - - -
125D PHE* 3.6 23.8 - + - -
139D TRP* 3.5 27.9 - + - -
161D LEU* 4.1 6.5 - - + -
169D TYR* 3.2 43.1 - + + +
170D ARG 3.4 12.8 - - - -
171D CYS* 3.5 25.0 - - + -
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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