Contacts of the strand formed by residues 121 - 127 (chain H) in PDB entry 1R9T
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 LEU 121 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537A ARG* 3.8 23.6 - - + +
540A PHE* 4.1 15.9 - - + -
565A ILE* 4.9 4.9 - - + -
23H VAL* 3.4 36.6 - - + -
41H ASP* 3.3 29.6 - - + +
43H ASN 4.1 7.9 - - - +
95H TYR* 3.9 13.9 - - - +
97H MET* 4.1 14.8 - - + -
118H PHE* 2.5 52.1 + - + +
119H GLY 2.9 3.2 + - - +
120H GLY* 1.3 74.9 - - - +
122H LEU* 1.3 63.6 + - - +
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Residues in contact with LEU 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537A ARG* 5.2 2.7 - - - +
598A LEU* 3.7 35.9 - - + +
599A SER* 5.2 0.7 - - - -
613A ILE 4.1 1.1 - - - +
614A PHE* 3.7 27.6 - - + -
25H ARG* 3.7 2.9 + - - +
39H THR 3.4 6.0 - - - +
40H LEU* 3.7 2.9 - - - +
41H ASP* 2.7 46.7 + - - +
97H MET* 5.2 0.2 - - - +
102H TYR* 3.0 26.7 - - + +
116H TYR 3.1 20.0 - - - +
117H SER* 3.0 32.1 - - - +
118H PHE* 5.0 2.0 - - - -
120H GLY 4.4 6.3 - - - +
121H LEU* 1.3 77.0 - - - +
123H MET* 1.3 60.9 + - - +
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Residues in contact with MET 123 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598A LEU* 4.5 4.2 - - - +
38H LEU* 3.3 24.2 - - + -
39H THR 3.4 1.1 - - - -
40H LEU* 2.8 39.9 - - + -
57H VAL* 5.5 3.1 - - + -
59H ILE* 4.4 10.3 - - + -
102H TYR* 4.8 0.3 - - - -
114H VAL 3.0 2.1 - - - +
115H TYR* 2.9 17.8 - - - -
116H TYR* 2.6 85.0 + - + +
118H PHE* 4.0 7.4 - - + -
122H LEU* 1.3 78.2 - - - +
124H ARG* 1.4 61.0 - - - +
125H LEU* 4.4 7.0 - - + +
142H LEU* 3.5 24.2 - - + -
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Residues in contact with ARG 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598A LEU* 4.2 14.4 - - + +
27H GLU* 5.5 2.5 - - - -
37H LYS* 3.7 6.8 - - - +
38H LEU* 3.0 28.0 - - - +
39H THR* 2.9 41.7 + - - +
105H GLU* 3.8 9.3 + - - -
107H VAL* 4.7 11.5 - - - +
113H ALA* 4.8 5.1 - - + +
114H VAL 3.1 4.3 - - - -
115H TYR* 3.5 37.9 + - + -
123H MET* 1.4 70.0 - - - +
125H LEU* 1.3 65.7 + - - +
126H GLU* 3.3 39.4 + - - +
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Residues in contact with LEU 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H PHE* 4.1 30.5 - - + -
10H PHE* 4.4 9.4 - - + -
37H LYS 3.2 23.1 - - - +
38H LEU* 3.1 37.0 - - + -
57H VAL* 5.9 1.6 - - + -
59H ILE* 5.6 4.7 - - + -
112H ILE 3.8 0.2 - - - +
113H ALA* 2.6 9.0 - - - -
114H VAL* 2.0 63.2 + - + +
116H TYR* 5.4 1.3 - - + -
123H MET* 4.3 11.4 - - + +
124H ARG* 1.3 76.2 - - - +
126H GLU* 1.3 53.8 + - - +
130H ARG* 4.1 15.0 - - - +
134H ASN* 4.3 17.9 - - - +
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Residues in contact with GLU 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H GLN 3.2 20.8 - - - +
36H CYS* 3.1 14.5 - - - +
37H LYS* 2.7 50.4 + - + +
107H VAL* 3.9 26.9 - - + +
111H LEU* 4.0 19.2 - - + +
112H ILE 2.9 12.3 - - - +
113H ALA* 3.7 6.1 - - - -
124H ARG* 3.3 30.1 + - - +
125H LEU* 1.3 76.3 - - - +
127H GLY* 1.4 50.3 - - - +
130H ARG* 2.0 21.7 + - - +
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Residues in contact with GLY 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35H GLN* 3.7 21.8 - - - -
36H CYS* 4.1 1.8 - - - -
111H LEU* 3.4 7.8 - - - +
112H ILE* 2.8 28.7 + - - +
126H GLU* 1.4 66.4 - - - +
128H ASN* 1.4 66.7 + - - +
129H TYR* 4.1 2.9 - - - -
130H ARG* 2.5 24.2 - - - +
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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