Contacts of the strand formed by residues 93 - 99 (chain D) in PDB entry 4GKH
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 ASP 93 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14C ARG* 5.3 2.3 + - - -
16C ASN* 4.7 14.0 + - + +
56D HIS* 2.6 29.6 + - - +
57D GLY 3.4 3.6 - - - -
58D LYS* 2.7 32.4 + - - +
62D ALA* 3.9 3.8 - - - -
88D ILE 4.0 0.4 - - - +
89D ARG* 3.5 3.8 - - - -
90D THR* 2.9 43.4 + - - +
92D ASP* 1.3 91.1 - - - +
94D ALA* 1.3 60.9 + - - +
95D TRP* 4.0 15.1 + - + +
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Residues in contact with ALA 94 (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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55D LYS 3.6 0.8 - - - +
56D HIS* 3.3 8.5 - - - -
57D GLY 2.9 29.1 + - - -
62D ALA* 3.5 32.5 - - + +
65D VAL* 3.9 15.9 - - + -
66D THR* 4.0 9.9 - - - +
87D PHE* 4.1 3.8 - - + -
88D ILE 3.3 7.2 - - - +
89D ARG* 4.0 4.5 - - - -
93D ASP* 1.3 74.9 - - - +
95D TRP* 1.3 62.2 + - - +
96D LEU 4.2 0.4 - - - -
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Residues in contact with TRP 95 (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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13C PRO* 4.9 4.3 - - + -
14C ARG* 3.5 15.7 - - - -
15C LEU* 3.4 31.9 - - + -
16C ASN* 4.5 17.0 - - + +
19D LEU* 4.6 17.7 - - + -
41D TYR* 4.4 13.2 - + - -
54D LEU* 3.9 37.2 - - + -
55D LYS 3.3 4.0 - - - -
56D HIS* 3.4 56.2 + + + -
86D HIS 3.9 0.7 - - - +
87D PHE* 3.2 9.2 - - - -
88D ILE* 2.9 56.3 + - + +
90D THR* 5.8 1.1 - - + -
93D ASP* 4.0 12.6 + - + +
94D ALA* 1.3 79.4 - - - +
96D LEU* 1.3 60.3 + - - +
97D LEU 4.1 0.2 - - - -
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Residues in contact with LEU 96 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53D PHE 3.5 2.1 - - - +
54D LEU* 3.4 5.1 - - - +
55D LYS* 2.8 44.4 + - + +
65D VAL* 3.7 31.9 - - + +
68D GLU* 3.6 24.0 - - - +
69D MSE 3.9 22.0 - - + +
72D LEU* 4.2 11.4 - - + -
84D ILE* 4.1 18.2 - - + -
86D HIS 3.8 1.1 - - - +
87D PHE* 3.9 15.0 - - + -
94D ALA 4.2 0.4 - - - -
95D TRP* 1.3 71.3 - - - +
97D LEU* 1.3 60.7 + - - +
98D THR* 3.8 21.8 + - + +
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Residues in contact with LEU 97 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19D LEU* 4.2 9.2 - - + -
22D ASP* 5.0 2.7 - - - +
23D LEU* 4.0 23.3 - - + -
43D LEU* 4.0 27.4 - - + -
52D LEU* 4.0 19.5 - - + -
53D PHE 3.4 13.0 - - - +
54D LEU* 4.1 16.8 - - + +
84D ILE* 3.8 1.6 - - - +
85D LYS* 2.8 44.5 + - + -
86D HIS* 2.8 34.9 + - + +
95D TRP 4.1 0.2 - - - -
96D LEU* 1.3 72.5 - - - +
98D THR* 1.3 62.7 + - - +
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Residues in contact with THR 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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52D LEU* 3.4 10.1 - - - +
53D PHE* 2.8 45.4 + - - +
72D LEU* 4.0 19.5 - - + -
82D PRO* 4.0 10.2 - - + +
83D THR 3.2 12.6 - - - +
84D ILE* 4.3 2.9 - - + -
85D LYS* 4.3 1.1 - - - +
96D LEU* 3.8 28.2 + - + +
97D LEU* 1.3 81.4 - - - +
99D THR* 1.3 68.5 + - - +
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Residues in contact with THR 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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50D PRO* 5.3 9.4 - - + -
51D GLU 4.5 1.1 - - - -
52D LEU* 3.7 13.5 - - + -
53D PHE* 4.8 1.8 - - - -
82D PRO* 3.5 20.3 - - - +
83D THR* 2.9 38.6 + - - -
85D LYS* 3.8 35.4 - - + +
98D THR* 1.3 78.8 + - - +
100D ALA* 1.3 66.2 + - - +
101D ILE* 3.9 0.5 + - - +
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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