Contacts of the strand formed by residues 126 - 131 (chain L) in PDB entry 6R90
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 THR 126 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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987K GLU* 4.1 5.2 - - - +
119L TRP* 3.2 19.8 - - - -
120L HIS* 3.0 45.4 + - + +
123L HIS* 3.3 19.6 - - + +
124L PRO 3.4 0.9 - - - +
125L SER* 1.3 78.3 - - - +
127L VAL* 1.3 61.8 + - - +
138L LEU* 5.2 8.1 - - + -
139L TRP 3.3 5.8 - - - +
140L ASN* 3.2 35.9 - - + +
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Residues in contact with VAL 127 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117L LEU* 3.9 18.6 - - + -
118L ALA 3.0 24.7 - - - +
119L TRP* 3.5 33.7 - - + -
120L HIS 4.5 2.9 - - - +
126L THR* 1.3 76.5 - - - +
128L ALA* 1.3 60.9 + - - +
129L VAL* 5.6 3.5 - - + +
137L MET 4.0 0.5 - - - +
138L LEU* 3.5 8.5 - - - +
139L TRP* 2.9 60.1 + - + +
141L PHE* 4.4 7.6 - - + -
164L PHE* 4.5 0.4 - - - -
408L ALA* 4.7 2.5 - - + -
415L ILE* 5.3 6.5 - - + -
417L ILE* 5.3 1.3 - - + -
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Residues in contact with ALA 128 (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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117L LEU* 3.5 4.4 - - - +
118L ALA 2.9 32.4 + - - +
127L VAL* 1.3 73.5 - - - +
129L VAL* 1.3 63.6 + - - +
136L ILE* 5.3 0.2 - - + -
137L MET 3.4 4.7 - - - -
138L LEU* 4.0 0.4 - - + -
162L LEU* 4.2 15.0 - - + -
164L PHE* 3.4 28.6 - - + -
172L PHE* 6.0 0.2 - - + -
186L PHE* 3.7 26.5 - - + -
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Residues in contact with VAL 129 (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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110L PHE* 4.8 7.0 - - + -
114L ALA* 4.4 12.6 - - + -
116L SER 3.2 15.3 - - - +
117L LEU* 4.0 14.8 - - + -
127L VAL* 5.6 3.8 - - + +
128L ALA* 1.3 77.4 - - - +
130L GLY* 1.3 66.3 + - - +
135L ASP 3.9 0.5 - - - +
136L ILE* 3.3 6.8 - - - +
137L MET* 2.9 56.6 + - + +
139L TRP* 6.4 0.4 - - + -
162L LEU* 4.1 6.1 - - - -
410L ALA* 5.6 1.8 - - + -
415L ILE* 3.3 39.5 - - + -
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Residues in contact with GLY 130 (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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110L PHE* 5.2 0.9 - - - -
114L ALA* 3.9 1.6 - - - -
115L THR* 2.8 31.7 + - - -
116L SER* 2.9 19.3 + - - +
129L VAL* 1.3 78.4 - - - +
131L SER* 1.3 56.7 + - - -
135L ASP 3.6 5.4 - - - -
136L ILE* 4.0 13.7 - - - -
159L ILE* 4.9 7.9 - - - -
162L LEU* 4.1 6.3 - - - +
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Residues in contact with SER 131 (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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110L PHE* 3.5 14.1 - - - -
112L ARG 3.4 13.5 - - - -
113L ARG 3.1 12.6 - - - -
114L ALA* 4.1 1.8 - - - +
115L THR* 2.5 22.8 + - - +
130L GLY* 1.3 70.5 - - - -
132L LYS* 1.3 59.7 + - - +
133L GLY* 2.9 11.3 + - - -
134L GLY 4.1 0.5 + - - -
135L ASP* 2.6 44.5 + - - +
136L ILE* 4.8 1.0 - - - +
159L ILE* 3.2 17.8 + - - +
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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