Contacts of the helix formed by residues 97 - 113 (chain A) in PDB entry 1RRM
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 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A ASP* 5.6 0.2 + - - -
42A LEU* 4.7 1.4 - - - +
96A GLY* 1.3 72.5 - - - -
98A GLY* 1.3 65.7 + - - -
99A SER 3.2 2.7 - - - -
100A PRO* 3.2 8.1 - - - +
101A GLN* 3.1 30.9 + - - +
140A THR* 3.3 4.4 + - - -
141A THR* 3.5 17.4 - - - +
389A APR 3.2 22.6 + - - -
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Residues in contact with GLY 98 (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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97A GLY* 1.3 72.3 - - - -
99A SER* 1.3 57.3 + - - +
102A ASP* 2.8 36.1 + - - +
144A THR* 3.5 20.5 + - - +
146A ALA* 4.3 7.6 - - - -
389A APR 3.0 36.3 + - - -
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Residues in contact with SER 99 (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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39A ASP* 5.9 0.4 - - - -
68A VAL* 3.6 6.1 - - - -
69A VAL 3.7 11.7 - - - -
70A PRO* 4.1 1.3 - - - -
71A ASN 3.0 20.4 + - - -
72A PRO* 3.3 20.5 - - - +
98A GLY* 1.3 76.4 - - - +
100A PRO* 1.3 69.3 - - - +
103A THR* 2.8 28.1 + - - -
389A APR 2.6 35.2 + - - -
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Residues in contact with PRO 100 (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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37A VAL* 3.5 17.3 - - - +
38A THR* 3.9 11.7 - - - -
39A ASP* 3.9 19.7 - - - +
68A VAL* 3.8 18.4 - - + -
94A ALA* 4.7 1.6 - - - -
95A ILE 3.8 24.2 - - - +
96A GLY* 4.1 7.2 - - - -
97A GLY 3.2 12.8 - - - +
99A SER* 1.3 95.2 - - - +
101A GLN* 1.3 55.6 + - - +
103A THR* 3.6 0.2 - - - -
104A CYS* 2.9 30.7 + - - +
389A APR 3.5 8.7 - - - +
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Residues in contact with GLN 101 (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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94A ALA* 4.0 20.4 - - + +
96A GLY 3.2 23.1 + - - +
97A GLY* 3.1 19.8 + - - +
98A GLY 4.0 0.2 - - - +
100A PRO* 1.3 78.3 - - - +
102A ASP* 1.3 58.3 - - - +
104A CYS* 3.4 3.3 + - - +
105A LYS* 3.0 31.7 + - + +
135A ILE* 6.1 0.2 - - - +
137A ALA* 3.5 11.7 - - - +
138A ILE 4.8 0.7 - - - -
139A PRO* 3.4 26.4 - - - +
141A THR* 5.8 0.2 + - - -
144A THR* 4.5 2.4 + - - -
146A ALA* 3.6 23.3 - - + +
147A GLU* 3.2 35.7 + - - +
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Residues in contact with ASP 102 (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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72A PRO* 4.5 3.6 - - + -
98A GLY* 2.8 24.8 + - - +
99A SER 4.0 2.2 - - - +
101A GLN* 1.3 74.4 - - - +
103A THR* 1.3 66.5 + - - +
105A LYS* 3.3 3.8 + - - +
106A ALA* 3.1 22.7 + - - +
146A ALA* 3.7 17.5 - - - +
151A ASN 3.9 3.6 - - - +
152A TYR* 3.4 33.4 - - + +
153A VAL* 2.9 41.5 + - - +
154A ILE* 4.1 3.4 - - + +
389A APR 3.9 8.7 + - - -
390A PGO 5.5 1.6 + - - +
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Residues in contact with THR 103 (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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37A VAL* 4.3 2.0 - - + -
65A TYR* 4.8 1.6 - - + -
68A VAL* 3.6 24.5 - - + +
72A PRO* 3.1 20.6 - - - +
76A VAL* 4.1 16.3 - - + +
77A VAL* 4.4 12.6 - - + -
99A SER 2.8 22.2 + - - -
100A PRO 3.6 4.5 - - - -
102A ASP* 1.3 76.4 - - - +
104A CYS* 1.3 63.4 + - - +
106A ALA* 3.3 7.7 + - - +
107A ILE* 3.0 44.6 + - + +
154A ILE* 4.7 5.4 - - - -
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Residues in contact with CYS 104 (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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37A VAL* 3.9 23.5 - - + +
92A LEU* 3.5 33.5 - - - +
94A ALA* 3.8 25.4 - - + -
100A PRO 2.9 17.6 + - - +
101A GLN 3.5 6.3 - - - +
103A THR* 1.3 78.3 - - - +
105A LYS* 1.3 55.5 + - - +
107A ILE* 3.3 3.5 + - - +
108A GLY* 2.9 27.5 + - - -
135A ILE* 3.9 13.7 - - + +
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Residues in contact with LYS 105 (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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101A GLN* 3.0 17.4 + - - +
102A ASP* 3.3 9.6 + - - +
104A CYS* 1.3 76.2 - - - +
106A ALA* 1.3 65.1 + - - +
108A GLY* 3.4 0.7 + - - -
109A ILE* 3.0 30.1 + - - +
132A SER* 4.4 0.3 + - - -
135A ILE* 3.8 14.4 - - + -
146A ALA* 2.8 28.7 + - - +
149A THR* 2.7 32.0 + - - -
151A ASN 2.9 28.6 + - - +
152A TYR* 3.7 21.8 - - + -
170A ASP* 3.7 30.3 - - + +
172A PRO* 4.1 9.6 - - + -
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Residues in contact with ALA 106 (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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77A VAL* 3.7 28.9 - - + -
102A ASP 3.1 13.1 + - - +
103A THR 3.3 8.9 + - - +
105A LYS* 1.3 78.0 - - - +
107A ILE* 1.3 56.6 + - - +
109A ILE* 3.3 0.9 + - - +
110A ILE* 3.0 40.0 + - + +
119A VAL* 5.1 2.5 - - + -
122A LEU* 5.3 0.7 - - + -
152A TYR* 3.8 26.2 - - + -
154A ILE* 4.2 3.8 - - + -
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Residues in contact with ILE 107 (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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35A LEU* 5.4 1.1 - - + -
37A VAL* 4.3 18.4 - - + -
65A TYR* 4.9 0.7 - - + -
77A VAL* 3.8 20.0 - - + +
80A GLY* 3.6 28.3 - - - +
81A LEU* 3.9 16.7 - - + +
84A PHE* 4.0 30.7 - - + -
92A LEU* 4.3 9.2 - - + -
103A THR* 3.0 37.2 + - + +
104A CYS* 3.6 4.3 - - - +
106A ALA* 1.3 76.3 - - - +
108A GLY* 1.3 63.9 + - - +
110A ILE* 4.9 1.1 - - - -
111A SER* 3.0 24.9 + - - -
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Residues in contact with GLY 108 (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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92A LEU* 3.6 19.9 - - - +
104A CYS 2.9 16.2 + - - -
105A LYS 3.8 0.2 - - - -
107A ILE* 1.3 75.4 - - - +
109A ILE* 1.3 62.2 + - - +
112A ASN 3.7 10.9 + - - -
132A SER* 3.1 21.5 - - - -
133A VAL* 3.0 25.2 + - - +
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Residues in contact with ILE 109 (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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105A LYS 3.0 14.1 + - - +
106A ALA 3.8 2.7 - - - +
108A GLY* 1.3 75.0 - - - +
110A ILE* 1.3 63.5 + - - +
112A ASN 3.2 2.1 + - - -
113A ASN* 2.9 40.3 + - + +
116A PHE* 5.3 0.2 - - + -
122A LEU* 4.1 15.5 - - + -
128A THR* 3.7 25.8 - - + -
132A SER* 3.8 19.1 - - - +
152A TYR* 3.3 26.5 - - + +
167A ASP* 3.5 19.3 - - - +
169A HIS* 4.6 2.5 - - + +
170A ASP* 3.3 28.9 - - + +
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Residues in contact with ILE 110 (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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77A VAL* 3.8 15.3 - - + -
81A LEU* 3.5 28.5 - - + -
106A ALA 3.0 18.8 + - - +
107A ILE* 4.1 2.7 - - - +
109A ILE* 1.3 75.7 - - - +
111A SER* 1.3 63.7 + - - +
113A ASN 3.0 25.9 + - - +
114A PRO* 3.1 9.2 - - + +
116A PHE* 3.7 21.8 - - + +
117A ALA* 3.9 22.4 - - + +
119A VAL* 3.8 24.2 - - + -
122A LEU* 3.9 18.4 - - + -
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Residues in contact with SER 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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81A LEU* 4.0 15.6 - - - +
84A PHE* 3.3 27.3 - - - -
85A GLN* 5.0 8.3 + - - +
107A ILE 3.0 19.5 + - - -
108A GLY 3.9 0.4 - - - -
109A ILE 3.2 0.2 - - - -
110A ILE* 1.3 79.1 - - - +
112A ASN* 1.3 61.0 + - - +
114A PRO* 4.3 6.2 - - - +
133A VAL* 3.8 18.9 - - - +
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Residues in contact with ASN 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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108A GLY 3.7 2.3 + - - +
109A ILE 3.2 3.1 + - - +
110A ILE 3.2 0.6 - - - -
111A SER* 1.3 80.9 + - - +
113A ASN* 1.3 71.8 + - - +
114A PRO* 3.6 7.6 - - - +
130A LYS* 3.6 18.8 - - + +
131A PRO 2.9 28.7 + - - +
132A SER 3.5 2.0 + - - -
133A VAL* 3.3 33.6 - - - +
134A PRO* 5.3 0.6 - - - +
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Residues in contact with ASN 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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109A ILE* 2.9 35.1 + - - +
110A ILE* 3.1 9.5 - - - +
112A ASN* 1.3 85.0 - - - +
114A PRO* 1.3 62.2 - - - +
115A GLU* 3.0 18.3 + - - +
116A PHE* 3.2 33.1 + - + +
128A THR* 3.8 12.0 - - + -
129A ASN* 3.3 9.9 + - - +
130A LYS* 3.0 45.4 + - - +
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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