Contacts of the strand formed by residues 142 - 149 (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 SER 142 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63D KZ4 2.9 40.4 + - - +
140D GLU 3.7 0.2 + - - -
141D PRO* 1.3 75.4 - - - +
143D THR* 1.3 63.1 + - - +
157D VAL* 4.0 8.7 - - - +
159D THR* 3.7 17.3 - - - -
192D ASP* 3.3 5.4 - - - +
193D HIS* 2.8 41.7 + - - +
145F LYS* 5.7 4.9 - - - -
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Residues in contact with THR 143 (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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142D SER* 1.3 74.4 + - - +
144D GLU* 1.3 62.1 + - - +
145D LYS* 3.6 10.8 - - - +
157D VAL* 3.3 14.4 - - - +
190D PHE* 3.9 27.6 - - + -
191D VAL 3.5 3.8 - - - +
192D ASP* 2.6 26.4 + - - +
216D HIS* 4.0 1.8 - - - +
143F THR* 3.7 41.9 - - - +
145F LYS* 3.7 13.1 + - - +
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Residues in contact with GLU 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D KZ4 5.9 1.3 - - - -
66D ARG* 3.1 17.3 + - - -
142D SER 4.1 0.6 - - - -
143D THR* 1.3 72.7 - - - +
145D LYS* 1.3 66.1 + - - +
146D LEU* 3.7 18.9 - - + +
155D GLY* 3.5 16.7 - - - +
156D ASP 3.9 11.9 - - - +
157D VAL* 3.7 19.4 - - + +
175D THR* 4.7 2.3 + - - -
177D TYR* 2.5 26.4 + - - -
190D PHE* 3.1 10.4 - - - +
191D VAL* 2.8 37.8 + - - +
193D HIS* 2.8 27.9 + - + +
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Residues in contact with LYS 145 (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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143D THR* 3.6 16.8 - - - +
144D GLU* 1.3 73.3 - - - +
146D LEU* 1.3 60.8 + - - +
147D TYR* 4.1 6.6 - - + -
154D LYS 3.8 0.3 - - - +
155D GLY* 3.2 4.0 - - - -
156D ASP* 2.8 47.3 + - + +
157D VAL* 5.6 1.1 - - - -
188D TYR* 3.5 27.6 + - + +
189D HIS 3.7 3.1 - - - -
190D PHE* 3.6 22.2 - - + -
141F PRO 4.4 1.0 + - - -
142F SER* 3.5 16.6 - - - +
143F THR* 3.3 44.3 + - - +
145F LYS* 4.2 4.0 - - - +
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Residues in contact with LEU 146 (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* 5.0 1.3 - - + -
71D TYR* 4.6 0.9 - - - +
79D PHE* 4.2 11.9 - - + -
144D GLU* 3.7 33.4 - - + +
145D LYS* 1.3 77.2 - - - +
147D TYR* 1.3 62.4 + - - +
153D LEU* 4.0 19.7 - - + -
154D LYS 3.1 7.0 - - - +
177D TYR* 3.7 30.1 - - + -
187D ASP 4.2 0.2 - - - +
188D TYR* 3.4 6.8 - - - -
189D HIS* 2.8 58.0 + - + +
190D PHE 4.1 0.9 - - - -
191D VAL* 3.6 31.0 - - + +
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Residues in contact with TYR 147 (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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145D LYS* 4.1 8.3 - - + -
146D LEU* 1.3 79.6 - - - +
148D VAL* 1.3 69.1 + - - +
149D ARG* 4.2 31.8 + - + -
153D LEU* 3.4 8.3 - - - +
154D LYS* 2.8 66.3 + - + +
156D ASP* 3.0 38.8 + - - -
174D LYS* 5.7 0.3 - - - +
187D ASP 5.3 1.3 - - - -
188D TYR* 3.5 36.1 - + + +
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Residues in contact with VAL 148 (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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147D TYR* 1.3 82.1 - - - +
149D ARG* 1.3 67.9 + - - +
150D ASP 4.7 0.7 - - - +
151D GLY 4.1 10.8 - - - +
152D VAL 3.3 15.3 - - - +
153D LEU* 4.3 2.9 - - + -
185D LEU* 3.8 38.6 - - + -
186D PRO* 3.3 33.4 + - + +
188D TYR 5.8 0.2 - - - +
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Residues in contact with ARG 149 (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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147D TYR* 3.8 28.3 + - + -
148D VAL* 1.3 75.0 + - - +
150D ASP* 1.3 77.0 + - + +
151D GLY 3.2 1.3 - - - -
152D VAL* 3.0 27.6 + - - +
154D LYS* 3.8 32.8 + - + +
96F GLU* 2.8 43.6 + - - -
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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