Contacts of the strand formed by residues 159 - 163 (chain A) in PDB entry 1M9H
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 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A LEU* 3.9 19.7 - - + -
14A ILE* 5.2 3.1 - - + -
104A LEU* 4.0 15.0 - - + -
106A LEU* 3.7 22.7 - - + -
137A GLY* 3.3 2.6 - - - -
138A VAL 2.9 24.6 + - - -
157A PRO* 3.2 7.0 - - - +
158A ALA* 1.3 93.4 - - + +
160A ASN* 1.3 66.4 + - - +
161A GLN 4.2 2.9 - - - +
182A VAL* 3.6 6.3 - - - -
183A LYS* 3.0 17.0 - - + +
185A GLU* 3.6 32.8 - - + +
228A VAL* 6.3 0.4 - - + -
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Residues in contact with ASN 160 (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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138A VAL* 3.2 29.2 - - + +
139A SER* 3.4 3.3 - - - -
140A ASN 3.4 0.9 + - - -
141A HIS 2.9 39.8 + - - -
146A LEU* 3.9 10.1 - - + +
159A VAL* 1.3 75.4 - - - +
161A GLN* 1.3 62.0 + - - +
162A ILE* 3.5 17.0 + - - +
173A ILE* 3.5 14.1 - - + +
177A ALA* 5.8 0.4 - - + -
182A VAL* 4.2 10.8 - - + -
183A LYS 2.9 8.3 + - - -
184A ILE* 3.6 18.1 - - + +
185A GLU 3.2 18.0 + - - -
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Residues in contact with GLN 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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45A ASP* 3.2 21.0 + - - -
75A LYS* 3.3 11.0 + - - +
106A LEU* 3.7 11.6 - - + +
138A VAL 3.0 13.2 + - - +
139A SER* 2.8 27.7 + - - +
140A ASN 2.8 12.8 + - - -
159A VAL* 4.1 1.0 - - - +
160A ASN* 1.3 71.8 + - - +
162A ILE* 1.3 57.7 + - - +
185A GLU* 2.8 48.8 + - + +
187A TRP* 3.6 11.8 - - + -
230A PHE* 3.3 16.6 - - + -
300A NAD 2.8 38.5 + - - +
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Residues in contact with ILE 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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140A ASN* 3.9 14.1 - - - +
141A HIS 4.5 2.7 - - - +
160A ASN* 3.5 33.0 - - - +
161A GLN* 1.3 78.7 - - - +
163A GLU* 1.3 60.5 + - - +
164A LEU* 3.3 27.1 + - + -
170A GLN* 3.6 33.2 - - + +
173A ILE* 4.1 18.8 - - + -
174A THR* 4.3 7.0 - - + -
184A ILE* 4.4 5.8 - - + -
185A GLU 2.9 8.0 + - - +
186A SER* 3.6 1.2 - - - -
187A TRP* 2.8 35.5 + - - +
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Residues in contact with GLU 163 (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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140A ASN* 4.3 1.0 + - - -
162A ILE* 1.3 73.7 - - - +
164A LEU* 1.3 64.4 + - - +
165A HIS* 3.1 23.7 + - + +
168A TYR* 3.6 16.5 - - + +
170A GLN* 2.6 38.3 + - - +
187A TRP* 3.2 39.1 - - + +
188A GLY* 5.4 0.7 - - - +
269A ARG* 3.6 8.3 - - - +
270A VAL* 2.7 30.0 + - + +
271A SER* 3.1 35.1 + - - -
272A GLY 4.5 2.4 - - - +
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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