Contacts of the strand formed by residues 119 - 125 (chain D) in PDB entry 4MJI
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 119 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117D ASP* 2.8 18.5 + - + +
118D PRO* 1.3 71.5 - - - +
120D VAL* 1.3 61.4 + - - +
121D TYR* 3.3 40.0 - - + +
135D LEU 3.1 13.6 - - - +
136D PHE* 4.3 4.8 - - - -
137D THR 3.2 17.2 + - - +
138D ASP* 4.5 3.1 - - - +
196D ASP 3.9 4.0 - - - -
197D THR* 3.7 11.2 - - + -
139E HIS* 5.6 2.2 - - + -
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Residues in contact with VAL 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D ALA* 1.3 70.2 - - - +
121D TYR* 1.3 63.9 + - - +
134D CYS* 3.9 19.1 - - + -
135D LEU 3.6 5.2 - - - +
136D PHE* 3.7 27.8 - - + -
184D CYS* 3.9 32.5 - - + +
188D PHE* 3.8 25.6 - - + -
193D ILE* 6.3 1.1 - - + -
196D ASP 4.2 2.8 + - - +
197D THR 3.3 19.0 + - - +
198D PHE* 3.8 24.4 - - - +
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Residues in contact with TYR 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D ALA* 3.3 37.9 - - + +
120D VAL* 1.3 78.0 - - - +
122D GLN* 1.3 60.9 + - - +
123D LEU* 4.7 5.8 - - + -
134D CYS* 3.0 9.2 - - - -
135D LEU* 2.9 38.4 + - + +
137D THR* 3.5 23.3 - - + -
184D CYS* 3.8 5.8 - - - -
197D THR* 3.7 17.0 - - + -
198D PHE* 4.5 4.7 - + - -
133E SER* 3.6 16.8 - - - +
135E ALA* 3.5 37.0 - - + -
136E GLU* 3.8 26.1 - - + -
139E HIS* 3.8 19.2 - - - +
140E THR* 4.0 10.6 - - - +
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Residues in contact with GLN 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D TYR* 1.3 75.0 - - - +
123D LEU* 1.3 61.4 + - - +
132D SER* 3.6 30.2 + - - -
133D VAL 3.9 3.4 - - - -
183D ALA* 4.4 17.0 - - - +
184D CYS* 3.3 25.5 - - - +
133E SER* 2.9 25.7 + - - -
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Residues in contact with LEU 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D TYR* 4.4 4.9 - - + +
122D GLN* 1.3 81.4 - - - +
124D ARG* 1.3 60.2 + - - +
125D ASP 4.0 0.2 - - - -
131D LYS 3.7 7.3 - - - +
132D SER* 4.5 1.4 - - - -
133D VAL* 3.0 47.6 + - + +
135D LEU* 3.3 44.4 - - + +
130E PHE* 4.3 4.9 - - + -
131E GLU 2.6 27.4 - - - +
132E PRO* 3.6 16.6 - - + -
133E SER* 3.6 11.0 - - - +
136E GLU* 5.1 2.0 - - - +
144E THR 3.9 7.4 - - - +
146E VAL* 4.0 16.8 - - + -
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Residues in contact with ARG 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D GLN 4.3 0.2 - - - -
123D LEU* 1.3 72.9 - - - +
125D ASP* 1.3 75.3 + - - +
128D SER 4.3 10.5 - - - +
129D SER* 5.3 7.6 - - - +
131D LYS 4.9 0.4 - - - +
130E PHE* 4.2 0.2 - - - -
131E GLU* 2.8 45.5 + - + +
134E GLU* 5.5 4.9 + - - -
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Residues in contact with ASP 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D ARG* 1.3 72.9 - - - +
126D SER* 1.3 72.2 + - - +
127D LYS 3.4 0.2 + - - -
128D SER* 2.8 35.3 + - - +
130D ASP* 2.4 43.3 + - - +
131D LYS 3.3 15.2 - - - +
128E ALA* 5.4 3.8 - - + -
129E VAL 3.5 12.8 - - - +
130E PHE* 3.4 33.5 - - + +
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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