Contacts of the strand formed by residues 168 - 179 (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 HIS 168 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96D GLU* 3.6 0.2 - - - +
140D GLU* 2.4 45.9 + - + +
160D ALA* 4.0 15.9 - - + -
161D LEU 3.3 15.7 - - - +
162D SER* 3.7 10.4 - - - -
163D LEU* 4.2 8.9 - - - +
167D GLY* 1.3 84.3 - - - -
169D TYR* 1.3 56.6 + - - +
170D ARG* 6.0 0.4 - - + -
147F TYR* 4.2 36.2 - - + +
148F VAL 4.9 5.2 + - - -
149F ARG* 2.8 28.8 + - - +
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Residues in contact with TYR 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D TYR* 3.2 38.0 - + + +
96D GLU* 3.3 15.7 - - + -
97D ASP* 2.8 41.9 + - + -
125D PHE* 3.7 4.9 - - - -
130D PRO* 3.7 25.4 - - + -
131D VAL* 3.6 27.1 - - + +
136D THR* 4.9 0.9 - - + -
160D ALA* 3.3 2.7 - - - -
161D LEU* 2.8 49.6 + - + +
163D LEU* 3.7 22.4 - - + -
168D HIS* 1.3 72.7 - - - +
170D ARG* 1.3 62.9 + - - +
171D CYS* 5.1 0.7 - - - +
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Residues in contact with ARG 170 (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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94D ASN 4.7 0.2 - - - -
95D TYR* 3.4 11.4 - - - +
96D GLU* 2.6 54.6 + - + +
158D ASN* 2.5 56.1 - - - +
159D THR 3.1 19.1 + - - +
160D ALA* 4.2 9.0 - - + -
168D HIS 5.7 0.2 - - - -
169D TYR* 1.3 74.6 - - - +
171D CYS* 1.3 64.8 + - - +
172D ASP* 2.7 25.2 + - - +
145F LYS* 6.5 0.9 - - - -
147F TYR* 3.9 36.4 + - + +
149F ARG* 4.6 3.1 - - - +
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Residues in contact with CYS 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D MET* 3.7 3.6 - - - -
94D ASN 3.5 22.9 - - - -
95D TYR* 3.5 35.9 - - + -
139D TRP* 3.9 16.4 - - + -
157D VAL 3.8 1.0 - - - +
158D ASN* 3.7 0.2 - - - -
159D THR* 2.9 36.0 + - - +
170D ARG* 1.3 79.1 + - - +
172D ASP* 1.3 66.0 + - - +
173D PHE* 3.3 25.6 - - + -
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Residues in contact with ASP 172 (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 3.6 4.2 - - - +
94D ASN* 2.9 45.2 + - + +
157D VAL 3.7 0.2 - - - -
158D ASN* 2.5 36.0 + - - +
170D ARG* 2.7 29.4 + - - +
171D CYS* 1.3 71.6 + - - +
173D PHE* 1.3 63.0 + - - +
174D LYS* 4.0 16.2 + - + +
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Residues in contact with PHE 173 (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* 3.4 31.6 - - + -
63D KZ4 3.6 28.9 - + + -
91D ARG* 4.0 20.4 - - - -
92D SER 3.6 4.3 - - - +
93D MET* 3.6 18.8 - - + -
139D TRP* 3.9 23.8 - + - -
155D GLY 4.3 1.1 - - - +
156D ASP* 3.4 5.9 - - - +
157D VAL* 2.9 42.7 + - + +
159D THR* 4.0 10.1 - - + -
171D CYS* 3.3 29.6 - - + -
172D ASP* 1.3 77.6 - - - +
174D LYS* 1.3 68.2 + - - +
175D THR* 4.2 4.7 - - - +
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Residues in contact with LYS 174 (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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90D GLU 3.9 0.3 - - - +
91D ARG* 3.2 4.0 - - - +
92D SER* 3.0 40.2 + - - +
147D TYR* 5.7 0.2 - - - +
155D GLY 3.6 2.2 - - - -
156D ASP* 3.4 29.4 - - - +
158D ASN* 5.5 2.0 + - - -
172D ASP* 4.9 17.4 + - - +
173D PHE* 1.3 78.6 + - - +
175D THR* 1.3 61.8 + - - +
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Residues in contact with THR 175 (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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89D TRP* 4.2 6.5 - - + -
90D GLU 3.2 11.9 - - - +
91D ARG* 2.8 34.9 + - - +
144D GLU* 4.7 2.1 + - - -
154D LYS* 3.3 10.4 - - - +
155D GLY 2.8 36.9 + - - +
156D ASP* 4.5 0.7 + - - +
173D PHE* 4.8 3.6 - - - +
174D LYS* 1.3 73.1 + - - +
176D THR* 1.3 67.6 + - - +
177D TYR* 3.5 42.8 + - + +
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Residues in contact with THR 176 (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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89D TRP* 3.1 5.5 - - - +
90D GLU* 2.9 46.7 + - - +
152D VAL* 3.9 22.4 - - + -
153D LEU 3.7 2.2 - - - -
154D LYS* 3.2 27.5 - - + +
175D THR* 1.3 72.4 - - - +
177D TYR* 1.3 61.7 + - - +
178D LYS* 3.9 28.1 + - + +
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Residues in contact with TYR 177 (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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66D ARG* 2.8 32.2 + - + -
78D TYR* 3.4 15.7 + - + -
79D PHE* 3.4 39.3 - + + -
87D TYR* 4.0 6.5 - + + -
88D SER 3.6 4.3 - - - +
89D TRP* 3.7 23.1 - + + -
91D ARG* 4.9 0.2 - - - -
144D GLU* 2.5 24.3 + - - -
146D LEU* 3.7 19.5 - - + -
152D VAL* 3.5 6.8 - - - +
153D LEU* 2.7 50.1 + - + +
154D LYS 4.4 0.4 - - - -
155D GLY 4.0 8.5 - - - -
175D THR* 3.5 24.1 + - + +
176D THR* 1.3 73.1 - - - +
178D LYS* 1.3 60.5 + - - +
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Residues in contact with LYS 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D TYR* 3.7 1.8 - - - -
87D TYR* 3.3 3.7 - - - -
88D SER* 2.8 48.9 + - - +
89D TRP* 6.3 0.2 - - - -
90D GLU* 2.9 31.1 + - + +
152D VAL* 4.2 18.6 - - + -
176D THR* 3.9 24.0 - - + +
177D TYR* 1.3 77.7 - - - +
179D ALA* 1.3 67.3 + - - +
180D LYS* 3.6 1.9 + - - +
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Residues in contact with ALA 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D TYR* 2.9 25.5 + - + +
82D SER* 3.2 25.8 - - - +
87D TYR* 3.6 9.4 - - - -
152D VAL* 5.7 0.2 - - - +
178D LYS* 1.3 77.2 - - - +
180D LYS* 1.3 62.3 + - - +
181D LYS 3.3 20.5 + - - +
183D VAL* 4.1 8.5 - - + -
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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