Contacts of the strand formed by residues 198 - 206 (chain A) in PDB entry 1R1M
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 ARG 198 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A SER* 4.2 14.2 + - - -
77A LEU 3.3 14.6 - - - +
78A SER* 3.7 7.9 - - - +
79A ALA* 3.6 8.6 - - - +
118A HIS* 2.8 60.9 + - + +
135A ARG* 5.8 0.4 - - - +
162A GLN* 5.5 5.7 + - - +
164A GLN* 6.1 2.8 - - - +
195A PRO 3.1 25.5 + - - +
196A ASP* 3.9 15.0 + - - +
197A ARG* 1.3 76.2 - - - +
199A VAL* 1.3 66.8 + - - +
200A ASP* 2.9 39.4 + - - +
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Residues in contact with VAL 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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75A ILE 3.6 2.1 - - - +
77A LEU* 2.9 33.2 + - + +
79A ALA* 5.9 0.2 - - - -
82A LEU* 3.5 25.4 - - + -
83A PHE* 4.4 2.0 - - + -
115A VAL* 3.3 34.5 - - + -
116A GLU 3.2 9.2 - - - +
117A GLY* 4.5 3.1 - - - -
135A ARG* 4.1 33.7 - - + +
136A ALA* 4.4 1.6 - - - -
139A VAL* 3.9 14.6 - - + -
198A ARG* 1.3 79.4 - - - +
200A ASP* 1.3 64.3 + - - +
201A VAL* 4.1 1.5 + - + -
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Residues in contact with ASP 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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74A THR* 4.0 17.1 - - + +
75A ILE 3.4 2.5 - - - -
76A SER* 2.8 30.1 + - - -
114A ARG 3.6 1.6 - - - +
115A VAL* 3.4 2.8 - - - +
116A GLU* 2.7 50.6 + - - +
118A HIS* 3.6 13.1 + - + -
198A ARG* 2.9 41.8 + - - -
199A VAL* 1.3 72.6 - - - +
201A VAL* 1.3 62.5 + - - +
202A LYS* 3.8 6.5 + - + -
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Residues in contact with VAL 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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74A THR* 3.4 2.3 - - - -
75A ILE* 2.8 55.0 + - + +
77A LEU* 4.7 10.5 - - + -
98A LEU* 5.1 0.2 - - + -
101A LEU* 4.3 12.3 - - + -
105A LEU* 5.3 0.2 - - + -
113A VAL* 3.8 28.5 - - + -
114A ARG 3.7 2.2 - - - -
115A VAL* 4.4 9.6 - - + +
139A VAL* 4.1 25.6 - - + -
143A LEU* 4.1 12.6 - - + -
199A VAL* 4.8 2.2 - - + +
200A ASP* 1.3 75.4 - - - +
202A LYS* 1.3 59.5 + - - +
203A ILE* 4.0 14.8 - - + -
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Residues in contact with LYS 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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73A GLU 3.2 5.4 - - - +
74A THR* 3.0 34.9 + - + +
112A SER* 3.6 2.4 + - - +
113A VAL* 3.4 1.9 - - - -
114A ARG* 2.8 54.2 + - + +
116A GLU* 3.5 38.8 - - + +
200A ASP* 4.7 6.1 + - + -
201A VAL* 1.3 72.1 - - - +
203A ILE* 1.3 62.4 + - - +
204A ARG 4.2 0.3 + - - -
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Residues in contact with ILE 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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71A VAL 3.6 1.2 - - - +
72A ASP* 3.3 4.7 - - - +
73A GLU* 2.8 55.2 + - + +
75A ILE* 3.3 33.7 - - + -
101A LEU* 4.3 5.8 - - + -
104A ARG* 4.8 2.5 - - - +
105A LEU* 3.7 43.5 - - + -
108A THR* 5.6 0.4 - - + -
110A ILE* 4.1 16.2 - - + -
112A SER 3.3 8.7 - - - +
113A VAL* 4.3 6.5 - - + -
201A VAL* 4.0 17.3 - - + -
202A LYS* 1.3 76.7 - - - +
204A ARG* 1.3 67.4 + - - +
205A SER* 4.6 3.4 - - - +
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Residues in contact with ARG 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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70A TYR* 3.5 47.8 - - + +
71A VAL 3.5 4.3 - - - -
72A ASP* 2.7 41.0 + - - +
110A ILE* 3.9 1.0 - - - -
111A GLN* 2.8 51.3 + - + +
112A SER* 3.0 25.9 + - - +
202A LYS 4.2 0.2 + - - -
203A ILE* 1.3 74.3 - - - +
205A SER* 1.3 62.6 + - - +
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Residues in contact with SER 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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70A TYR* 3.2 8.3 - - - -
71A VAL* 2.9 46.1 + - - +
73A GLU* 4.4 9.0 + - - -
108A THR* 3.9 23.2 - - - +
109A ASN 3.3 15.5 - - - -
110A ILE* 4.0 4.3 - - - +
111A GLN 4.2 0.9 - - - +
203A ILE* 4.7 4.0 - - - +
204A ARG* 1.3 75.0 - - - +
206A ILE* 1.3 68.0 + - - +
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Residues in contact with ILE 206 (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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68A PRO* 4.2 20.2 - - + -
69A GLN 3.2 8.5 - - - +
70A TYR* 3.7 25.8 - - + -
71A VAL* 5.7 0.4 - - - -
109A ASN* 2.9 52.7 + - - +
110A ILE 4.6 2.2 - - - +
111A GLN* 3.9 24.7 - - + +
205A SER* 1.3 80.3 + - - +
207A VAL* 1.3 73.0 + - - +
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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