Contacts of the strand formed by residues 81 - 90 (chain D) in PDB entry 1C9T
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 GLN 81 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65D VAL 3.1 6.8 - - - +
66D ARG* 3.1 2.1 - - - -
67D LEU* 3.0 48.3 + - + +
70D GLU* 4.6 0.8 + - - -
79D ASN* 5.4 6.3 + - - +
80D GLU* 1.3 82.2 - - - +
82D PHE* 1.3 66.6 + - - +
83D ILE* 3.8 7.9 - - + +
112D ALA* 4.2 10.9 - - - +
113D SER* 2.8 37.8 + - - -
115D ASN* 6.1 0.6 - - - +
118D VAL* 3.2 28.9 - - - +
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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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34D ASN* 5.7 5.2 - - - -
64D GLN* 5.7 16.6 - - + +
65D VAL 3.4 5.4 - - - -
66D ARG* 3.3 45.8 - - + -
70D GLU* 4.2 2.0 - - - -
76D VAL* 6.3 0.7 - - + -
80D GLU* 3.4 34.5 + - + -
81D GLN* 1.3 79.3 - - - +
83D ILE* 1.3 62.3 + - - +
84D SER* 4.4 0.3 + - - -
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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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64D GLN* 3.6 3.3 - - - -
65D VAL* 2.8 42.5 + - - +
67D LEU* 3.7 24.2 - - + -
81D GLN* 4.4 10.5 - - + +
82D PHE* 1.3 77.4 - - - +
84D SER* 1.3 77.3 + - - +
108D LEU* 3.7 21.8 - - + -
109D LYS* 4.5 1.6 - - + -
110D SER* 3.7 43.5 - - - +
111D ALA 4.7 2.0 - - - +
112D ALA* 4.0 14.8 - - - -
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Residues in contact with SER 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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63D ILE 4.1 5.6 - - - -
64D GLN* 4.5 13.9 + - - +
82D PHE 4.3 0.2 - - - -
83D ILE* 1.3 80.0 - - - +
85D ALA* 1.3 62.5 + - - +
108D LEU* 3.6 1.5 - - - -
109D LYS* 2.7 60.1 + - - +
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Residues in contact with ALA 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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62D GLY* 5.6 3.6 - - - -
63D ILE* 3.2 28.6 + - + +
65D VAL* 4.9 3.6 - - + -
84D SER* 1.3 75.0 - - - +
86D SER* 1.3 65.0 + - - +
87D LYS 4.9 0.4 - - - +
88D SER* 3.9 16.5 + - - +
106D ILE* 3.6 28.3 - - + -
107D LYS 3.4 4.3 - - - +
108D LEU* 4.4 1.6 - - - +
109D LYS* 4.9 1.9 - - - -
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Residues in contact with SER 86 (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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85D ALA* 1.3 73.5 - - - +
87D LYS* 1.3 83.1 + - - +
88D SER* 4.2 0.5 + - - -
107D LYS* 2.6 20.5 + - - -
108D LEU 4.4 2.2 - - - -
109D LYS* 3.6 26.2 - - - +
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Residues in contact with LYS 87 (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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51D TRP* 4.9 0.4 - - + -
86D SER* 1.3 100.6 - - - +
88D SER* 1.3 62.3 + - - +
89D ILE* 3.7 25.3 + - + +
105D LEU 4.0 0.2 - - - +
106D ILE* 3.6 2.1 - - - +
107D LYS* 2.8 52.5 + - + +
245D ASN* 3.7 28.5 + - + +
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Residues in contact with SER 88 (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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59D TYR* 3.8 36.1 - - - -
60D LYS 4.8 2.7 + - - -
62D GLY* 5.6 1.7 + - - -
63D ILE* 4.7 11.4 + - - +
85D ALA* 3.9 20.4 + - - +
86D SER 4.2 1.2 + - - -
87D LYS* 1.3 73.6 + - - +
89D ILE* 1.3 60.7 + - - +
90D VAL 3.7 2.6 + - - -
104D MET* 4.8 4.7 - - - -
105D LEU 3.6 5.2 - - - -
106D ILE* 4.5 11.4 - - - +
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Residues in contact with ILE 89 (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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51D TRP* 3.6 31.4 - - + -
87D LYS* 4.0 17.5 - - + -
88D SER* 1.3 71.5 - - - +
90D VAL* 1.3 68.8 + - - +
92D PRO* 6.0 0.2 - - + -
104D MET* 3.5 2.1 - - - -
105D LEU* 2.7 42.6 + - + +
237D TRP* 3.8 18.3 - - + -
241D THR* 3.9 9.6 - - + -
245D ASN* 3.8 25.8 - - - +
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Residues in contact with VAL 90 (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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56D ALA* 3.9 19.1 - - + +
59D TYR* 3.5 44.9 - - + -
88D SER 3.7 1.6 + - - -
89D ILE* 1.3 82.7 - - - +
91D HIS* 1.3 77.7 + - - +
92D PRO* 3.4 6.9 - - - +
94D TYR* 4.1 14.1 - - + -
104D MET* 3.9 14.1 - - + -
237D TRP* 4.3 1.1 - - - -
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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