Contacts of the strand formed by residues 75 - 84 (chain D) in PDB entry 4CDC
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 TYR 75 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314B PHE* 4.9 2.3 - - - -
436C ILE* 3.5 17.5 + - + +
437C PRO* 2.8 31.5 + - + -
438C LYS* 3.8 8.1 - - - -
439C LEU* 3.9 34.3 + - + -
70D ILE 3.7 0.9 - - - +
71D VAL* 3.4 3.1 - - - +
72D LEU 2.9 32.5 + - - +
73D ASN* 3.1 25.7 - - + -
74D ASP* 1.3 78.4 - - - +
76D LYS* 1.3 61.9 + - - +
77D TRP* 4.1 9.2 - - - +
102D VAL* 4.1 18.2 - - + -
103D HIS* 3.3 8.1 - - - +
104D ASP* 3.3 33.8 - - + +
105D VAL* 4.4 0.4 - - - +
109D ASN* 4.5 20.3 + - + +
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Residues in contact with LYS 76 (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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69D GLU* 4.1 7.1 + - - +
70D ILE 3.2 7.0 - - - +
71D VAL* 4.0 23.1 - - + +
75D TYR* 1.3 75.2 - - - +
77D TRP* 1.3 61.6 + - - +
101D TRP 3.7 1.7 - - - +
102D VAL* 3.3 5.0 - - - -
103D HIS* 2.7 54.8 + - + +
105D VAL* 4.1 30.7 - - + +
285E LYS* 4.2 9.2 + - - +
288E GLN* 3.2 27.5 + - - +
321E TYR* 3.6 27.7 + - - +
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Residues in contact with TRP 77 (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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439C LEU* 3.5 27.3 - - + +
17D PHE* 3.6 39.3 - + + -
19D VAL* 3.8 20.2 - - + -
40D VAL* 4.2 17.9 - - + -
42D VAL* 5.2 5.1 - - + +
68D PHE* 4.4 1.6 - - + -
69D GLU* 3.2 8.7 - - - +
70D ILE* 2.8 64.4 + - + +
72D LEU* 4.5 9.6 + - + +
75D TYR* 4.1 14.7 + - - +
76D LYS* 1.3 77.1 - - - +
78D PHE* 1.3 62.0 + - - +
101D TRP 3.6 4.0 - - - -
102D VAL* 3.5 28.5 - - + +
113D PHE* 3.7 35.4 - + + -
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Residues in contact with PHE 78 (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* 3.9 10.8 - - + -
67D GLY* 5.2 1.1 - - - -
68D PHE* 3.2 15.3 - - - +
69D GLU* 4.5 2.5 - - + -
77D TRP* 1.3 77.5 - - - +
79D ALA* 1.3 81.0 + - - +
80D PHE* 3.6 24.7 - + - -
100D GLY* 3.4 0.7 - - - -
101D TRP* 2.9 55.8 + + - +
113D PHE* 3.5 4.0 - - - -
270E TYR* 3.7 24.0 - + - -
281E LEU* 3.5 41.5 - - + -
285E LYS* 3.5 34.8 - - + +
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Residues in contact with ALA 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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67D GLY* 3.3 2.9 - - - -
68D PHE* 3.2 34.9 + - + -
78D PHE* 1.3 89.0 - - - +
80D PHE* 1.3 60.3 + - - +
97D THR* 3.8 26.7 - - + +
98D MET 4.0 2.5 - - - +
99D THR 5.2 0.4 - - - -
100D GLY* 3.7 19.7 - - - -
101D TRP* 5.1 1.3 - - - -
113D PHE* 3.8 13.0 - - + -
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Residues in contact with PHE 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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2D THR* 4.2 16.6 - - + -
66D GLN* 3.4 32.1 - - + +
67D GLY* 4.0 0.2 - - - -
78D PHE* 3.6 21.5 - + - -
79D ALA* 1.3 75.7 - - - +
81D PHE* 1.3 67.1 + - - +
83D TYR* 5.1 0.2 - - + -
97D THR* 3.4 5.4 - - - -
98D MET* 3.0 40.3 + - + +
99D THR 5.4 0.6 + - - -
101D TRP* 4.6 8.7 - + - -
269E GLN 3.6 20.6 - - - -
270E TYR 3.5 23.3 - - - -
272E GLN* 3.6 21.5 - - - -
278E PHE* 6.2 1.1 - + - -
281E LEU* 3.9 16.6 - - + -
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Residues in contact with PHE 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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2D THR* 5.0 0.3 + - - -
4D ALA* 4.4 8.2 - - + +
6D CYS* 3.5 41.7 - - + -
7D THR 5.0 1.3 - - - -
10D ASP* 5.8 0.7 - - + -
11D LEU* 4.2 21.5 - - + -
15D TRP* 4.5 6.5 - + - -
62D ILE* 4.2 16.2 - - + -
65D ASN 3.7 9.2 - - - -
66D GLN 2.8 31.0 + - - +
67D GLY* 3.3 30.5 - - - -
68D PHE* 4.0 19.7 - + - -
80D PHE* 1.3 77.1 - - - +
82D LYS* 1.3 65.6 + - - +
83D TYR* 3.5 15.1 - - - -
93D TYR 4.4 2.0 - - - +
94D CYS 4.0 21.1 - - - -
96D GLU 3.7 9.4 - - - +
97D THR* 4.3 0.4 - - + +
98D MET* 3.7 2.9 - - - +
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Residues in contact with LYS 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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4D ALA* 5.0 0.2 - - - +
80D PHE 3.6 1.4 + - - -
81D PHE* 1.3 73.5 - - - +
83D TYR* 1.3 67.2 + - - +
84D LYS* 3.3 33.9 - - - +
92D THR* 3.7 5.0 - - - +
93D TYR* 3.0 45.1 + - + +
96D GLU* 3.0 56.4 + - + +
97D THR* 3.7 13.9 - - - +
98D MET* 3.7 18.8 - - - +
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Residues in contact with TYR 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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2D THR* 3.6 37.5 - - + +
3D PRO* 3.7 27.1 - - + +
4D ALA* 5.0 3.1 - - + +
80D PHE* 5.1 1.6 - - + -
81D PHE 3.5 15.9 - - - -
82D LYS* 1.3 76.7 + - - +
84D LYS* 1.3 74.3 + - - +
90D VAL* 4.5 7.9 - - + -
91D THR 3.2 15.0 - - - +
92D THR* 4.3 9.9 - - - +
93D TYR* 4.8 1.1 - - - -
98D MET* 3.6 39.6 - - + +
272E GLN* 5.4 4.5 + - - +
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Residues in contact with LYS 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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82D LYS* 3.3 28.0 - - - +
83D TYR* 1.3 84.3 - - - +
89D LYS 3.6 7.6 - - - +
90D VAL* 3.4 17.0 - - - +
91D THR* 3.1 33.7 + - - +
93D TYR* 4.3 25.0 + - + +
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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