Contacts of the strand formed by residues 198 - 205 (chain A) in PDB entry 6EKL
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 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A GLU 3.9 0.2 - - - +
102A ILE* 3.6 0.2 - - - -
103A THR* 2.9 54.6 + - + +
192A MET 3.4 7.4 - - - +
193A THR* 3.8 28.1 - - + +
194A SER 4.7 5.6 - - - +
197A LEU* 1.3 82.2 - - - +
199A MET* 1.3 61.5 + - - +
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Residues in contact with MET 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 4.3 14.6 - - - -
22A PHE* 3.5 39.5 - - + -
23A LEU* 5.6 0.4 - - - -
100A PHE* 4.4 11.0 - - + -
101A GLU 3.2 14.8 - - - +
102A ILE* 4.4 12.1 - - + -
122A LEU* 4.1 12.1 - - + +
123A LEU* 4.2 5.4 - - + -
126A PHE* 3.4 38.8 - - + -
191A THR* 3.3 5.0 - - - +
192A MET 3.0 32.6 + - - +
197A LEU* 4.2 13.4 - - + +
198A LYS* 1.3 76.3 - - - +
200A GLN* 1.3 66.7 - - - +
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Residues in contact with GLN 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A VAL 3.2 2.9 - - - +
100A PHE* 3.6 0.3 - - - -
101A GLU* 2.6 69.0 + - + +
126A PHE* 4.4 0.9 - - - -
190A LYS 3.4 3.6 - - - +
191A THR* 2.8 34.7 + - + +
199A MET* 1.3 78.3 - - - +
201A LEU* 1.3 63.1 + - - +
202A TYR* 4.2 15.6 + - + -
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Residues in contact with LEU 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A PHE* 4.4 6.5 - - + -
99A VAL 3.2 18.4 - - - +
100A PHE* 3.7 36.1 - - + +
126A PHE* 3.7 30.0 - - + +
129A LYS* 5.4 1.1 - - + -
130A ILE* 3.7 34.5 - - + -
188A PRO* 4.3 0.2 - - - +
189A LEU* 3.0 44.9 + - + -
190A LYS 2.8 15.6 + - - +
191A THR* 5.3 0.2 + - - -
200A GLN* 1.3 76.4 - - - +
202A TYR* 1.3 70.6 - - - +
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Residues in contact with TYR 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A LYS* 4.4 7.3 + - - -
97A LYS 3.7 0.2 - - - +
98A PHE* 3.7 2.3 - - - -
99A VAL* 2.8 63.5 + - + +
101A GLU* 3.9 23.4 + - + -
186A LEU* 4.1 15.3 - - + -
187A ILE 3.4 15.0 - - - +
188A PRO* 3.9 11.0 - - + -
189A LEU* 4.1 2.2 - - - +
200A GLN* 4.4 17.9 - - + -
201A LEU* 1.3 78.7 - - - +
203A VAL* 1.3 75.7 + - - +
204A GLU* 3.6 30.3 + - + -
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Residues in contact with VAL 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A GLU* 4.6 4.3 - - + -
97A LYS 3.2 13.2 - - - +
98A PHE* 3.6 37.2 - - + -
133A VAL* 4.3 7.9 - - + -
137A LEU* 4.0 24.5 - - + -
186A LEU* 3.5 3.5 - - - -
187A ILE* 2.8 46.4 + - + +
189A LEU* 3.7 17.7 - - + -
202A TYR* 1.3 80.3 - - - +
204A GLU* 1.3 75.8 + - - +
205A GLU* 4.5 0.7 - - + +
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Residues in contact with GLU 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A GLU* 3.3 4.7 - - - -
97A LYS* 2.9 62.3 + - + +
99A VAL* 4.4 9.5 - - + +
181A MET* 4.0 13.5 - - - +
184A PRO* 4.2 13.9 - - + +
185A ARG 3.4 5.6 - - - +
186A LEU* 3.4 27.1 - - + +
202A TYR* 3.6 22.8 + - + -
203A VAL* 1.3 72.6 - - - +
205A GLU* 1.3 60.7 + - - +
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Residues in contact with GLU 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A VAL 3.7 8.7 - - - +
96A GLU* 4.1 9.4 - - + +
137A LEU* 3.8 15.7 - - + +
138A ASP* 3.2 39.0 + - - +
181A MET* 3.9 1.8 - - - -
184A PRO* 3.4 3.2 - - - +
185A ARG* 2.8 73.0 + - + +
187A ILE* 4.0 13.2 - - + -
203A VAL* 4.0 1.5 - - + -
204A GLU* 1.3 75.5 - - - +
206A ARG* 1.3 76.2 + - + +
207A ALA 3.3 0.3 + - - -
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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