Contacts of the strand formed by residues 148 - 154 (chain A) in PDB entry 3NDM
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 TYR 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A GLY* 6.4 1.1 - - - -
106A LEU* 4.2 22.7 - - + -
107A LEU 3.0 22.2 - - - +
108A SER* 3.7 20.2 - - - -
109A LYS* 3.6 7.2 - - - -
144A GLN* 3.3 5.5 - - - +
145A ASP* 3.0 28.1 + - - -
147A ARG* 1.3 112.9 + - + +
149A LEU* 1.3 63.8 + - - +
150A TYR* 3.5 31.6 - - + -
378A GLU* 3.3 28.3 + - - +
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Residues in contact with LEU 149 (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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105A LYS 3.7 0.5 - - - +
106A LEU* 3.2 6.6 - - - +
107A LEU* 2.8 41.9 + - + +
109A LYS* 3.5 15.4 - - + +
112A MET* 3.7 23.6 - - + -
121A PHE* 4.0 26.9 - - + -
143A PHE 3.6 1.1 - - - -
144A GLN* 3.3 26.5 - - + +
148A TYR* 1.3 73.4 - - - +
150A TYR* 1.3 60.5 + - - +
151A MET* 5.5 0.8 - - + +
394A PHE* 3.9 13.5 - - + -
397A PHE* 3.0 44.6 - - + -
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Residues in contact with TYR 150 (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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73A ALA* 3.2 33.4 - - + +
104A MET* 4.0 14.1 - - + -
105A LYS 3.5 4.0 - - - -
106A LEU* 3.5 37.7 - - + -
142A ALA* 3.2 6.9 - - - +
143A PHE* 2.7 71.1 + + + +
144A GLN* 4.0 3.6 - - - -
145A ASP* 2.5 31.9 + - - -
148A TYR* 3.5 30.5 - - + +
149A LEU* 1.3 76.3 - - - +
151A MET* 1.3 65.4 + - - +
152A VAL 4.1 0.7 - - - -
397A PHE* 3.8 2.1 - - - -
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Residues in contact with MET 151 (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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103A ALA 3.2 4.3 - - - +
104A MET* 3.1 21.5 - - - +
105A LYS* 3.0 31.5 + - + +
107A LEU* 5.2 11.4 - - + -
121A PHE* 4.2 4.7 - - + +
124A GLU* 4.1 24.9 - - + +
125A ARG* 3.6 42.2 - - + +
128A MET* 5.0 7.4 - - - +
139A LEU* 4.0 17.7 - - + -
141A TYR 3.6 4.3 - - - -
142A ALA* 5.1 1.6 - - + -
149A LEU 5.5 1.1 - - - -
150A TYR* 1.3 78.0 - - - +
152A VAL* 1.3 62.2 + - - +
153A MET* 3.5 11.0 + - + +
397A PHE* 3.9 19.5 - - + -
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Residues in contact with VAL 152 (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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76A TYR* 3.3 34.3 - - + +
102A TYR* 3.5 35.0 - - + -
103A ALA 3.9 2.7 - - - -
104A MET* 3.9 22.2 - - + +
139A LEU* 3.1 2.8 - - - +
140A PHE* 2.8 27.8 + - + +
141A TYR* 2.8 37.3 + - + +
143A PHE* 4.0 11.2 - - + -
151A MET* 1.3 69.8 - - - +
153A MET* 1.3 59.4 + - - +
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Residues in contact with MET 153 (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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90A VAL* 4.4 8.5 - - + -
102A TYR* 3.2 4.3 - - - +
103A ALA* 2.6 64.7 + - + +
105A LYS* 4.2 20.0 - - + +
124A GLU* 5.8 0.7 - - - +
128A MET* 3.2 37.0 - - + +
137A VAL* 4.1 11.2 - - + -
138A GLN 3.2 11.2 - - - +
139A LEU* 3.8 14.1 - - + -
140A PHE* 4.2 5.2 - - - -
151A MET* 3.7 17.7 - - - +
152A VAL* 1.3 78.4 - - - +
154A GLU* 1.3 61.5 + - - +
155A TYR 3.2 0.3 + - - -
215A ALA* 5.2 3.4 - - + +
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Residues in contact with GLU 154 (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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101A VAL 5.6 0.2 - - - -
102A TYR* 4.9 1.8 - - - -
103A ALA* 4.2 3.9 - - - +
136A VAL 4.6 0.5 - - - +
137A VAL* 3.5 15.5 - - + +
138A GLN* 3.0 53.1 + - - +
140A PHE* 3.7 23.7 - - + -
153A MET* 1.3 71.5 - - - +
155A TYR* 1.3 68.6 + - - +
156A MET* 3.2 13.9 + - + +
213A LYS* 2.9 38.6 + - - +
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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