Contacts of the strand formed by residues 92 - 98 (chain D) in PDB entry 1EVW
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 LYS 92 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88D ASN* 3.0 5.1 - - - -
89D ILE* 2.8 41.9 + - + +
90D ASN* 3.2 11.1 - - + -
91D GLY* 1.3 78.9 - - - +
93D THR* 1.3 63.6 + - - +
94D CYS* 3.4 3.1 + - - -
115D SER* 4.1 27.4 - - - +
117D ASP* 5.0 13.1 + - + +
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Residues in contact with THR 93 (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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87D ASP* 3.6 15.1 + - + +
88D ASN* 4.3 1.9 - - - +
91D GLY 3.9 2.9 + - - -
92D LYS* 1.3 73.0 - - - +
94D CYS* 1.3 72.7 + - - +
95D THR* 4.4 8.9 - - + +
115D SER* 3.6 14.6 - - - -
116D ALA* 4.1 6.6 + - - +
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Residues in contact with CYS 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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151C VAL* 3.8 16.6 - - - -
86D PRO* 5.1 0.7 - - - -
87D ASP* 3.5 7.3 + - - +
88D ASN 3.7 9.6 - - - -
89D ILE* 3.5 38.1 - - - -
92D LYS 3.6 5.4 - - - -
93D THR* 1.3 81.0 - - - +
95D THR* 1.3 69.1 + - - +
113D TRP* 3.4 40.6 - - + +
114D GLU 3.7 13.0 - - - +
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Residues in contact with THR 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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93D THR* 4.4 13.2 - - + +
94D CYS* 1.3 79.5 - - - +
96D ALA* 1.3 68.0 + - - +
112D CYS 3.3 0.3 - - - +
113D TRP* 3.1 21.1 - - - -
114D GLU 3.0 31.5 + - - +
115D SER 4.6 2.4 + - - -
116D ALA* 5.0 11.3 - - + +
119D ASN* 4.1 8.0 + - - +
14N G 3.1 34.6 + - + +
15N A 3.8 8.3 - - - +
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Residues in contact with ALA 96 (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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78D HIS* 3.5 40.6 - - + +
82D PHE* 4.5 1.8 - - + -
95D THR* 1.3 77.8 + - - +
97D SER* 1.3 60.4 + - - +
98D HIS* 4.9 0.6 + - + -
111D LEU* 4.4 7.6 - - + -
112D CYS 3.4 5.4 - - - +
113D TRP* 3.7 7.2 - - + -
119D ASN* 3.9 0.2 + - - -
14N G 3.1 29.7 + - - +
15N A 3.1 16.8 + - - +
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Residues in contact with SER 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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95D THR* 3.8 0.6 + - - -
96D ALA* 1.3 73.6 - - - +
98D HIS* 1.3 62.9 + - - +
99D LEU 3.4 0.5 + - - -
111D LEU* 3.4 7.3 - - - +
112D CYS* 2.7 34.6 + - - +
114D GLU* 2.4 43.5 + - - -
119D ASN* 3.1 25.7 + - - +
122D ARG* 3.9 8.5 - - - -
14N G 3.0 4.3 - - - -
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Residues in contact with HIS 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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61D ARG* 6.0 0.4 - - - -
78D HIS* 3.2 32.4 + + - -
96D ALA 4.9 1.1 + - - -
97D SER* 1.3 75.6 + - - +
99D LEU* 1.3 63.3 + - - +
100D CYS* 3.2 11.4 - - - -
101D HIS* 3.7 37.5 + - - +
102D ASN 2.9 27.5 + - - -
103D THR* 3.2 16.6 + - + -
105D CYS* 3.1 20.5 + - + -
110D HIS 3.7 3.6 - - - -
111D LEU* 4.0 12.0 - - + +
119D ASN* 5.0 1.0 - - - +
122D ARG* 4.8 2.1 - - - -
13G A 4.9 0.2 + - - -
14N G 2.3 46.0 + - - +
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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