Contacts of the strand formed by residues 158 - 162 (chain A) in PDB entry 3N4E
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 ALA 158 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A CYS 3.9 1.8 + - - -
129A TYR* 3.3 17.2 - - + -
130A SER 3.2 7.6 + - - -
156A PRO* 3.1 24.0 - - - +
157A ALA* 1.3 78.3 - - - +
159A VAL* 1.3 65.5 + - - +
193A VAL* 3.3 30.5 - - + +
221A TRP* 4.6 9.4 - - + -
322A PRO* 4.1 13.0 - - + -
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Residues in contact with VAL 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A TYR* 4.7 2.0 - - - -
130A SER* 3.7 6.1 - - - +
132A ILE* 3.8 26.2 - - + -
147A VAL* 4.0 10.8 - - + -
151A VAL* 3.5 30.1 - - + -
156A PRO* 4.1 5.8 - - + -
158A ALA* 1.3 79.0 - - - +
160A LYS* 1.3 55.2 + - - +
161A ILE* 4.1 13.7 - - + -
188A LEU* 3.8 23.1 - - + -
193A VAL 2.9 8.1 + - - +
194A ILE* 3.1 9.7 - - + +
195A GLY 2.7 29.6 + - - -
221A TRP* 4.7 1.5 - - - -
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Residues in contact with LYS 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A TYR* 2.6 39.7 + - + -
130A SER 2.9 10.9 + - - +
131A SER* 3.5 17.4 - - - -
132A ILE* 2.9 28.6 + - - +
159A VAL* 1.3 73.2 - - - +
161A ILE* 1.3 62.9 + - - +
162A ARG* 3.8 13.1 + - + +
195A GLY 3.3 15.9 - - - +
197A ASP* 3.9 13.2 - - + -
221A TRP* 3.6 19.7 - - + +
223A GLU* 2.8 43.6 + - + +
269A GLN* 4.7 0.8 - - - +
324A GLU* 3.0 14.5 + - - -
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Residues in contact with ILE 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A ILE* 3.4 6.5 - - + -
135A ASN* 3.6 14.8 - - - +
143A VAL* 4.9 2.5 - - + -
147A VAL* 3.7 29.4 - - + -
159A VAL* 4.1 11.9 - - + -
160A LYS* 1.3 74.8 - - - +
162A ARG* 1.3 59.8 + - - +
163A TRP* 3.7 27.7 - - + -
180A LYS 4.5 0.9 - - - +
181A ALA* 4.3 7.2 - - - -
184A VAL* 4.0 20.6 - - + -
194A ILE* 4.9 0.7 - - + -
195A GLY 3.0 13.5 + - - +
196A PHE* 3.6 7.1 - - + -
197A ASP 2.9 22.5 + - - -
219A TYR* 3.6 23.1 - - + +
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Residues in contact with ARG 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A SER* 3.0 39.2 + - - +
132A ILE 2.7 13.1 + - - +
133A GLY* 3.4 9.5 - - - +
134A GLY 3.6 2.1 + - - -
135A ASN* 2.8 27.7 + - - +
160A LYS* 3.8 13.2 - - - +
161A ILE* 1.3 73.0 - - - +
163A TRP* 1.3 65.5 + - - +
164A ASP* 3.3 28.2 + - - +
197A ASP* 3.4 32.1 - - + -
199A ASN* 3.5 11.7 + - - +
300A THR* 5.5 6.5 - - - +
324A GLU* 4.4 2.9 + - - -
326A ALA* 4.5 6.9 - - - +
327A ASP* 2.8 30.3 + - - -
500A CA 4.3 3.8 - - - -
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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