Contacts of the strand formed by residues 143 - 149 (chain L) in PDB entry 6AHU
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 143 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2J ALA* 4.1 17.3 - - + -
101L ILE 3.3 19.8 + - - +
102L ASP* 4.3 16.1 - - + +
103L GLU 5.1 0.6 - - - -
104L ASP 3.1 28.9 + - - +
118L SER* 3.6 18.2 + - - +
119L LEU 3.5 26.8 - - - +
120L ASP* 3.5 9.0 - - - +
134L SER* 3.9 21.6 + - - -
135L GLN* 5.2 12.3 + - + +
141L ILE* 3.7 11.0 - - - +
142L MET* 1.3 90.8 - - + +
144L PHE* 1.3 72.0 + - - +
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Residues in contact with PHE 144 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118L SER* 3.5 2.8 + - - -
119L LEU* 2.7 40.5 + - - +
120L ASP 4.5 4.7 - - - -
121L LYS* 4.5 23.1 - - + -
124L TYR* 3.6 61.5 - + + -
125L GLU* 5.9 0.7 - - + -
132L HIS* 3.7 5.8 - - - +
133L PRO* 3.7 37.7 - - + -
134L SER 5.0 0.7 - - - +
141L ILE* 3.7 33.7 - - + -
143L LYS* 1.3 79.0 - - - +
145L ILE* 1.3 61.1 + - - +
146L VAL* 4.3 0.4 - - - -
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Residues in contact with ILE 145 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101L ILE* 6.3 0.4 - - + -
116L ILE* 3.7 24.9 - - + -
117L LEU 3.4 8.5 - - - +
118L SER* 3.7 23.1 - - - +
131L GLY* 3.4 1.8 - - - -
132L HIS* 3.2 45.2 + - + +
134L SER* 3.4 28.9 - - - +
144L PHE* 1.3 78.1 - - - +
146L VAL* 1.3 64.8 + - - +
147L SER* 4.9 1.3 - - - +
321L PRO* 5.5 4.9 - - + +
322L VAL* 5.2 6.1 - - + -
328L GLU* 3.6 30.7 - - + +
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Residues in contact with VAL 146 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115L LEU 3.6 0.2 - - - +
116L ILE* 3.4 1.9 - - - -
117L LEU* 3.0 46.4 + - + +
119L LEU* 4.9 8.3 - - + -
124L TYR* 3.7 36.1 - - + -
129L LEU* 3.7 30.5 - - + +
130L GLN 3.3 17.7 - - - +
131L GLY* 3.8 3.6 - - - -
144L PHE 4.3 0.9 - - - -
145L ILE* 1.3 75.5 - - - +
147L SER* 1.3 61.4 + - - +
148L ILE* 3.8 22.4 - - + -
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Residues in contact with SER 147 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114L LYS* 4.5 11.8 - - - +
115L LEU 4.0 2.2 - - - -
116L ILE* 3.4 29.5 - - - +
130L GLN 4.5 4.5 + - - +
132L HIS* 5.9 5.7 - - - -
145L ILE* 4.2 3.2 + - - -
146L VAL* 1.3 74.5 - - - +
148L ILE* 1.3 63.7 + - - +
149L ASP* 4.1 2.4 + - - +
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Residues in contact with ILE 148 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78L ILE* 6.0 0.2 - - + -
114L LYS* 3.3 1.5 - - - -
115L LEU* 2.5 57.1 + - + +
117L LEU* 4.1 14.8 - - + -
129L LEU* 3.8 30.1 - - + -
146L VAL* 3.8 11.0 - - + -
147L SER* 1.3 76.5 + - - +
149L ASP* 1.3 58.4 + - - +
150L LEU* 3.4 21.8 + - + -
153L LEU* 4.2 5.4 - - + -
165L ILE* 3.8 41.1 - - + -
169L PHE* 4.6 5.6 - - + -
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Residues in contact with ASP 149 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112L ASN 3.8 6.1 - - - +
113L GLY 3.1 20.6 - - - +
114L LYS* 3.7 27.1 - - + +
147L SER* 4.0 3.2 + - - +
148L ILE* 1.3 70.6 - - - +
150L LEU* 1.3 62.0 + - - +
151L MET* 3.4 8.9 + - - +
152L GLU* 3.3 42.8 + - - +
153L LEU* 3.4 24.1 + - - +
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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