Contacts of the strand formed by residues 87 - 95 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65C ASN* 2.6 33.9 + - - -
66C ARG 3.0 18.4 + - - -
67C VAL 3.9 0.2 + - - -
78C TYR* 5.3 1.3 - + + -
79C PHE* 3.7 35.6 - + + -
82C SER* 4.1 9.4 - - - +
83C PHE* 3.9 28.0 - + - -
86C GLY* 1.3 76.5 - - - +
88C SER* 1.3 72.6 + - - +
89C TRP* 3.8 21.1 - + - -
107C ILE* 3.0 45.5 + - + +
177C TYR* 4.0 8.9 - + + -
178C LYS 3.2 15.7 - - - +
179C ALA* 3.7 9.9 - - - +
180C LYS* 3.8 8.4 - - - +
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Residues in contact with SER 88 (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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87C TYR* 1.3 81.0 - - - +
89C TRP* 1.3 64.4 + - - +
90C GLU* 5.3 2.6 + - - +
105C ASN 3.2 12.8 - - - -
106C ASP* 3.7 19.3 - - - -
178C LYS* 2.8 49.8 + - - +
180C LYS* 4.3 6.0 + - - +
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Residues in contact with TRP 89 (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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60C VAL* 3.7 40.6 - - + -
63C KZ4 2.7 28.2 + - - -
87C TYR* 3.8 21.1 - + - -
88C SER* 1.3 77.4 - - - +
90C GLU* 1.3 74.5 + - - +
91C ARG* 3.5 52.3 - - + -
103C ALA* 3.7 17.5 - - + -
104C THR* 3.3 7.4 - - - -
105C ASN* 2.9 58.1 + - + +
107C ILE* 4.2 4.3 - - + -
175C THR* 4.2 2.7 - - + -
176C THR 3.1 14.1 - - - +
177C TYR* 3.8 21.8 - + + -
178C LYS* 6.0 0.4 - - - -
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Residues in contact with GLU 90 (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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19A ASN* 3.2 32.8 - - - +
20A GLY* 5.4 0.2 - - - -
123A VAL* 3.9 13.5 - - + -
124A ASN* 2.9 38.5 + - - +
88C SER* 5.3 4.0 + - - +
89C TRP* 1.3 78.8 - - - +
91C ARG* 1.3 63.1 + - - +
103C ALA 3.4 5.6 - - - -
104C THR* 4.2 11.0 - - + -
175C THR* 3.2 4.9 - - - +
176C THR* 2.8 33.8 + - - +
178C LYS* 2.8 39.3 + - + +
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Residues in contact with ARG 91 (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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123A VAL* 3.8 7.7 - - - +
124A ASN* 4.2 0.7 - - - +
59C THR* 2.7 41.4 + - - -
60C VAL* 4.1 2.6 - - - +
63C KZ4 2.7 28.5 + - - +
66C ARG* 3.5 13.5 - - - +
89C TRP* 3.5 38.7 - - + +
90C GLU* 1.3 77.3 - - - +
92C SER* 1.3 68.3 + - - +
93C MET* 3.8 26.0 - - + +
101C CYS 3.8 0.5 - - - +
102C ASN* 3.4 4.0 - - - -
103C ALA 2.8 33.1 + - - +
173C PHE* 4.0 14.5 - - - -
174C LYS 3.2 10.1 - - - +
175C THR* 2.9 27.1 + - - +
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Residues in contact with SER 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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98A GLY 5.8 0.4 - - - -
100A ILE* 3.3 23.5 - - - +
124A ASN* 3.7 8.8 - - - +
91C ARG* 1.3 74.9 - - - +
93C MET* 1.3 63.5 + - - +
94C ASN* 4.0 3.5 + - - +
100C ILE* 3.7 14.7 - - - +
101C CYS 3.4 3.6 - - - -
102C ASN* 3.0 18.4 + - - -
172C ASP 3.4 3.9 - - - +
173C PHE* 3.5 1.9 - - - -
174C LYS* 3.0 38.5 + - - +
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Residues in contact with MET 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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56C ILE 4.6 8.7 - - - +
59C THR* 3.9 17.7 - - - -
60C VAL* 3.8 24.7 - - + -
91C ARG* 3.8 25.4 - - + +
92C SER* 1.3 74.4 - - - +
94C ASN* 1.3 59.2 + - - +
95C TYR* 3.6 16.6 - - + -
100C ILE* 3.4 5.7 - - - -
101C CYS* 2.7 57.7 + - + +
103C ALA* 3.9 17.3 - - + -
120C PHE* 4.3 1.6 - - + -
139C TRP* 6.1 0.7 - - - -
171C CYS* 3.7 14.1 - - - -
172C ASP 3.5 3.4 - - - -
173C PHE* 3.6 23.6 - - + -
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Residues in contact with ASN 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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94A ASN* 4.5 16.8 - - - +
100A ILE* 6.1 1.0 - - - +
92C SER* 5.2 2.7 - - - +
93C MET* 1.3 69.6 - - - +
95C TYR* 1.3 69.4 + - - +
96C GLU* 4.9 0.2 - - - -
98C GLY* 5.0 0.9 - - - -
100C ILE* 3.1 32.2 - - + +
171C CYS* 3.4 2.8 - - - -
172C ASP* 2.9 49.0 + - + +
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Residues in contact with TYR 95 (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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56C ILE* 3.4 35.6 + - + +
93C MET* 3.6 22.1 - - + +
94C ASN* 1.3 84.8 - - - +
96C GLU* 1.3 65.6 + - - +
97C ASP* 3.2 2.7 - - - +
98C GLY* 3.1 13.0 + - - -
99C GLY 2.9 23.1 + - - +
101C CYS* 4.1 9.3 - - - -
125C PHE* 3.6 23.1 - + - -
139C TRP* 3.6 20.1 - + - -
161C LEU* 4.0 7.2 - - + -
169C TYR* 3.2 44.6 - + + +
170C ARG 3.5 5.8 - - - -
171C CYS* 3.6 30.4 - - + -
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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