Contacts of the strand formed by residues 109 - 116 (chain A) in PDB entry 1R9F
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 GLY 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A GLY 3.8 1.2 - - - +
65A PHE* 3.8 1.0 - - - -
66A GLY* 2.9 35.1 + - - +
108A ILE* 1.3 74.0 - - - +
110A CYS* 1.3 59.4 + - - -
111A THR* 5.9 0.4 - - - +
125A GLY 3.8 4.9 - - - -
12B U 3.9 8.3 - - - -
13B A 3.3 26.4 + - - -
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Residues in contact with CYS 110 (chain A).
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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63A TRP* 5.2 1.6 - - + -
64A GLY 3.2 6.7 - - - +
65A PHE* 4.0 20.2 - - + -
103A PHE* 4.8 4.3 - - - -
108A ILE* 4.0 7.9 - - - -
109A GLY* 1.3 79.3 - - - -
111A THR* 1.3 62.5 + - - +
123A VAL 4.0 0.2 - - - +
124A SER* 3.3 4.3 - - - -
125A GLY 2.8 36.3 + - - +
127A SER* 3.8 32.5 - - - -
130A LEU* 4.4 15.0 - - + -
133A LEU* 3.8 16.7 - - + +
12B U 4.3 0.9 + - - -
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Residues in contact with THR 111 (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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62A SER* 3.7 3.4 - - - +
63A TRP* 3.3 10.9 - - - -
64A GLY* 2.7 54.4 + - - +
69A VAL* 6.0 0.9 - - + -
109A GLY 5.9 0.4 - - - +
110A CYS* 1.3 77.1 - - - +
112A TYR* 1.3 61.3 + - - +
113A SER* 4.0 2.0 + - - +
122A THR* 3.1 27.0 - - - +
123A VAL 3.3 6.1 + - - -
124A SER* 4.0 6.7 - - - -
9C U 5.7 1.1 - - - +
10C U 3.9 31.8 + - - +
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Residues in contact with TYR 112 (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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61A GLU* 2.7 31.5 + - + +
62A SER 3.2 13.9 - - - -
63A TRP* 3.4 39.2 - + + -
90A TRP* 3.5 22.4 - + - -
111A THR* 1.3 74.1 + - - +
113A SER* 1.3 74.8 + - - +
114A ILE* 3.6 29.1 - - + +
121A ILE* 5.1 0.7 - - + -
122A THR* 3.2 3.3 - - - +
123A VAL* 2.8 42.8 + - + +
137A ALA* 3.6 37.9 - - + -
140A SER* 5.5 0.9 - - - -
141A LYS* 3.4 14.8 - - + +
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Residues in contact with SER 113 (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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61A GLU* 3.0 6.3 - - - +
62A SER* 2.8 46.4 + - - +
111A THR* 4.0 1.9 + - - +
112A TYR* 1.3 78.2 - - - +
114A ILE* 1.3 62.1 + - - +
120A SER* 5.3 1.6 - - - -
121A ILE 3.3 5.4 - - - -
122A THR* 3.0 25.8 + - - +
10C U 3.6 5.2 + - - -
11C C 3.3 26.7 - - - -
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Residues in contact with ILE 114 (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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59A PHE* 3.7 24.7 - - + -
60A LYS 3.2 11.2 - - - +
61A GLU* 4.5 0.2 - - + -
112A TYR* 3.6 29.4 - - + +
113A SER* 1.3 77.3 - - - +
115A ARG* 1.3 65.3 + - - +
120A SER* 3.3 2.9 + - - -
121A ILE* 3.0 35.4 + - + +
140A SER 5.0 1.1 - - - +
141A LYS* 3.8 29.2 - - + +
144A MSE 3.0 50.2 - - + +
145A LEU* 4.3 7.6 - - + -
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Residues in contact with ARG 115 (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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59A PHE* 3.4 4.9 - - - +
60A LYS* 2.8 52.6 + - + +
114A ILE* 1.3 75.8 - - - +
116A PHE* 1.3 70.7 + - - +
117A ARG 5.2 0.2 - - - +
118A GLY* 4.1 27.1 + - - +
119A VAL 3.3 10.5 - - - +
120A SER* 4.4 5.2 - - - -
11C C 5.5 0.2 - - - +
12C C 3.0 36.1 + - - +
13C G 3.0 42.1 + - - -
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Residues in contact with PHE 116 (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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56A PRO* 3.9 23.3 - - + -
58A GLY* 3.9 11.4 - - - -
59A PHE* 3.7 21.1 - - + +
76A TYR* 3.7 37.5 - + - -
78A ARG* 4.6 11.7 - - + -
114A ILE* 5.1 0.4 - - + -
115A ARG* 1.3 76.9 - - - +
117A ARG* 1.3 107.2 + - + +
118A GLY 3.4 1.6 - - - -
119A VAL* 2.9 22.1 + - - +
144A MSE 3.6 39.7 - - + +
145A LEU* 4.0 10.5 - - + -
147A MSE 4.2 5.4 - - + +
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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