Contacts of the strand formed by residues 139 - 144 (chain C) 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 LEU 139 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C ARG* 4.2 11.7 - - + +
128C MET* 2.6 29.5 + - + +
129C ALA* 3.9 21.7 - - + +
138C GLN* 1.3 76.7 - - - +
140C PHE* 1.3 64.7 + - - +
141C TYR 2.7 32.5 - - - +
142C ALA* 4.0 16.8 - - + -
151C MET* 3.8 27.4 - - + -
152C VAL 2.9 30.1 - - - +
153C MET* 3.8 5.4 - - + +
399C TYR* 3.9 17.7 + - + -
401C SER 4.7 1.7 - - - +
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Residues in contact with PHE 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C TYR* 3.2 39.0 - + + +
138C GLN* 3.4 39.3 - - + -
139C LEU* 1.3 81.2 - - - +
141C TYR* 1.3 88.7 + - + +
152C VAL 2.8 8.2 + - - +
153C MET 4.1 1.6 - - - -
154C GLU* 3.5 43.1 - - + -
399C TYR* 4.1 3.2 - - - +
401C SER 3.0 28.1 + - - +
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Residues in contact with TYR 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C MET* 3.2 32.1 - - + -
76C TYR* 3.2 22.7 - - - -
95C HIS* 4.5 8.2 - + - -
102C TYR* 4.5 15.8 + + - -
139C LEU* 2.7 15.7 - - - +
140C PHE* 1.3 107.6 - - + +
142C ALA* 1.3 57.6 + - - +
143C PHE* 4.7 0.7 - - + -
151C MET* 3.4 0.2 - - - -
152C VAL* 2.7 50.4 + - + -
399C TYR 3.5 5.4 - - - +
400C TYR* 4.4 5.4 - + + -
401C SER 4.2 21.5 - - - -
402C ASN 4.5 6.0 - - - -
7D PHE* 2.6 37.4 - + - -
11D PHE* 4.5 8.7 - + - -
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Residues in contact with ALA 142 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125C ARG* 4.9 1.8 - - - +
139C LEU* 4.0 14.1 - - + -
141C TYR* 1.3 76.5 - - - +
143C PHE* 1.3 67.9 + - - +
150C TYR 3.2 13.7 - - - +
151C MET* 4.7 0.4 - - + -
397C PHE* 4.0 18.8 - - + +
398C THR* 3.3 3.2 - - - +
399C TYR* 2.7 51.7 + - + +
400C TYR* 4.8 2.6 - - - -
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Residues in contact with PHE 143 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C MET* 3.4 59.2 - - + +
72C LYS* 4.8 0.4 - - - -
73C ALA* 4.0 20.2 - - - -
76C TYR* 4.6 5.2 - + - -
104C MET* 4.2 11.0 - - - -
142C ALA* 1.3 81.8 - - - +
144C GLN* 1.3 65.6 + - - +
149C LEU* 3.6 1.4 - - - -
150C TYR* 2.7 76.8 + + + +
152C VAL* 4.1 14.8 - - + -
397C PHE* 4.0 5.1 - - - -
398C THR* 3.7 21.0 - - + +
400C TYR* 5.2 2.5 - - + +
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Residues in contact with GLN 144 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C ASP* 2.9 36.3 + - - +
35C ASP* 4.9 11.0 - - - +
39C TYR* 5.3 0.2 + - - -
70C ARG* 5.8 0.7 - - - +
109C LYS* 2.7 33.2 + - - +
143C PHE* 1.3 84.9 - - - +
145C ASP* 1.3 62.0 + - - +
148C TYR 3.2 10.8 - - - +
149C LEU* 3.7 10.8 - - + -
150C TYR* 4.0 3.4 - - - -
391C GLN* 4.3 2.3 - - - +
394C PHE* 2.9 33.5 + - - +
395C VAL* 4.4 0.4 - - - +
397C PHE* 4.1 1.3 - - + +
398C THR* 3.7 15.1 + - - +
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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