Contacts of the strand formed by residues 144 - 148 (chain A) in PDB entry 1X0X
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 MET 144 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A PHE* 3.5 14.4 - - + -
115A GLY* 3.1 42.0 - - - +
116A ILE* 4.4 1.8 - - - -
117A SER 4.9 2.0 - - - -
133A SER* 3.7 23.3 - - - +
136A ILE* 3.8 18.6 - - + -
137A GLY* 3.7 13.9 - - - -
142A ILE* 3.2 39.7 + - + +
143A PRO* 1.3 76.0 - - - +
145A SER* 1.3 68.8 + - - +
168A CYS* 5.3 1.0 - - - -
169A LYS* 5.5 5.9 + - - +
194A VAL* 4.6 15.3 - - - +
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Residues in contact with SER 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLY 2.8 8.6 + - - -
116A ILE* 3.3 6.9 - - - -
117A SER* 2.7 28.9 + - - -
144A MET* 1.3 78.8 + - - +
146A VAL* 1.3 67.0 + - - +
166A ILE* 4.7 0.9 - - - -
167A GLY 3.3 13.5 - - - -
168A CYS* 3.1 29.0 - - - -
173A GLN* 4.4 3.3 + - - +
177A LEU* 3.5 26.6 - - - +
194A VAL* 4.7 1.6 - - - -
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Residues in contact with VAL 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ILE* 3.9 4.7 - - - -
117A SER* 3.2 14.1 - - - +
133A SER* 3.9 10.5 - - - -
145A SER* 1.3 82.8 - - - +
147A LEU* 1.3 59.7 + - - +
148A MET* 4.2 8.3 - - + -
165A THR 3.7 0.5 - - - +
166A ILE* 3.2 5.9 - - - +
167A GLY* 2.8 38.1 + - - +
194A VAL* 3.8 31.9 - - + +
197A VAL* 3.9 14.4 - - + -
198A GLU* 3.4 36.1 - - + +
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Residues in contact with LEU 147 (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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14A TRP* 4.5 10.7 + - + +
18A ILE* 5.8 0.2 - - + -
116A ILE* 3.7 12.5 - - + +
117A SER 3.0 7.3 + - - -
118A LEU* 3.7 24.8 - - + +
120A LYS* 5.3 0.7 - - - -
146A VAL* 1.3 72.8 - - - +
148A MET* 1.3 76.2 + - - +
151A ASN* 4.0 9.6 - - - +
164A THR* 2.9 38.8 - - + +
165A THR 3.4 2.0 - - - -
166A ILE* 3.8 27.1 - - + -
181A MET* 3.4 36.8 - - + -
186A PHE* 4.3 9.0 - - + -
2001A NAD 6.2 0.2 - - - -
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Residues in contact with MET 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A SER* 3.5 18.6 - - - +
118A LEU 3.6 7.6 - - - -
119A ILE 3.3 24.5 - - - +
120A LYS* 3.8 32.1 - - - +
146A VAL* 4.0 8.7 - - + -
147A LEU* 1.3 89.9 - - - +
149A GLY* 1.3 58.8 + - - +
164A THR* 3.3 4.5 - - - -
165A THR* 2.8 39.5 + - - +
197A VAL* 3.7 23.1 - - + +
198A GLU* 4.2 15.9 - - + +
201A GLY* 4.1 10.3 - - - -
256A CYS* 3.4 20.9 - - + +
260A ASP* 5.8 0.2 - - - +
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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