Contacts of the strand formed by residues 88 - 95 (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 GLY 88 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84C ARG* 3.8 6.6 - - - +
85C GLY 3.2 22.1 + - - +
86C ALA 3.3 3.8 + - - -
87C PHE* 1.3 81.8 - - - +
89C GLU* 1.3 72.3 + - - +
106C LEU* 3.6 10.5 - - - -
107C LEU* 4.8 0.4 - - - -
108C SER* 5.0 1.1 - - - -
900C 3ND 4.1 3.3 - - - +
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Residues in contact with GLU 89 (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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81C VAL* 3.6 19.2 - - - +
83C GLY 3.5 13.2 - - - +
84C ARG* 3.9 22.7 + - - +
88C GLY* 1.3 79.8 - - - +
90C VAL* 1.3 60.2 + - - +
91C GLN* 3.4 32.7 - - - +
104C MET 4.0 0.5 - - - +
105C LYS* 3.0 1.4 - - - -
106C LEU* 2.6 49.4 + - + +
374C ASP 4.9 6.2 - - - +
900C 3ND 3.7 15.6 - - - +
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Residues in contact with VAL 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C VAL* 3.6 1.2 - - - +
82C ILE* 3.4 10.2 + - + -
83C GLY 3.0 29.6 + - - +
89C GLU* 1.3 75.1 - - - +
91C GLN* 1.3 77.0 + - - +
103C ALA* 4.0 11.4 - - + -
104C MET 3.7 5.6 - - - +
105C LYS* 3.3 38.6 - - + +
153C MET* 4.0 7.4 - - + -
900C 3ND 3.7 53.7 - - + +
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Residues in contact with GLN 91 (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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78C VAL* 3.3 30.2 - - + +
80C LYS 3.8 8.1 - - - +
81C VAL* 4.4 10.3 - - + -
82C ILE* 4.0 6.3 - - - +
89C GLU* 3.4 26.4 - - - +
90C VAL* 1.3 75.4 - - - +
92C LEU* 1.3 67.7 + - - +
93C VAL* 4.2 4.4 - - + +
103C ALA* 3.1 9.0 - - - +
104C MET* 2.8 46.2 + - - +
106C LEU* 3.1 39.7 - - - +
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Residues in contact with LEU 92 (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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79C VAL* 3.0 47.3 + - + +
80C LYS 3.2 7.1 + - - +
82C ILE* 3.4 16.5 - - + +
91C GLN* 1.3 74.6 - - - +
93C VAL* 1.3 73.0 + - - +
101C VAL* 3.5 20.2 - - + -
102C TYR 3.4 16.6 - - - +
155C TYR* 3.6 33.9 - - + -
363C ILE* 3.8 25.6 - - + -
365C THR* 3.6 20.0 - - + -
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Residues in contact with VAL 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C TYR* 4.3 24.0 - - + -
77C GLU 3.0 20.9 - - - +
78C VAL* 3.2 18.2 - - + -
79C VAL* 3.5 4.7 - - - -
91C GLN* 4.1 12.8 - - - +
92C LEU* 1.3 88.2 - - - +
94C ARG* 1.3 58.9 + - - +
95C HIS 3.9 0.9 + - - -
100C LYS 3.8 0.2 - - - +
101C VAL* 3.3 7.1 - - - +
102C TYR* 2.9 42.8 + - + +
104C MET* 3.8 31.4 - - + +
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Residues in contact with ARG 94 (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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76C TYR* 4.9 0.4 - - - -
77C GLU* 3.1 39.5 + - + +
79C VAL* 4.1 6.8 - - + +
93C VAL* 1.3 70.5 - - - +
95C HIS* 1.3 53.6 + - - +
96C LYS* 2.6 20.4 + - - -
99C ARG* 3.1 73.7 + - - +
100C LYS 3.0 4.0 - - - +
101C VAL* 3.1 18.6 - - + +
362C ASP* 2.7 31.1 + - - -
363C ILE* 3.5 31.9 - - - +
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Residues in contact with HIS 95 (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* 4.7 1.4 - - + +
75C ASP* 3.5 18.7 + - + -
76C TYR* 3.7 35.8 + + + -
93C VAL 3.9 2.6 + - - -
94C ARG* 1.3 66.9 - - - +
96C LYS* 1.3 54.1 + - - +
97C SER* 2.7 31.0 + - - -
98C THR* 3.5 17.2 + - - +
99C ARG* 2.7 32.6 + - - -
100C LYS 2.6 22.5 + - - +
102C TYR* 4.1 21.0 - + + -
141C TYR* 4.5 4.9 - + - -
7D PHE* 3.4 33.1 - + - -
10D ARG* 4.7 5.4 - - - -
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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