Contacts of the strand formed by residues 154 - 161 (chain E) in PDB entry 6NZD
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 GLY 154 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149E LEU 3.7 2.9 - - - +
151E SER* 3.1 34.1 + - - -
152E ASP 3.2 3.6 + - - -
153E ASN* 1.3 79.7 - - - +
155E ASN* 1.3 66.7 + - - -
156E ILE* 4.2 1.3 + - - +
169E HIS* 4.1 3.7 + - - -
170E LYS 3.6 10.8 - - - -
171E MET* 3.8 14.0 - - - +
172E ALA* 4.7 4.7 - - - -
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Residues in contact with ASN 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ILE* 3.5 40.7 - - + +
125A PRO* 5.8 1.8 - - - +
128A ASP* 5.1 4.9 + - - -
148E CYS* 5.6 0.2 - - + -
149E LEU 3.3 5.4 - - - +
150E GLU* 3.4 25.1 + - - +
151E SER 4.0 3.3 + - - +
154E GLY* 1.3 76.2 - - - -
156E ILE* 1.3 62.0 + - - +
157E MET* 3.8 12.1 + - + +
168E VAL 3.3 2.8 - - - +
169E HIS* 3.4 1.3 - - - -
170E LYS* 2.9 38.1 + - + +
172E ALA* 4.2 21.6 - - - +
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Residues in contact with ILE 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D LEU* 3.4 34.5 - - + -
56D HIS* 4.0 22.9 - - + +
119E LEU* 4.2 12.8 - - + -
127E ILE* 5.4 1.8 - - + -
147E VAL 3.5 2.1 - - - +
148E CYS* 3.2 3.5 - - - -
149E LEU* 2.8 49.0 + - + +
154E GLY 5.4 1.6 - - - +
155E ASN* 1.3 73.7 - - - +
157E MET* 1.3 60.9 + - - +
158E ILE* 4.2 21.8 - - + +
167E ALA* 4.3 12.6 - - + -
168E VAL 3.4 5.6 - - - +
169E HIS* 3.9 21.1 - - + +
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Residues in contact with MET 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ILE* 4.2 22.7 - - + -
128A ASP* 3.5 24.5 - - + +
129A LEU* 3.4 34.8 - - + -
132A VAL* 3.5 39.0 - - + +
146E VAL* 4.0 7.4 - - + -
147E VAL 3.5 4.3 - - - -
148E CYS* 3.9 12.6 - - - +
155E ASN* 4.2 13.2 - - + +
156E ILE* 1.3 76.6 - - - +
158E ILE* 1.3 61.3 + - - +
166E VAL 3.8 0.9 - - - +
167E ALA* 3.3 1.7 - - - -
168E VAL 2.8 36.1 + - - +
170E LYS* 5.1 9.2 - - - -
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Residues in contact with ILE 158 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A VAL* 5.0 0.2 - - - -
127E ILE* 3.7 26.5 - - + +
130E LEU* 4.0 30.5 - - + -
131E ALA* 4.0 12.1 - - + +
145E PRO 3.9 0.7 - - - +
146E VAL* 3.2 7.9 - - - +
147E VAL* 2.7 49.6 + - + +
149E LEU* 5.2 4.7 - - + -
156E ILE* 4.2 17.0 - - + +
157E MET* 1.3 78.1 - - - +
159E GLN* 1.3 63.0 + - - +
165E THR* 3.5 26.5 - - + -
166E VAL 3.3 4.9 - - - +
167E ALA* 3.9 14.8 - - + -
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Residues in contact with GLN 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A VAL* 4.6 10.4 - - + +
133A SER* 3.3 35.3 + - - +
136A ALA* 4.2 14.7 - - + +
131E ALA* 5.4 0.9 - - - -
144E ILE* 3.2 32.5 + - + +
145E PRO 3.5 10.5 - - - +
146E VAL* 3.5 22.6 - - + +
157E MET 4.4 0.2 - - - -
158E ILE* 1.3 75.6 - - - +
160E LYS* 1.3 75.6 + - - +
161E HIS* 3.9 4.2 + - + -
165E THR* 3.6 4.0 - - - -
166E VAL 2.9 31.6 + - - +
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Residues in contact with LYS 160 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E SER* 4.8 11.2 - - - -
131E ALA* 4.1 19.2 - - + +
132E GLN* 4.2 34.8 - - + +
135E ALA* 6.2 2.5 - - + -
144E ILE* 3.4 28.4 - - + +
145E PRO 4.8 0.6 + - - -
159E GLN* 1.3 80.4 - - - +
161E HIS* 1.3 64.0 + - - +
162E ASP* 2.9 32.7 + - - +
163E GLY* 5.1 0.2 - - - -
164E ILE 3.4 4.9 - - - +
165E THR* 3.5 21.2 - - - +
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Residues in contact with HIS 161 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A SER* 4.9 3.6 - - - -
136A ALA* 4.2 16.4 - - + +
137A ALA* 3.7 33.7 - - + +
140A TYR* 3.4 34.4 - + + -
159E GLN* 3.9 3.6 + - + -
160E LYS* 1.3 74.1 - - - +
162E ASP* 1.3 82.5 + - - +
163E GLY 3.2 1.4 + - - -
164E ILE* 2.6 37.0 + - + +
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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