Contacts of the strand formed by residues 101 - 108 (chain B) 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 VAL 101 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92B LEU* 3.3 31.9 - - + -
93B VAL 2.9 9.9 - - - +
94B ARG* 3.7 31.6 - - + +
99B ARG 4.0 0.9 - - - +
100B LYS* 1.3 79.2 - - - +
102B TYR* 1.3 66.7 + - - +
155B TYR* 4.2 11.5 + - + +
362B ASP* 4.2 17.3 - - + +
363B ILE* 3.9 24.0 - - + -
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Residues in contact with TYR 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B TYR* 3.9 14.8 - + - -
92B LEU* 3.1 20.8 - - - +
93B VAL* 2.8 20.1 + - + -
95B HIS* 4.4 6.2 - + + -
98B THR* 5.3 0.9 + - - -
100B LYS* 3.5 51.2 + - + +
101B VAL* 1.3 79.9 - - - +
103B ALA* 1.3 61.4 + - - +
140B PHE* 3.3 42.9 - + + -
141B TYR* 3.9 32.0 + + - -
152B VAL* 3.4 28.9 - - + -
153B MET 3.3 9.0 - - - +
154B GLU* 4.6 1.1 - - - -
155B TYR* 3.9 8.1 - - - +
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Residues in contact with ALA 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B ILE* 4.1 9.9 - - + -
90B VAL* 4.5 3.4 - - + -
91B GLN 3.2 8.3 - - - +
92B LEU* 4.6 0.2 - - - +
102B TYR* 1.3 74.0 - - - +
104B MET* 1.3 59.0 + - - +
153B MET* 2.5 51.9 + - + +
155B TYR* 3.8 8.5 - - + +
900B 3ND 3.7 37.9 - - + +
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Residues in contact with MET 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B ALA* 5.0 6.3 - - + +
76B TYR* 4.2 30.1 - - + -
90B VAL* 4.3 0.4 - - - -
91B GLN* 2.6 53.7 + - - +
93B VAL* 3.9 17.9 - - + -
102B TYR 4.1 0.6 - - - -
103B ALA* 1.3 71.7 - - - +
105B LYS* 1.3 57.2 + - - +
106B LEU* 3.2 27.6 + - + +
143B PHE* 4.0 25.6 - - + -
150B TYR* 4.0 15.9 - - + -
151B MET 3.1 17.3 - - - +
152B VAL* 4.2 11.0 - - + -
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Residues in contact with LYS 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B GLU 3.3 11.7 - - - +
90B VAL* 3.9 12.5 - - + +
104B MET* 1.3 72.1 - - - +
106B LEU* 1.3 61.7 + - - +
107B LEU* 3.5 34.3 + - + +
120B PHE* 5.4 3.6 - - - -
124B GLU* 3.1 37.0 + - - +
149B LEU 3.6 0.9 - - - +
150B TYR* 3.3 4.3 - - - -
151B MET* 2.9 43.1 + - + +
153B MET* 3.5 24.2 - - + +
215B ALA 5.2 0.2 + - - -
216B ASP* 3.6 21.4 + - - +
900B 3ND 3.7 25.3 - - + -
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B GLY* 3.2 5.5 - - - -
89B GLU* 2.7 44.0 + - + +
91B GLN* 3.5 29.6 - - - +
104B MET* 3.2 24.5 - - + +
105B LYS* 1.3 75.1 - - - +
107B LEU* 1.3 67.1 + - - +
148B TYR* 4.0 24.7 - - + -
149B LEU 3.1 3.4 - - - +
150B TYR* 3.1 45.1 - - + +
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Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B PHE* 3.8 22.2 - - + +
88B GLY* 5.0 0.2 - - - -
105B LYS* 3.5 34.8 - - + +
106B LEU* 1.3 81.7 - - - +
108B SER* 1.3 61.2 + - - +
112B MET* 3.4 19.7 - - + -
120B PHE* 4.6 13.0 - - + -
121B PHE* 4.1 26.2 - - + -
124B GLU* 5.8 1.1 - - - +
148B TYR* 3.1 15.6 - - - +
149B LEU* 2.7 44.7 + - + +
151B MET* 4.9 13.2 - - + -
900B 3ND 4.4 3.8 - - + -
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Residues in contact with SER 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B PHE 2.9 20.7 + - - -
88B GLY* 5.3 0.9 - - - -
107B LEU* 1.3 72.5 - - - +
109B LYS* 1.3 65.5 + - - +
110B PHE* 3.5 9.2 + - - +
111B GLU* 3.1 34.3 + - - +
112B MET* 2.8 27.6 + - - +
147B ARG 4.0 4.4 + - - -
148B TYR* 4.3 12.2 - - - -
378B GLU* 5.8 2.6 - - - +
379B GLU* 5.6 1.4 + - - +
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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