Contacts of the strand formed by residues 138 - 143 (chain D) in PDB entry 4MNE
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 GLU 138 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96D ARG* 5.6 0.5 + - - -
98D LEU* 3.7 37.6 - - + +
99D ILE 3.4 18.2 - - - +
100D HIS* 4.1 13.9 - - - +
101D LEU* 4.3 1.8 - - - +
134D TYR* 3.6 11.6 - - - -
135D SER* 3.1 39.7 + - - +
136D ASP* 4.1 13.3 - - - +
137D GLY* 1.3 82.1 - - - +
139D ILE* 1.3 62.8 + - - +
140D SER* 3.8 1.7 + - - -
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Residues in contact with ILE 139 (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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97D LYS 3.4 3.1 - - - +
98D LEU* 3.5 2.2 - - - -
99D ILE* 3.0 42.9 + - + +
101D LEU* 3.7 26.0 - - + -
103D ILE* 4.7 2.5 - - + -
108D ARG* 4.4 9.9 - - + +
111D ILE* 4.2 16.8 - - + -
112D ILE* 4.0 30.7 - - + -
115D LEU* 4.2 13.0 - - + -
133D PHE 3.7 2.7 - - - +
134D TYR* 4.2 15.3 - - + -
138D GLU* 1.3 72.0 - - - +
140D SER* 1.3 70.1 + - - +
141D ILE* 4.0 18.7 + - + -
215D LEU* 5.6 1.6 - - + -
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Residues in contact with SER 140 (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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96D ARG* 2.9 37.0 + - - -
97D LYS 3.2 4.5 - - - -
98D LEU* 3.1 12.3 - - - +
132D ALA* 3.2 9.0 - - - +
133D PHE* 2.8 59.7 + - - -
135D SER* 6.0 0.2 - - - -
138D GLU* 3.8 2.7 + - - +
139D ILE* 1.3 71.5 - - - +
141D ILE* 1.3 62.5 + - - +
142D CYS 4.0 0.4 - - - -
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Residues in contact with ILE 141 (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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95D ALA 3.4 3.5 - - - +
96D ARG* 4.6 0.2 - - - -
97D LYS* 2.9 35.5 + - + +
99D ILE* 4.1 19.7 - - + -
115D LEU* 3.8 32.3 - - + -
118D LEU* 5.0 0.9 - - + -
129D PHE* 4.0 22.2 - - + -
131D GLY 3.7 2.5 - - - -
132D ALA* 4.6 0.4 - - + -
139D ILE* 4.1 5.8 - - + -
140D SER* 1.3 77.0 - - - +
142D CYS* 1.3 64.6 + - - +
143D MET* 3.6 6.5 + - + +
215D LEU* 4.6 2.0 - - + -
903D 573 3.6 55.6 - - + +
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Residues in contact with CYS 142 (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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68D PHE* 4.1 12.6 - - - -
94D MET* 3.7 28.0 - - - -
95D ALA 3.5 4.5 - - - -
96D ARG* 4.2 17.3 - - - +
129D PHE* 3.8 3.8 - - - -
130D TYR* 2.8 26.8 + - + -
131D GLY* 2.7 26.4 + - - +
133D PHE* 3.9 28.3 - - - -
140D SER* 5.0 0.2 - - - -
141D ILE* 1.3 73.1 - - - +
143D MET* 1.3 59.1 + - - +
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Residues in contact with MET 143 (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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82D VAL* 4.8 1.3 - - + -
95D ALA* 2.7 47.6 + - + +
97D LYS* 3.6 33.4 - - + +
127D VAL* 4.2 4.3 - - + -
128D GLY 3.5 13.2 - - - +
129D PHE* 4.6 2.5 - - + -
130D TYR* 3.4 11.6 - - - +
141D ILE* 3.7 15.5 - - + +
142D CYS* 1.3 75.6 - - - +
144D GLU* 1.3 61.5 + - - +
145D HIS 3.1 0.2 + - - -
207D CYS* 3.8 24.2 - - - -
901D ACP 3.3 39.5 - - - +
903D 573 3.8 20.9 - - + -
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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