Contacts of the strand formed by residues 152 - 163 (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 VAL 152 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C TYR* 4.1 10.5 - - - +
148C VAL* 3.3 7.6 - - - +
149C ARG 2.9 36.7 + - - +
150C ASP* 4.1 8.1 - - + +
151C GLY* 1.3 83.7 - - - +
153C LEU* 1.3 61.1 + - - +
154C LYS* 4.5 6.5 - - - -
176C THR* 3.8 25.6 - - + -
177C TYR 3.3 10.5 - - - +
178C LYS* 4.1 21.8 - - + -
179C ALA 5.4 0.7 - - - +
185C LEU* 4.7 4.0 - - - -
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Residues in contact with LEU 153 (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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78C TYR* 3.8 45.1 + - + -
79C PHE* 3.8 24.2 - - + -
146C LEU* 3.9 16.6 - - + -
147C TYR* 3.4 32.5 - - - +
148C VAL* 4.1 13.0 - - + +
152C VAL* 1.3 76.5 - - - +
154C LYS* 1.3 69.4 + - - +
176C THR* 3.7 0.5 - - - +
177C TYR* 2.8 39.9 + - + +
186C PRO* 4.3 17.0 - - + +
189C HIS* 4.6 2.9 - - + -
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Residues in contact with LYS 154 (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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126A PRO* 6.0 5.9 - - - +
145C LYS 3.8 0.2 - - - +
146C LEU* 3.1 8.1 - - - +
147C TYR* 2.7 64.7 + - + +
149C ARG* 3.8 44.2 - - + +
152C VAL* 4.5 8.1 - - + +
153C LEU* 1.3 77.2 - - - +
155C GLY* 1.3 58.7 - - - +
156C ASP* 4.9 1.3 - - - +
175C THR 3.3 4.9 - - - +
176C THR* 3.2 44.6 - - + +
177C TYR* 4.3 4.7 - - - -
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Residues in contact with GLY 155 (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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144C GLU* 3.5 22.4 - - - -
145C LYS 3.3 6.5 - - - -
146C LEU* 4.4 0.4 - - - -
154C LYS* 1.3 75.7 - - - +
156C ASP* 1.3 64.2 + - - +
157C VAL* 4.5 0.6 + - - -
173C PHE* 3.9 0.9 - - - +
174C LYS* 3.5 1.4 - - - -
175C THR* 2.7 44.1 + - - -
177C TYR* 4.0 6.6 - - - -
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Residues in contact with ASP 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C GLU* 4.3 0.6 - - - +
145C LYS* 2.9 42.4 + - + +
147C TYR* 2.8 26.3 + - + -
154C LYS* 4.9 0.9 - - - +
155C GLY* 1.3 83.4 + - - +
157C VAL* 1.3 62.4 + - - +
173C PHE 3.4 6.3 - - - +
174C LYS* 3.3 25.6 - - + +
175C THR 4.4 1.0 + - - +
158E ASN* 4.8 4.3 - - + +
170E ARG* 2.3 47.9 + - - +
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Residues in contact with VAL 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C KZ4 3.5 24.5 - - + -
142C SER* 4.0 18.8 - - - -
143C THR 3.2 28.3 - - - +
144C GLU* 3.7 17.7 - - + -
145C LYS* 4.6 4.3 - - - +
155C GLY 5.8 0.2 - - - +
156C ASP* 1.3 78.2 - - - +
158C ASN* 1.3 75.3 + - - +
159C THR* 3.8 2.6 + - + -
171C CYS 3.9 0.3 - - - +
172C ASP* 3.7 0.3 - - - -
173C PHE* 2.8 49.0 + - + +
145E LYS* 4.7 1.3 - - - +
158E ASN* 3.9 2.2 + - - -
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Residues in contact with ASN 158 (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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142C SER* 5.7 0.2 - - - -
145C LYS* 5.3 0.2 - - - +
157C VAL* 1.3 74.4 + - - +
159C THR* 1.3 59.3 - - - +
170C ARG* 2.9 27.5 + - - +
171C CYS 3.6 0.4 - - - -
172C ASP* 2.3 48.5 + - - +
173C PHE 4.3 0.4 + - - +
174C LYS* 5.2 1.6 - - - +
145E LYS* 3.3 33.8 - - - +
156E ASP* 4.8 7.1 - - + +
157E VAL 4.6 0.2 - - - -
158E ASN* 2.2 52.3 + - - +
172E ASP* 3.6 5.0 - - - +
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Residues in contact with THR 159 (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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63C KZ4 4.1 10.2 + - + +
139C TRP* 3.6 25.1 - - + -
140C GLU 4.1 8.7 + - - -
141C PRO 4.4 2.6 + - - -
142C SER* 3.7 28.0 - - - -
157C VAL* 4.3 3.1 - - + +
158C ASN* 1.3 75.3 - - - +
160C ALA* 1.3 75.0 + - - +
170C ARG* 2.8 18.4 + - - -
171C CYS 2.9 24.5 + - - +
173C PHE* 3.9 20.0 - - + -
145E LYS* 5.4 0.2 - - - -
188E TYR* 4.2 8.0 + - - -
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Residues in contact with ALA 160 (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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139C TRP* 3.5 12.0 - - - -
140C GLU* 3.1 27.3 + - - +
159C THR* 1.3 84.8 + - - +
161C LEU* 1.3 58.5 + - - +
168C HIS* 4.0 16.6 - - + -
169C TYR 3.3 11.4 - - - +
170C ARG* 4.1 13.0 - - - +
188E TYR* 4.0 28.5 + - + +
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Residues in contact with LEU 161 (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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55C ASP* 3.6 27.1 - - + +
56C ILE* 5.0 4.9 - - + -
95C TYR* 4.0 9.6 - - + +
136C THR* 4.0 17.0 - - + -
138C LYS 3.3 20.9 - - - +
139C TRP* 3.5 49.1 - - + +
160C ALA* 1.3 73.8 - - - +
162C SER* 1.3 65.0 + - - +
163C LEU* 5.1 0.4 - - + -
168C HIS* 3.2 6.9 - - - -
169C TYR* 2.8 60.3 + - + +
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Residues in contact with SER 162 (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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136C THR* 3.6 3.8 - - - -
137C VAL* 2.8 54.2 + - - +
138C LYS* 2.8 22.5 + - - +
140C GLU* 3.8 21.7 + - - +
160C ALA 4.2 0.8 + - - -
161C LEU* 1.3 76.1 - - - +
163C LEU* 1.3 57.1 + - - +
167C GLY 3.8 6.5 - - - -
168C HIS* 3.8 8.1 - - - -
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Residues in contact with LEU 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C PRO* 3.8 20.6 - - + -
135C ARG* 3.6 28.7 - - + +
136C THR* 4.4 5.8 - - + -
137C VAL* 3.6 7.9 - - - +
161C LEU 4.4 0.7 - - - +
162C SER* 1.3 80.9 - - - +
164C GLU* 1.3 66.2 + - - +
165C GLY 3.0 3.6 + - - +
166C GLY* 3.2 31.8 + - - +
167C GLY* 3.0 12.2 + - - +
168C HIS 4.2 16.8 - - - +
169C TYR* 3.7 28.7 - - + -
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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