Contacts of the helix formed by residues 89 - 107 (chain B) in PDB entry 4RG1
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 SER 89 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A GLU* 2.7 31.0 + - - -
168A PHE* 5.9 0.7 - - - -
87B ALA* 3.4 4.3 + - - +
88B GLN* 1.3 80.0 - - - +
90B PRO* 1.4 71.1 - - - +
91B GLU* 3.5 5.6 + - - -
92B LEU* 3.0 22.0 + - - +
93B ARG* 2.9 28.9 + - - +
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Residues in contact with PRO 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B SER* 1.4 87.9 - - - +
91B GLU* 1.3 69.1 - - - +
93B ARG* 3.3 14.3 - - + +
94B THR* 3.2 24.3 + - - -
141B GLN* 5.2 0.7 + - - -
168B PHE* 3.4 29.6 - - + -
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Residues in contact with GLU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A GLU* 3.6 20.5 - - - +
92A LEU* 5.7 3.6 - - + -
89B SER* 3.6 6.6 + - - -
90B PRO* 1.3 90.9 - - - +
92B LEU* 1.3 57.8 + - - +
94B THR* 3.4 4.3 + - - -
95B TYR* 2.9 28.0 + - - +
168B PHE* 3.6 36.8 - - + -
171B LEU* 3.6 29.1 - - + +
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Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A GLU* 3.5 28.9 - - + +
92A LEU* 3.9 22.0 - - + -
95A TYR* 3.8 41.6 + - + -
168A PHE* 4.9 0.7 - - + -
172A LEU* 3.7 32.3 - - + -
87B ALA* 3.8 9.4 - - + +
88B GLN* 4.4 3.4 - - + +
89B SER* 3.0 27.7 + - - +
91B GLU* 1.3 73.9 - - - +
93B ARG* 1.3 59.6 + - - +
95B TYR* 3.6 3.8 - - + +
96B LEU* 2.8 31.4 + - - +
99B GLN* 5.5 0.2 + - - -
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Residues in contact with ARG 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B LEU* 3.2 49.8 + - + +
85B ASP* 3.2 23.6 + - - +
87B ALA* 3.5 12.3 - - + +
89B SER 2.9 13.3 + - - +
90B PRO* 3.3 16.4 - - - +
92B LEU* 1.3 77.7 - - - +
94B THR* 1.3 61.3 + - - +
96B LEU* 3.4 3.8 + - - +
97B ALA* 3.2 18.5 + - - +
137B GLN* 4.5 6.1 - - - +
138B ALA* 3.6 31.7 - - - +
141B GLN* 2.5 32.7 + - - +
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Residues in contact with THR 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B PRO 3.2 9.8 + - - -
91B GLU 3.7 7.4 - - - -
93B ARG* 1.3 73.9 - - - +
95B TYR* 1.3 66.7 + - - +
97B ALA* 3.2 4.7 + - - +
98B GLY 3.1 16.6 + - - -
141B GLN* 3.8 14.4 + - - +
145B ILE* 4.1 18.5 - - + +
165B ASP 4.3 5.6 + - - +
166B LEU* 6.1 0.4 - - - -
168B PHE* 3.4 47.8 - - - +
169B ALA* 4.3 0.9 - - - +
171B LEU* 5.3 1.3 - - + -
172B LEU* 3.2 27.9 - - + +
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Residues in contact with TYR 95 (chain B).
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* 3.7 30.7 - - + -
95A TYR* 3.8 24.0 - + - -
99A GLN* 4.2 8.7 + - - -
352A ARG* 3.5 17.0 + - - -
354A GLU* 4.1 4.5 + - - -
91B GLU 2.9 17.6 + - - +
92B LEU* 3.6 10.3 - - - +
93B ARG 3.3 0.2 - - - -
94B THR* 1.3 77.6 - - - +
96B LEU* 1.3 56.7 + - - +
98B GLY 3.1 0.7 + - - -
99B GLN* 2.9 37.3 + - + +
171B LEU* 3.4 27.5 - - + +
172B LEU* 4.5 2.0 - - - -
173B ASN* 3.3 18.5 + - - -
402B PGO 2.8 44.8 - - + +
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Residues in contact with LEU 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A TYR* 4.7 3.8 - - - +
83B ILE* 3.4 44.4 - - + +
84B LEU* 4.0 13.0 - - + -
86B ASN* 5.6 0.7 - - + -
87B ALA* 4.5 12.1 - - + +
92B LEU 2.8 21.0 + - - +
93B ARG 3.6 4.5 - - - +
94B THR 3.3 0.2 - - - -
95B TYR* 1.3 71.9 - - - +
97B ALA* 1.3 64.4 + - - +
99B GLN* 3.0 27.1 + - - +
100B ILE* 3.1 13.5 + - - +
354B GLU* 3.4 46.0 - - + +
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Residues in contact with ALA 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B LEU* 4.0 6.4 - - + +
93B ARG 3.2 7.9 + - - +
94B THR 3.2 9.2 + - - +
96B LEU* 1.3 77.3 - - - +
98B GLY* 1.3 63.7 + - - +
100B ILE* 3.2 6.6 + - - +
101B ALA* 3.1 17.7 + - - +
142B LEU* 3.7 27.6 - - + -
145B ILE* 3.6 35.9 - - + -
146B LEU* 3.7 7.8 - - + +
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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
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94B THR 3.1 4.6 + - - -
95B TYR 3.1 4.0 + - - -
97B ALA* 1.3 79.6 - - - +
99B GLN* 1.3 56.7 + - - +
101B ALA* 3.7 1.0 - - - +
102B ARG* 2.9 26.3 + - - +
145B ILE* 4.3 0.2 - - - +
149B LEU* 3.8 10.8 - - - -
172B LEU* 3.7 11.3 - - - +
402B PGO 3.3 35.1 + - - -
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Residues in contact with GLN 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A TYR* 2.8 35.8 + - - -
99A GLN* 3.4 18.7 + - - +
355A GLU* 5.5 0.4 - - - +
95B TYR* 2.9 28.4 + - + +
96B LEU* 3.0 28.4 + - - +
98B GLY* 1.3 75.7 - - - +
100B ILE* 1.3 57.6 + - - +
102B ARG* 4.0 1.4 - - - +
103B ALA* 3.0 30.3 + - - +
354B GLU* 3.6 27.7 - - + +
358B LEU* 5.8 0.9 - - - +
402B PGO 3.2 17.3 - - - +
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Residues in contact with ILE 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LEU* 3.6 42.0 - - + -
83B ILE* 3.8 16.4 - - + -
96B LEU 3.1 13.6 + - - +
97B ALA* 3.2 9.6 + - - +
99B GLN* 1.3 74.2 - - - +
101B ALA* 1.3 66.2 + - - +
103B ALA* 3.3 5.3 + - + +
104B CYS* 3.0 36.2 + - - -
112B ILE* 4.7 0.9 - - + -
142B LEU* 4.5 5.8 - - + -
146B LEU* 4.2 16.6 - - + -
354B GLU* 3.7 26.7 - - + +
357B ILE* 3.7 15.0 - - + -
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Residues in contact with ALA 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ALA 3.1 7.1 + - - +
98B GLY 3.3 7.6 + - - +
100B ILE* 1.3 77.3 - - - +
102B ARG* 1.3 59.2 + - - +
104B CYS* 3.4 2.1 + - - +
105B ALA* 2.9 28.8 + - - +
112B ILE* 4.7 1.8 - - - -
146B LEU* 3.6 17.2 - - + +
149B LEU* 3.7 23.1 - - + -
175B LEU* 3.8 7.4 - - + +
262B TYR* 3.4 27.8 - - - +
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Residues in contact with ARG 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348A SER* 2.9 26.1 + - - -
350A THR* 2.7 25.8 + - - -
351A ILE* 3.7 3.2 - - - +
352A ARG* 3.9 11.3 - - - +
355A GLU* 2.8 48.2 + - - +
98B GLY 2.9 19.2 + - - +
99B GLN 4.1 1.8 - - - +
101B ALA* 1.3 73.1 - - - +
103B ALA* 1.3 59.4 + - - +
105B ALA* 3.2 2.5 + - - +
106B ILE* 2.8 44.0 + - - +
173B ASN* 3.5 28.9 - - - +
174B PRO 2.9 20.8 + - - -
175B LEU* 3.7 21.8 + - + -
176B ASP* 4.7 3.6 + - - -
402B PGO 3.8 8.7 - - - +
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Residues in contact with ALA 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355A GLU* 5.2 0.4 + - - -
99B GLN 3.0 18.3 + - - +
100B ILE* 3.7 5.8 - - + +
102B ARG* 1.3 77.3 - - - +
104B CYS* 1.3 63.7 + - - +
106B ILE* 3.5 1.3 + - - +
107B PHE* 3.3 29.1 + - - +
354B GLU 4.8 3.4 - - - +
357B ILE* 3.8 25.6 - - + -
358B LEU* 3.6 34.5 - - + -
361B LEU* 4.4 0.5 - - - +
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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
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77B VAL* 4.1 30.7 - - - -
100B ILE* 3.0 26.9 + - - +
101B ALA 3.8 1.8 - - - +
103B ALA* 1.3 78.5 - - - +
105B ALA* 1.3 60.6 + - - +
107B PHE 3.3 1.9 + - - -
108B CYS 3.2 3.8 + - - -
109B VAL* 2.9 42.4 + - + +
112B ILE* 3.7 34.8 - - + -
259B TYR* 4.4 1.1 - - - -
262B TYR* 4.8 2.2 - - + -
357B ILE* 4.6 7.4 - - - -
361B LEU* 4.9 0.2 - - - -
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Residues in contact with ALA 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347A GLY* 3.1 19.8 - - - +
348A SER* 4.8 2.5 - - - -
101B ALA 2.9 17.3 + - - +
102B ARG* 3.8 4.0 - - - +
104B CYS* 1.3 71.5 - - - +
106B ILE* 1.3 67.6 + - - +
108B CYS 3.0 10.4 + - - -
175B LEU* 4.2 24.7 - - + +
177B SER* 3.9 20.6 - - - +
259B TYR* 3.6 18.5 + - + +
262B TYR* 4.9 1.1 - - + -
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Residues in contact with ILE 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A CYS* 3.6 26.2 - - - -
345A GLY 4.5 0.2 - - - +
346A GLN* 3.5 8.1 - - + -
347A GLY 2.9 24.4 + - - +
348A SER* 4.0 19.7 - - - +
351A ILE* 3.9 26.5 - - + -
355A GLU* 3.6 36.3 - - + +
359A ILE* 3.9 10.8 - - + -
102B ARG* 2.8 29.1 + - - +
103B ALA 3.9 4.0 - - - +
105B ALA* 1.3 75.6 - - - +
107B PHE* 1.3 62.3 + - + +
108B CYS* 3.4 1.7 + - - -
358B LEU* 4.6 7.9 - - + -
365B GLN* 5.5 0.5 + - - -
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Residues in contact with PHE 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343A CYS* 4.0 7.9 - - - -
359A ILE* 3.8 40.6 - - + -
75B LEU* 3.8 14.5 - - + +
103B ALA 3.3 16.5 + - - +
104B CYS 3.3 3.1 + - - +
105B ALA 3.1 0.8 - - - -
106B ILE* 1.3 78.9 - - + +
108B CYS* 1.3 71.1 + - - +
109B VAL* 3.3 2.9 + - + -
358B LEU* 3.9 18.4 - - + -
361B LEU* 3.6 41.1 - - + -
362B ALA* 3.6 32.1 - - + -
365B GLN* 3.8 34.4 + - + +
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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