Contacts of the strand formed by residues 120 - 124 (chain M) in PDB entry 3INU
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 SER 120 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117M LYS* 6.1 1.0 - - - -
118M GLY 3.9 1.4 + - - -
119M PRO* 1.3 74.5 - - - +
121M VAL* 1.3 61.6 + - - +
122M PHE* 3.6 31.9 + - - -
143M LEU 3.4 3.5 - - - +
144M VAL* 3.6 0.5 - - - -
145M LYS* 2.8 38.9 + - - +
146M ASP* 5.0 4.0 + - - +
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Residues in contact with VAL 121 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119M PRO* 4.1 5.6 + - + +
120M SER* 1.3 75.6 - - - +
122M PHE* 1.3 63.1 + - - +
142M CYS* 3.7 22.0 - - + -
143M LEU 3.7 2.7 - - - -
144M VAL* 4.5 7.4 - - + +
208M CYS* 4.3 0.4 - - - -
210M VAL* 4.0 31.9 - - + -
219M VAL* 3.5 38.3 - - + +
221M LYS* 3.4 42.8 + - + +
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Residues in contact with PHE 122 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120M SER* 3.6 30.7 - - - -
121M VAL* 1.3 76.6 - - - +
123M PRO* 1.3 71.5 - - + +
142M CYS* 3.6 3.7 - - - -
143M LEU* 2.8 56.4 + - + +
145M LYS* 4.2 15.0 - - + -
146M ASP* 6.0 0.2 - - - -
221M LYS* 4.5 2.5 - - - -
121N SER* 3.8 6.5 - - - +
123N GLU* 4.0 13.5 - - + -
124N GLN* 3.4 65.3 - - + +
127N SER* 5.2 5.8 - - - -
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Residues in contact with PRO 123 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121M VAL 4.3 0.7 - - - +
122M PHE* 1.3 95.4 - - + +
124M LEU* 1.3 66.3 + - - +
125M ALA* 3.8 5.5 + - + +
141M GLY 3.9 0.4 - - - +
142M CYS* 4.9 0.2 - - - -
143M LEU* 5.2 0.9 - - - +
221M LYS* 4.1 22.3 - - + -
222M LYS 4.6 3.1 - - - +
225M VAL* 3.7 27.4 - - + -
226M GLU 5.4 2.5 - - - +
119N PRO 5.5 1.6 - - - +
121N SER* 3.5 31.9 + - - +
123N GLU* 4.7 7.9 - - + +
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Residues in contact with LEU 124 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123M PRO* 1.3 75.5 - - - +
125M ALA* 1.3 65.4 + - - +
126M PRO* 3.3 6.5 - - - +
140M LEU* 3.6 2.4 - - - +
141M GLY* 2.6 51.7 + - - +
142M CYS 3.8 15.3 - - - +
143M LEU* 3.9 15.0 - - + +
188M SER* 4.3 12.8 - - - -
189M SER 4.6 1.3 - - - +
190M VAL* 4.7 9.2 - - + -
225M VAL* 3.9 2.0 - - - +
118N PHE* 3.6 41.4 - - + -
119N PRO 5.6 3.4 - - - +
131N SER 5.8 1.1 - - - +
133N VAL* 3.7 27.4 - - + -
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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