Contacts of the strand formed by residues 101 - 108 (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 VAL 101 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C LEU* 3.5 27.8 - - + -
93C VAL 3.3 11.9 - - - +
94C ARG* 3.1 39.7 - - + +
99C ARG 3.8 1.1 - - - +
100C LYS* 1.3 83.8 - - - +
102C TYR* 1.3 70.2 + - - +
154C GLU* 5.5 0.2 - - - -
155C TYR* 4.1 12.8 + - + +
362C ASP* 3.7 19.3 - - + +
363C ILE* 4.2 9.9 - - + -
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Residues in contact with TYR 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C TYR* 5.0 4.7 - + - -
92C LEU* 3.4 8.1 - - - +
93C VAL* 2.9 35.4 + - + +
95C HIS* 4.1 23.4 - + + -
98C THR* 5.0 0.2 + - - -
100C LYS* 3.4 53.5 + - + +
101C VAL* 1.3 81.0 - - - +
103C ALA* 1.3 62.1 + - - +
104C MET 4.1 0.7 - - - -
140C PHE* 3.2 45.5 - + + +
141C TYR* 4.5 17.0 + + - -
152C VAL* 3.5 26.0 - - + -
153C MET 3.0 8.5 - - - +
154C GLU* 4.8 0.7 - - - -
155C TYR* 4.1 8.7 - - - +
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Residues in contact with ALA 103 (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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82C ILE* 4.2 4.7 - - + -
90C VAL* 4.0 4.9 - - + -
91C GLN 3.1 9.6 - - - +
92C LEU* 4.7 0.2 - - - +
102C TYR* 1.3 72.3 - - - +
104C MET* 1.3 59.3 + - - +
105C LYS 3.9 0.4 - - - -
153C MET* 2.5 47.3 + - - +
155C TYR* 3.9 8.9 - - + +
900C 3ND 3.2 39.7 - - + +
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Residues in contact with MET 104 (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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73C ALA* 5.2 5.4 - - + +
76C TYR* 3.6 33.0 - - + -
90C VAL* 3.6 0.3 - - - -
91C GLN* 2.8 49.1 + - + +
93C VAL* 3.8 17.9 - - + +
102C TYR 4.1 0.6 - - - -
103C ALA* 1.3 70.1 - - - +
105C LYS* 1.3 59.8 + - - +
106C LEU* 3.4 36.7 - - + +
143C PHE* 4.2 5.2 - - - -
150C TYR* 3.6 26.5 - - + -
151C MET 3.2 13.2 - - - +
152C VAL* 3.9 16.8 - - + -
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Residues in contact with LYS 105 (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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89C GLU 3.0 10.5 - - - +
90C VAL* 3.3 30.4 - - + +
103C ALA 3.8 0.8 + - - -
104C MET* 1.3 72.8 - - - +
106C LEU* 1.3 69.8 + - - +
107C LEU* 4.1 25.8 - - + +
120C PHE* 5.8 2.6 - - - -
124C GLU* 2.6 38.8 + - - +
149C LEU 3.8 0.3 - - - +
150C TYR* 3.6 2.9 - - - -
151C MET* 3.0 37.8 + - + +
153C MET* 4.0 13.7 - - + -
215C ALA 5.1 1.2 + - - +
216C ASP* 3.5 24.6 + - - +
900C 3ND 4.0 18.5 - - + +
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Residues in contact with LEU 106 (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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88C GLY* 3.6 4.5 - - - -
89C GLU* 2.6 41.6 + - + +
91C GLN* 3.1 28.3 - - - +
104C MET* 3.4 37.0 - - + +
105C LYS* 1.3 79.4 - - - +
107C LEU* 1.3 69.5 + - - +
148C TYR* 4.4 25.4 - - + -
149C LEU 3.2 4.3 - - - +
150C TYR* 3.5 26.9 - - + +
900C 3ND 4.7 0.2 - - - +
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Residues in contact with LEU 107 (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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87C PHE* 3.8 26.9 - - + +
88C GLY* 5.2 0.7 - - - -
105C LYS* 4.1 28.0 - - + +
106C LEU* 1.3 83.4 - - - +
108C SER* 1.3 61.2 + - - +
112C MET* 4.1 10.1 - - + -
120C PHE* 4.3 17.3 - - + -
121C PHE* 4.2 24.9 - - + -
124C GLU* 5.7 0.9 - - - +
148C TYR* 3.1 31.7 - - - -
149C LEU* 2.8 31.9 + - + +
151C MET* 4.7 13.9 - - + -
397C PHE* 5.1 0.4 - - + -
900C 3ND 4.7 3.8 - - + -
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Residues in contact with SER 108 (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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87C PHE* 3.1 20.2 + - - +
88C GLY* 5.6 0.7 - - - -
107C LEU* 1.3 72.2 - - - +
109C LYS* 1.3 67.0 + - - +
110C PHE* 3.5 9.4 + - - +
111C GLU* 3.4 33.9 + - - +
112C MET* 2.8 27.6 + - - +
147C ARG 3.9 2.9 + - - -
148C TYR* 4.0 15.7 - - - -
378C GLU* 5.9 2.4 - - - +
379C GLU 5.2 1.6 + - - -
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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