Contacts of the strand formed by residues 135 - 143 (chain A) in PDB entry 2MJN
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 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A LEU* 3.2 19.0 - - - +
103A SER 3.6 18.8 - - - -
104A PRO* 3.1 20.5 + - - +
106A ILE 3.2 20.4 + - - -
126A VAL* 3.3 16.9 - - - +
128A LYS* 3.8 9.6 - - - +
134A LYS* 1.3 75.0 - - - +
136A LYS* 1.3 59.4 + - - +
137A GLY 3.0 16.4 + - - -
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Residues in contact with LYS 136 (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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127A VAL* 2.9 38.5 + - + +
128A LYS 4.0 17.9 - - - +
129A ASP* 4.0 8.5 - - + +
134A LYS 4.4 0.2 - - - +
135A SER* 1.3 74.4 - - - +
137A GLY* 1.3 57.4 + - - +
138A TYR* 2.8 46.6 + - + -
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Residues in contact with GLY 137 (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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100A GLY* 3.2 0.7 - - - -
101A ASP* 2.8 29.2 + - - -
102A LEU* 3.5 28.3 - - - -
135A SER* 3.0 8.9 + - - -
136A LYS* 1.3 79.7 - - - +
138A TYR* 1.3 63.4 + - - +
167A ARG* 5.0 0.9 + - - -
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Residues in contact with TYR 138 (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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98A PHE* 4.2 20.4 - + + -
99A VAL 3.2 13.0 - - - +
100A GLY* 4.4 0.9 - - - -
102A LEU* 3.6 14.3 - - - +
126A VAL* 3.7 2.6 - - - +
127A VAL* 3.0 54.6 + - + +
135A SER* 3.8 1.8 + - - -
136A LYS* 2.8 52.6 + - + -
137A GLY* 1.3 82.7 - - - +
139A GLY* 1.3 60.5 + - - +
140A PHE* 5.6 4.7 - + - -
167A ARG* 5.2 2.0 - - - +
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Residues in contact with GLY 139 (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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98A PHE* 3.5 5.2 - - - -
99A VAL* 2.8 38.9 + - - +
102A LEU* 4.6 1.3 - - - -
111A ILE* 5.4 0.4 - - - -
125A ARG 3.2 13.5 - - - -
126A VAL* 4.1 3.4 - - - -
127A VAL* 4.2 6.5 - - - -
138A TYR* 1.3 79.1 - - - +
140A PHE* 1.3 69.5 - - - -
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Residues in contact with PHE 140 (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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96A HIS* 4.8 9.9 - + + -
97A VAL 3.1 17.7 - - - +
98A PHE* 3.5 37.2 - + + -
99A VAL* 4.5 1.3 - - - +
111A ILE* 5.6 0.2 - - - +
125A ARG* 2.8 62.8 + - + +
127A VAL* 5.5 7.0 - - + -
138A TYR* 5.6 5.6 - + - -
139A GLY* 1.3 79.7 - - - -
141A VAL* 1.3 63.7 + - - +
171A ALA* 4.3 14.1 - - + -
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Residues in contact with VAL 141 (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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95A PHE 3.4 1.7 - - - +
96A HIS* 3.1 8.6 - - - -
97A VAL* 2.9 32.3 + - + +
99A VAL* 3.9 15.9 - - + -
111A ILE* 3.4 31.2 - - + -
115A PHE* 4.8 4.3 - - + -
121A ILE* 3.7 22.0 - - + -
123A ASP 3.6 11.2 - - - +
124A ALA* 3.8 4.5 - - + +
125A ARG* 5.3 0.2 - - - +
140A PHE* 1.3 80.2 - - - +
142A SER* 1.3 64.1 + - - +
143A PHE* 3.4 35.1 + - + -
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Residues in contact with SER 142 (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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94A HIS* 5.7 3.6 - - - -
95A PHE 3.4 5.4 - - - -
96A HIS* 2.8 25.8 + - - -
121A ILE* 3.5 3.6 - - - +
122A SER* 2.8 31.8 + - - -
123A ASP* 2.7 23.3 + - - +
125A ARG* 2.8 26.8 + - - +
141A VAL* 1.3 71.2 - - - +
143A PHE* 1.3 62.4 + - - +
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Residues in contact with PHE 143 (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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94A HIS* 2.8 25.0 + - - +
95A PHE* 2.8 25.0 + - + +
97A VAL* 3.5 27.1 - - + -
115A PHE* 4.0 13.9 - + + -
119A GLY* 3.6 33.2 - - - -
120A ARG 3.4 16.8 - - - +
121A ILE* 3.7 10.1 - - + -
122A SER* 3.8 1.1 - - - -
141A VAL* 3.4 26.5 - - + -
142A SER* 1.3 74.0 - - - +
144A PHE* 1.3 56.4 + - - +
145A ASN 3.3 16.4 - - - +
148A ASP* 3.9 4.3 - - + -
149A ALA* 3.4 21.1 - - + -
152A ALA* 3.6 22.4 - - + -
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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