Contacts of the strand formed by residues 84 - 92 (chain D) in PDB entry 4DOH
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 ILE 84 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C LEU* 4.4 13.5 - - + +
107C ARG* 3.3 36.6 - - + +
110C SER* 3.9 15.9 - - - +
69D GLU* 3.2 6.4 - - - +
70D TYR* 2.7 59.2 + - + +
71D GLN* 4.7 0.4 - - - -
75D GLU* 3.5 42.2 - - + +
82D ILE* 4.9 6.3 - - + +
83D TRP* 1.3 75.9 - - - +
85D PRO* 1.3 74.5 - - + +
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Residues in contact with PRO 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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103C HIS* 3.8 42.2 - - + +
106C LEU* 5.6 5.2 - - + -
107C ARG* 3.2 19.4 + - - +
68D VAL 3.9 0.4 - - - +
69D GLU* 3.9 17.7 - - + +
70D TYR* 4.3 0.2 - - - -
83D TRP 3.9 4.9 - - - +
84D ILE* 1.3 95.3 - - + +
86D SER* 1.3 66.9 + - - +
90D SER* 4.2 14.4 - - - +
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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
----------------------------------------------------------
107C ARG* 4.5 1.2 + - - -
68D VAL* 2.5 51.8 + - - +
69D GLU* 4.1 0.2 - - - +
70D TYR* 4.1 6.3 - - - -
84D ILE 3.7 2.8 + - - -
85D PRO* 1.3 73.5 - - - +
87D SER* 1.3 65.8 + - - +
88D TRP 3.2 1.5 + - - -
89D CYS* 3.5 21.0 + - - +
90D SER* 3.4 14.7 + - - -
97D CYS* 4.8 1.3 - - - -
99D VAL* 5.2 1.6 - - - -
102D ASP* 3.3 21.1 - - - -
111D LEU* 6.0 0.2 - - - -
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Residues in contact with SER 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C ARG* 3.5 35.7 + - - +
85D PRO 3.6 0.4 + - - -
86D SER* 1.3 72.3 - - - +
88D TRP* 1.3 86.3 + - - +
90D SER* 6.3 0.2 - - - -
101D ASP* 3.8 17.9 - - - +
102D ASP* 2.8 26.8 + - - -
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Residues in contact with TRP 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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86D SER* 3.2 0.4 - - - -
87D SER* 1.3 106.2 + - - +
89D CYS* 1.3 71.9 + - - +
90D SER 3.7 2.8 + - - -
92D THR* 3.3 20.6 - - - +
98D ASP* 3.4 31.7 + - + +
101D ASP* 2.8 35.6 + - + -
102D ASP* 4.7 0.4 + - - -
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Residues in contact with CYS 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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54D TRP* 5.8 0.7 - - + -
66D TYR* 4.1 1.6 - - + +
67D SER* 3.1 5.0 - - - -
68D VAL* 2.7 43.3 + - + -
86D SER* 3.5 16.4 + - - +
88D TRP* 1.3 94.5 - - - +
90D SER* 1.3 57.4 - - - +
91D LEU 3.5 2.2 - - - -
92D THR* 3.7 15.5 - - - +
97D CYS* 2.0 55.2 - - + -
98D ASP 4.2 0.9 - - - -
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Residues in contact with SER 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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103C HIS* 5.9 1.2 - - - -
67D SER* 3.6 7.4 - - - -
68D VAL 4.8 1.2 + - - -
85D PRO* 4.2 15.9 - - - +
86D SER* 3.4 17.4 + - - -
87D SER 6.3 0.2 - - - -
88D TRP 3.7 3.0 + - - -
89D CYS* 1.3 77.3 - - - +
91D LEU* 1.3 79.3 + - - +
92D THR* 4.8 1.0 - - - +
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Residues in contact with LEU 91 (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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65D TYR* 4.2 17.3 - - + -
66D TYR 2.6 21.1 + - - +
67D SER* 2.8 27.1 + - - +
90D SER* 1.3 84.0 - - - +
92D THR* 1.3 63.4 + - - +
114D ARG* 6.4 0.2 - - - +
116D THR* 3.1 36.3 - - + -
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Residues in contact with THR 92 (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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54D TRP* 5.9 0.9 - - - -
65D TYR* 3.4 5.0 - - - -
66D TYR* 2.6 40.6 + - - +
88D TRP 3.3 24.9 - - - +
89D CYS* 3.7 21.4 - - - +
90D SER 4.8 1.6 - - - +
91D LEU* 1.3 78.5 - - - +
93D GLU* 1.3 67.3 + - - +
94D GLY 3.9 5.0 + - - -
96D GLU 5.0 5.9 + - - -
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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