Contacts of the strand formed by residues 95 - 101 (chain D) in PDB entry 3N84
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 PHE 95 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95B PHE* 3.4 33.9 - + - -
118B TYR* 3.2 27.4 - - - -
128B LEU* 3.9 5.8 - - + -
61D PHE* 3.7 17.0 - + - -
85D ILE* 3.9 21.5 - - + -
86D ARG 3.5 7.2 - - - +
87D GLU* 3.6 25.8 - - + -
93D GLY 4.4 3.4 - - - -
94D ASP* 1.3 77.0 - - - +
96D SER* 1.3 63.5 + - - +
109D LYS* 4.0 4.3 - - - +
110D VAL* 3.0 47.2 + - + +
112D ARG* 6.2 0.9 - - - -
118D TYR* 4.1 17.9 - + - -
128D LEU* 3.9 15.5 - - + -
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Residues in contact with SER 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D LEU 3.9 0.3 - - - +
85D ILE* 3.5 6.4 - - - +
86D ARG* 2.9 67.3 + - - +
88D SER* 3.6 7.4 - - - +
94D ASP 4.4 0.2 + - - -
95D PHE* 1.3 76.4 + - - +
97D LEU* 1.3 61.8 + - - +
98D SER 4.0 0.4 - - - -
108D PHE 3.5 8.3 - - - -
109D LYS* 4.7 1.4 + - - -
110D VAL* 4.7 0.2 - - - -
1J PTR 2.9 33.8 + - - -
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Residues in contact with LEU 97 (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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83D PHE* 3.5 32.5 - - + -
84D LEU 3.4 17.3 - - - +
85D ILE* 3.9 14.8 - - + -
96D SER* 1.3 72.1 - - - +
98D SER* 1.3 58.4 + - - +
99D VAL* 3.9 9.4 - - + -
107D HIS* 3.3 2.5 - - - -
108D PHE* 2.8 49.0 + - + +
110D VAL* 4.6 5.3 - - + +
120D LEU* 4.2 13.5 - - + -
131D LEU* 4.2 16.8 - - + -
132D VAL* 5.3 0.2 - - + -
140D VAL* 3.6 29.8 - - + -
148D LEU* 4.2 9.4 - - + -
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Residues in contact with SER 98 (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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70D ALA* 4.1 9.0 - - - -
74D LEU* 3.4 19.3 - - - +
83D PHE* 3.2 6.9 - - - +
84D LEU* 3.0 35.9 + - - -
86D ARG* 2.9 23.0 + - - -
96D SER 3.9 0.6 + - - -
97D LEU* 1.3 72.5 - - - +
99D VAL* 1.3 58.8 + - - +
106D GLN 3.4 5.2 - - - -
107D HIS* 2.8 30.7 + - - -
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Residues in contact with VAL 99 (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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74D LEU* 3.9 1.0 - - - +
81D GLY* 3.6 32.5 - - - +
82D ALA 3.5 3.4 - - - -
83D PHE* 4.1 0.4 - - + -
97D LEU* 3.9 12.3 - - + -
98D SER* 1.3 80.4 - - - +
100D LYS* 1.3 68.2 + - - +
101D PHE* 4.4 0.6 - - + +
105D VAL* 3.4 6.3 - - - +
106D GLN* 2.7 43.1 + - + +
108D PHE* 3.8 25.4 - - + -
140D VAL* 4.5 1.8 - - + -
146D ILE* 3.7 17.9 - - + -
148D LEU* 3.8 23.1 - - + -
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Residues in contact with LYS 100 (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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74D LEU* 3.4 22.6 - - + +
75D SER* 3.0 32.7 + - - +
77D GLN* 3.2 22.9 + - + +
78D ARG 4.5 6.7 - - - -
79D HIS 3.5 26.0 - - - +
80D ASP* 3.5 11.4 - - - +
81D GLY 2.8 26.6 + - - -
82D ALA* 2.8 21.4 + - + +
99D VAL* 1.3 75.1 - - - +
101D PHE* 1.3 63.6 + - - +
102D GLY 3.4 20.6 + - - -
103D ASN 5.9 0.4 - - - -
104D ASP 4.0 8.3 + - - +
105D VAL* 4.6 4.5 - - + +
146D ILE* 4.6 0.3 - - - +
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Residues in contact with PHE 101 (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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3D GOL 3.8 41.0 + - - -
80D ASP* 3.7 10.1 - - + -
99D VAL 3.5 1.7 + - - +
100D LYS* 1.3 76.2 - - - +
102D GLY* 1.3 65.9 + - - +
103D ASN 3.5 0.3 + - - -
104D ASP* 3.0 28.9 + - + +
106D GLN* 3.4 41.1 - - + -
144D GLN* 3.8 30.5 - - + -
145D GLN 4.8 4.3 - - - -
146D ILE* 3.6 32.1 - - + -
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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