Contacts of the strand formed by residues 78 - 85 (chain D) in PDB entry 3N2N
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 78 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43D PHE* 3.6 33.0 - - + -
45D LEU* 3.8 23.6 - - + -
69D LEU 5.4 0.9 - - - +
73D PHE* 3.5 35.0 - - + +
75D SER* 3.0 9.1 + - - +
76D PRO 3.9 2.3 - - - +
77D GLN* 1.3 76.9 - - - +
79D ARG* 1.3 74.5 + - - +
80D MET* 3.7 25.1 - - + -
97D GLU* 4.1 0.3 - - - -
99D ARG* 2.8 32.6 + - - -
212D ILE* 4.4 7.9 - - + -
216D LEU* 4.2 13.7 - - + -
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Residues in contact with ARG 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D PHE 2.9 7.9 + - - +
44D ASP* 3.0 39.2 + - - +
45D LEU* 2.8 27.2 + - - +
76D PRO 4.5 2.7 - - - +
77D GLN 3.9 1.8 + - - +
78D LEU* 1.3 77.1 - - - +
80D MET* 1.3 63.1 + - - +
95D LEU* 3.5 23.9 + - + +
96D THR* 3.2 10.3 - - - +
97D GLU* 3.6 37.9 - - + +
134D GLU* 2.8 36.2 + - - -
141D THR* 5.6 3.0 - - - +
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Residues in contact with MET 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D LEU* 3.1 18.4 - - + +
47D PHE* 4.2 13.9 - - + -
69D LEU 5.6 0.2 - - - -
70D ALA* 3.9 36.6 - - + +
73D PHE 4.2 0.4 - - - +
78D LEU* 3.7 21.8 - - + -
79D ARG* 1.3 76.5 - - - +
81D SER* 1.3 61.4 + - - +
82D PHE* 3.9 16.2 - - + -
93D MET* 3.3 22.4 - - + +
95D LEU* 3.4 4.4 - - - -
96D THR 2.9 27.6 + - - +
99D ARG* 3.5 28.7 - - - +
102D ILE* 3.9 20.2 - - + -
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Residues in contact with SER 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D LEU 2.9 5.5 + - - +
46D TYR* 3.8 18.2 - - - -
47D PHE* 2.9 27.9 + - - +
80D MET* 1.3 75.5 - - - +
82D PHE* 1.3 66.4 + - - +
83D ILE* 4.0 4.8 - - - +
91D THR* 3.8 2.4 - - - +
93D MET* 2.7 21.9 + - - -
95D LEU* 3.6 15.7 - - - -
130D GLN* 2.9 27.0 + - - -
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Residues in contact with PHE 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D PHE* 3.7 21.8 - + + -
49D LEU* 4.9 2.5 - - + -
66D VAL* 3.6 21.1 - - + -
70D ALA* 4.8 0.2 - - + -
80D MET* 3.9 22.7 - - + -
81D SER* 1.3 77.3 - - - +
83D ILE* 1.3 62.8 + - - +
91D THR 3.8 0.5 - - - -
92D LEU* 2.9 38.0 + - + -
93D MET* 3.0 42.4 + - + +
102D ILE* 3.8 9.9 - - + -
105D GLY* 3.8 13.0 - - - -
106D LEU* 3.7 42.2 - - + -
109D LEU* 3.8 21.5 - - + -
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Residues in contact with ILE 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D TYR* 4.5 7.6 - - + -
47D PHE 2.8 16.3 + - - +
48D ILE* 4.3 10.5 - - + -
49D LEU* 2.7 36.4 + - - +
81D SER* 4.0 9.9 - - - +
82D PHE* 1.3 77.9 - - - +
84D VAL* 1.3 64.9 + - - +
90D THR 3.5 10.3 - - - +
91D THR* 4.0 13.7 - - - +
123D GLY* 3.6 29.2 - - - +
126D ARG* 3.7 10.5 - - + -
127D ALA* 3.6 39.7 - - + +
130D GLN* 3.8 12.3 - - - +
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Residues in contact with VAL 84 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D LEU* 3.3 13.2 - - + +
51D LYS* 3.8 25.1 - - + +
59D TRP* 4.4 7.4 - - + -
82D PHE 4.4 0.4 + - - -
83D ILE* 1.3 80.6 - - - +
85D PHE* 1.3 65.8 + - - +
88D ARG 3.9 1.0 - - - +
89D GLY* 3.4 0.9 - - - -
90D THR* 2.9 48.3 + - - +
92D LEU* 4.3 13.2 - - + -
109D LEU* 3.8 29.4 - - + -
112D VAL* 4.7 2.7 - - + -
222D ACT 3.7 21.8 - - - +
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Residues in contact with PHE 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D ILE* 3.6 34.8 - - + -
49D LEU 2.9 14.2 + - - -
50D ASP* 3.3 39.9 - - + -
51D LYS* 2.8 30.5 + - - +
52D SER 3.8 0.7 + - - -
84D VAL* 1.3 76.0 - - - +
86D SER* 1.3 62.0 + - - +
88D ARG 3.3 9.9 - - - +
89D GLY* 4.0 8.3 - - - -
118D THR* 3.6 20.4 - - + -
119D TYR 3.9 13.7 - - - +
120D MET* 3.4 53.6 - - + -
123D GLY* 4.3 5.6 - - - +
148D LEU 4.3 1.3 - - - -
149D THR* 4.3 2.0 - - - -
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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