Contacts of the helix formed by residues 97 - 113 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B GLY* 1.3 77.5 - - - +
98B GLY* 1.3 66.5 + - - -
99B SER 3.2 3.4 - - - -
100B PRO* 3.1 13.1 - - - +
101B GLN* 3.2 18.6 + - - +
140B THR* 3.3 4.9 + - - -
141B THR* 3.5 17.9 - - - +
144B THR* 5.2 0.2 - - - -
389B APR 3.2 23.2 + - - -
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Residues in contact with GLY 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B GLY* 1.3 72.1 - - - -
99B SER* 1.3 56.0 + - - +
102B ASP* 2.8 36.4 + - - +
144B THR* 3.5 19.9 + - - -
146B ALA* 4.4 8.5 - - - -
389B APR 3.0 35.6 + - - -
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Residues in contact with SER 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ASP* 5.7 0.4 - - - -
68B VAL* 3.6 5.8 - - - -
69B VAL 3.7 12.1 - - - -
70B PRO* 4.1 1.3 - - - -
71B ASN 3.1 19.9 + - - -
72B PRO* 3.4 22.1 - - - +
98B GLY* 1.3 76.9 - - - +
100B PRO* 1.3 70.0 - - - +
103B THR* 2.8 28.2 + - - -
389B APR 2.5 34.2 + - - -
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Residues in contact with PRO 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B VAL* 3.6 15.4 - - - +
38B THR* 3.9 9.4 - - - -
39B ASP* 3.8 20.2 - - - +
68B VAL* 3.7 19.7 - - + -
94B ALA* 4.8 1.1 - - - -
95B ILE 3.7 24.5 - - - +
96B GLY* 4.0 6.1 - - - -
97B GLY 3.1 13.9 - - - +
99B SER* 1.3 94.7 - - - +
101B GLN* 1.3 55.4 + - - +
103B THR* 3.3 1.7 + - - -
104B CYS* 2.8 31.3 + - - +
389B APR 3.5 8.1 - - - +
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Residues in contact with GLN 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ALA* 4.1 19.9 - - + +
96B GLY 3.1 25.0 + - - +
97B GLY* 3.2 18.9 + - - +
98B GLY 4.0 0.2 - - - +
100B PRO* 1.3 77.5 - - - +
102B ASP* 1.3 58.3 + - - +
104B CYS* 3.3 2.9 + - - +
105B LYS* 3.0 32.4 + - - +
135B ILE* 6.1 0.2 - - - +
137B ALA* 3.5 10.9 - - - +
138B ILE 4.8 0.7 - - - -
139B PRO* 3.4 26.8 - - - +
144B THR* 4.5 2.0 + - - -
146B ALA* 3.5 23.9 - - + +
147B GLU* 3.1 36.5 + - - +
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Residues in contact with ASP 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PRO* 4.5 3.8 - - + -
98B GLY* 2.8 25.8 + - - +
99B SER 4.0 2.2 - - - +
101B GLN* 1.3 69.8 - - - +
103B THR* 1.3 67.0 + - - +
105B LYS* 3.2 4.6 + - - +
106B ALA* 3.0 23.4 + - - +
146B ALA* 3.8 18.2 - - - +
151B ASN 3.8 3.8 - - - +
152B TYR* 3.5 34.0 - - + +
153B VAL* 3.0 40.4 + - - +
154B ILE* 4.5 3.1 - - + -
389B APR 3.8 10.1 + - - -
390B PGO 5.0 1.4 + - - +
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Residues in contact with THR 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B VAL* 4.2 2.7 - - + -
65B TYR* 4.7 1.6 - - + -
68B VAL* 3.7 25.4 - - + +
72B PRO* 3.1 20.1 - - - +
76B VAL* 4.0 16.6 - - + +
77B VAL* 4.4 10.3 - - + -
99B SER 2.8 21.6 + - - -
100B PRO 3.6 4.0 - - - -
102B ASP* 1.3 76.6 - - - +
104B CYS* 1.3 62.7 + - - +
106B ALA* 3.2 7.9 + - - +
107B ILE* 3.0 46.0 + - + +
154B ILE* 4.7 4.9 - - - +
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Residues in contact with CYS 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B VAL* 3.9 23.8 - - + +
92B LEU* 3.6 33.3 - - - +
94B ALA* 3.7 27.1 - - + -
100B PRO 2.8 18.3 + - - +
101B GLN 3.5 5.8 - - - +
103B THR* 1.3 76.9 - - - +
105B LYS* 1.3 56.9 + - - +
107B ILE* 3.2 5.0 + - - +
108B GLY* 2.9 26.9 + - - -
135B ILE* 3.9 13.5 - - + +
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Residues in contact with LYS 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B GLN* 3.0 17.1 + - - +
102B ASP* 3.2 9.6 + - - +
104B CYS* 1.3 75.1 - - - +
106B ALA* 1.3 63.4 + - - +
108B GLY* 3.4 1.2 + - - -
109B ILE* 3.0 31.1 + - - +
132B SER* 4.4 0.5 + - - -
135B ILE* 3.8 14.8 - - + -
146B ALA* 2.7 28.0 + - - +
149B THR* 2.7 32.8 + - - -
151B ASN 2.9 27.8 + - - +
152B TYR* 3.7 18.4 - - + -
170B ASP* 3.7 34.5 - - + +
172B PRO* 4.0 9.0 - - + -
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Residues in contact with ALA 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B VAL* 3.7 29.4 - - + -
102B ASP 3.0 12.3 + - - +
103B THR 3.2 8.7 + - - +
105B LYS* 1.3 75.0 - - - +
107B ILE* 1.3 63.5 + - - +
109B ILE* 3.4 0.7 + - - +
110B ILE* 3.0 35.9 + - + +
119B VAL* 5.2 2.5 - - + -
122B LEU* 5.3 0.2 - - + -
152B TYR* 3.9 26.8 - - + -
154B ILE* 4.4 3.8 - - + -
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Residues in contact with ILE 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 5.4 0.7 - - + -
37B VAL* 4.4 19.3 - - + -
65B TYR* 4.9 1.1 - - + -
77B VAL* 3.9 12.1 - - + +
80B GLY* 3.5 28.9 - - - +
81B LEU* 3.8 26.4 - - + +
84B PHE* 3.9 32.3 - - + -
92B LEU* 4.5 8.5 - - + -
103B THR* 3.0 31.8 + - + +
104B CYS* 3.2 6.9 + - - +
106B ALA* 1.3 77.6 - - - +
108B GLY* 1.3 57.5 + - - +
110B ILE* 5.0 0.4 - - - -
111B SER* 3.0 30.0 + - - -
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Residues in contact with GLY 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU* 3.7 17.9 - - - +
104B CYS 2.9 12.9 + - - -
107B ILE* 1.3 77.4 - - - +
109B ILE* 1.3 62.0 + - - +
112B ASN 3.6 10.6 + - - -
132B SER* 3.1 23.6 - - - -
133B VAL* 3.1 24.4 + - - +
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Residues in contact with ILE 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B LYS 3.0 20.8 + - - +
106B ALA 3.8 2.9 - - - +
108B GLY* 1.3 74.7 - - - +
110B ILE* 1.3 63.1 + - - +
112B ASN 3.2 2.6 + - - -
113B ASN* 2.8 41.2 + - + +
122B LEU* 4.0 11.0 - - + -
128B THR* 3.7 24.5 - - + +
132B SER* 3.7 20.0 - - - +
152B TYR* 4.0 21.1 - - + +
167B ASP* 3.7 13.9 - - - +
169B HIS* 3.7 27.4 - - + +
170B ASP* 3.8 14.1 - - + +
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Residues in contact with ILE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B VAL* 3.9 13.7 - - + -
81B LEU* 3.6 28.5 - - + -
85B GLN* 5.6 1.0 + - - +
106B ALA 3.0 18.1 + - - +
107B ILE 4.2 1.8 - - - +
109B ILE* 1.3 76.2 - - - +
111B SER* 1.3 63.7 + - - +
113B ASN 3.0 26.6 + - - +
114B PRO* 3.1 9.4 - - + +
116B PHE* 3.6 21.1 - - + +
117B ALA* 4.1 19.7 - - + +
119B VAL* 3.8 23.3 - - + -
122B LEU* 3.9 20.0 - - + -
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Residues in contact with SER 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU* 4.1 11.4 - - - +
84B PHE* 3.2 29.5 - - - -
85B GLN* 4.7 12.6 + - - +
107B ILE 3.0 19.2 + - - -
109B ILE 3.3 0.2 - - - -
110B ILE* 1.3 78.1 - - - +
112B ASN* 1.3 62.7 + - - +
114B PRO* 4.4 5.9 - - - +
133B VAL* 3.8 19.2 - - - +
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Residues in contact with ASN 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B GLY 3.6 3.9 + - - +
109B ILE 3.2 2.0 + - - -
110B ILE 3.1 0.2 - - - -
111B SER* 1.3 83.1 + - - +
113B ASN* 1.3 71.5 + - - +
114B PRO* 3.5 8.6 - - - +
115B GLU* 4.8 0.3 - - - +
130B LYS* 3.8 17.0 - - + +
131B PRO 2.8 29.0 + - - +
132B SER 3.5 1.6 + - - -
133B VAL* 3.4 31.6 - - - +
134B PRO* 5.5 0.6 - - - +
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Residues in contact with ASN 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ILE* 2.8 31.0 + - - +
110B ILE* 3.1 12.8 - - - +
112B ASN* 1.3 86.3 - - - +
114B PRO* 1.3 59.1 - - - +
115B GLU* 3.0 22.1 + - - +
116B PHE* 3.2 28.4 + - + +
128B THR* 3.8 15.1 - - + -
129B ASN* 3.2 10.9 + - - +
130B LYS* 2.9 46.2 + - - +
131B PRO 4.6 0.2 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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