Contacts of the strand formed by residues 114 - 120 (chain D) in PDB entry 6EKK
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 CYS 114 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82D HIS 3.1 20.5 + - - +
83D GLY* 3.1 7.3 - - - -
84D VAL 2.7 24.0 + - - -
112D ASP 3.6 4.2 + - - -
113D VAL* 1.3 75.9 - - - +
115D ARG* 1.3 61.8 + - - +
164D ILE* 4.2 2.7 - - + -
167D LEU* 3.6 43.1 - - + -
168D VAL* 4.0 6.5 - - + -
171D ALA* 3.7 18.8 - - - -
201D SO4 3.2 13.2 - - - +
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Residues in contact with ARG 115 (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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84D VAL* 3.2 21.3 - - + +
86D VAL* 4.6 2.5 - - + -
103D LEU* 4.3 19.7 + - + +
106D ILE* 3.4 28.8 - - + +
107D ASN* 3.9 18.8 + - - +
110D CYS 3.9 1.4 + - - -
111D ASP* 2.6 51.3 + - - +
113D VAL* 2.5 37.1 + - - -
114D CYS* 1.3 75.2 - - - +
116D ILE* 1.3 69.7 + - - +
142D MET 5.1 6.7 + - - -
144D ILE* 3.9 18.3 - - + +
145D GLN 4.8 0.3 + - - -
164D ILE* 4.2 2.4 - - - +
167D LEU* 4.2 1.2 - - - +
201D SO4 2.8 47.7 + - - +
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Residues in contact with ILE 116 (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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84D VAL 3.2 8.5 + - - +
85D ILE* 4.3 4.9 - - + -
86D VAL* 3.0 31.5 + - - +
115D ARG* 1.3 79.7 - - - +
117D LEU* 1.3 61.0 + - - +
118D VAL* 4.2 7.0 - - + -
144D ILE* 4.7 5.8 - - - -
145D GLN* 3.8 15.7 - - + +
147D PHE* 4.3 9.2 - - + -
160D MET* 3.5 50.7 - - + +
163D CYS* 3.8 15.3 - - - -
164D ILE* 3.8 17.9 - - + +
167D LEU* 3.6 22.9 - - + -
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Residues in contact with LEU 117 (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 VAL* 3.6 11.9 - - + +
88D TYR* 3.7 32.5 - - + -
96D PHE* 4.4 5.6 - - + -
99D VAL* 3.8 12.6 - - + -
103D LEU* 3.8 19.3 - - + -
116D ILE* 1.3 73.6 - - - +
118D VAL* 1.3 63.6 + - - +
135D ALA* 4.1 16.8 - - + +
138D PHE* 4.2 19.5 - - + -
139D ALA* 4.5 6.3 - - + -
144D ILE* 4.0 14.4 - - + +
145D GLN 2.9 13.7 + - - +
146D LEU* 3.4 18.7 - - + -
147D PHE* 2.8 26.9 + - - +
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Residues in contact with VAL 118 (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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24D LEU* 4.2 17.7 - - + -
85D ILE* 3.6 23.1 - - + -
86D VAL 2.8 13.1 + - - +
87D VAL* 3.4 8.0 - - + -
88D TYR* 2.8 33.3 + - - +
116D ILE* 4.2 6.7 - - + -
117D LEU* 1.3 79.1 - - - +
119D GLY* 1.3 60.7 + - - +
120D ASN 4.3 1.1 - - - +
147D PHE 3.1 7.2 - - - +
149D THR* 3.5 32.3 - - + +
160D MET* 3.5 26.7 - - + -
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Residues in contact with GLY 119 (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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88D TYR* 3.3 35.7 + - - -
90D VAL* 3.7 9.0 - - - +
118D VAL* 1.3 70.2 - - - +
120D ASN* 1.3 63.0 + - - -
122D ASN* 4.1 0.5 - - - +
146D LEU* 4.2 1.6 - - - +
147D PHE 2.8 11.5 + - - -
148D GLU* 3.2 6.7 - - - +
149D THR* 2.8 26.1 + - - +
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Residues in contact with ASN 120 (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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19D VAL 2.8 28.2 + - - +
20D GLY* 3.5 10.7 + - - -
24D LEU* 3.9 8.4 - - + +
87D VAL* 4.0 11.4 - - + -
88D TYR 2.9 13.1 + - - +
89D ASP* 3.6 0.7 - - - -
90D VAL* 3.0 22.0 + - - +
118D VAL* 3.6 1.4 + - + -
119D GLY* 1.3 71.4 - - - +
121D LYS* 1.3 80.6 + - - +
122D ASN 3.2 3.3 + - - -
149D THR* 3.1 17.9 + - - +
151D ALA* 3.0 24.8 + - - +
203D GDP 3.2 26.6 + - - -
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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