Contacts of the helix formed by residues 89 - 107 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A ALA* 3.4 4.1 + - - +
88A GLN* 1.3 79.7 - - - +
90A PRO* 1.3 71.6 - - - +
91A GLU* 3.5 10.6 + - - +
92A LEU* 3.0 32.1 + - - +
93A ARG* 2.8 30.1 + - - +
171B LEU* 5.3 6.2 - - - +
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Residues in contact with PRO 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A SER* 1.3 89.1 - - - +
91A GLU* 1.3 61.2 + - - +
93A ARG* 3.4 13.2 - - + +
94A THR* 3.2 25.3 + - - -
141A GLN* 5.4 0.5 + - - -
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Residues in contact with GLU 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A SER* 3.3 8.7 + - - +
90A PRO* 1.3 79.5 - - - +
92A LEU* 1.3 58.5 + - + +
94A THR* 3.4 6.0 + - - -
95A TYR* 3.0 25.7 + - - +
168A PHE* 4.0 29.9 - - + -
172A LEU* 4.4 2.3 - - + +
89B SER* 2.7 36.6 + - - -
91B GLU* 3.6 24.3 - - - +
92B LEU* 3.5 21.7 - - + +
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Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ALA* 3.9 5.5 - - + +
88A GLN* 4.4 18.2 - - + +
89A SER* 3.0 26.6 + - - +
91A GLU* 1.3 75.4 - - + +
93A ARG* 1.3 59.2 + - - +
95A TYR* 3.8 5.0 - - + +
96A LEU* 2.9 31.9 + - - +
91B GLU* 5.4 3.1 - - + +
92B LEU* 3.9 21.3 - - + -
95B TYR* 3.7 43.7 - - + -
171B LEU* 4.2 38.4 - - + +
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Residues in contact with ARG 93 (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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84A LEU* 3.2 46.8 + - + +
85A ASP* 3.1 24.7 + - - +
87A ALA* 3.7 11.6 - - + +
89A SER 2.8 13.8 + - - +
90A PRO* 3.4 17.0 - - - +
92A LEU* 1.3 77.6 - - - +
94A THR* 1.3 60.6 + - - +
96A LEU* 3.4 3.7 + - - +
97A ALA* 3.2 19.8 + - - +
137A GLN* 4.4 5.9 - - - +
138A ALA* 3.6 29.7 - - - +
141A GLN* 2.5 38.7 + - - +
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Residues in contact with THR 94 (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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90A PRO 3.2 12.3 + - - -
91A GLU* 3.6 9.8 - - - -
92A LEU 3.3 0.2 - - - -
93A ARG* 1.3 75.2 - - - +
95A TYR* 1.3 66.6 - - - +
97A ALA* 3.4 4.7 + - - +
98A GLY* 3.2 16.5 + - - -
141A GLN* 4.4 9.2 + - - -
145A ILE* 4.4 13.6 - - + +
168A PHE* 4.5 9.8 - - + -
169A ALA* 3.4 43.3 - - + +
172A LEU* 4.5 7.8 - - + +
173A ASN* 4.7 0.2 + - - -
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Residues in contact with TYR 95 (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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91A GLU 3.0 17.0 + - - +
92A LEU* 3.8 7.2 - - + +
94A THR* 1.3 75.7 - - - +
96A LEU* 1.3 57.9 + - - +
98A GLY 3.0 2.9 + - - -
99A GLN* 2.9 58.1 + - + +
172A LEU* 4.1 23.3 - - + +
173A ASN* 3.1 21.7 + - - +
92B LEU* 3.8 33.7 - - + -
95B TYR* 3.8 16.2 - + - -
96B LEU* 4.7 4.0 - - - +
99B GLN* 2.8 34.1 + - - -
352B ARG* 3.3 30.7 + - - -
354B GLU* 3.9 4.0 + - - -
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Residues in contact with LEU 96 (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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83A ILE* 3.5 41.1 - - + +
84A LEU* 4.0 16.2 - - + -
87A ALA* 4.5 11.0 - - + +
92A LEU 2.9 20.0 + - - +
93A ARG 3.6 4.7 - - - +
94A THR 3.3 0.2 - - - -
95A TYR* 1.3 75.5 - - - +
97A ALA* 1.3 62.1 + - - +
99A GLN* 3.1 24.8 + - - +
100A ILE* 3.1 15.4 + - + +
352A ARG* 4.5 13.5 - - - +
354A GLU* 3.5 45.1 - - + +
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Residues in contact with ALA 97 (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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84A LEU* 4.0 6.0 - - + +
93A ARG 3.2 11.2 + - - +
94A THR 3.6 4.0 - - - +
96A LEU* 1.3 75.1 - - - +
98A GLY* 1.3 58.0 + - - +
100A ILE* 3.3 6.2 + - - +
101A ALA* 3.1 21.7 + - - +
142A LEU* 3.8 26.7 - - + -
145A ILE* 3.5 42.0 - - + -
146A LEU* 3.7 8.3 - - - +
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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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94A THR 3.2 6.3 + - - -
95A TYR 3.0 9.1 + - - -
97A ALA* 1.3 76.9 - - - +
99A GLN* 1.3 59.4 + - - +
101A ALA* 3.3 1.6 + - - +
102A ARG* 2.9 35.5 + - - +
149A LEU* 3.8 16.0 - - - +
169A ALA 5.3 1.1 - - - -
173A ASN* 3.4 25.7 - - - +
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Residues in contact with GLN 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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95A TYR* 2.9 44.3 + - + +
96A LEU* 3.1 30.6 + - - +
98A GLY* 1.3 75.3 - - - +
100A ILE* 1.3 58.8 + - - +
102A ARG* 3.5 4.0 + - - +
103A ALA* 3.0 30.3 + - - +
173A ASN* 3.7 6.7 - - - +
354A GLU* 3.6 31.3 + - + +
355A GLU* 6.2 0.2 - - - +
358A LEU* 5.9 0.9 - - - +
95B TYR* 4.2 11.4 + - - -
99B GLN* 3.4 22.6 + - - +
352B ARG* 5.5 1.3 - - - +
355B GLU* 5.3 2.4 - - - +
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Residues in contact with ILE 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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79A LEU* 3.7 41.7 - - + -
83A ILE* 3.9 16.8 - - + -
96A LEU* 3.1 14.5 + - + +
97A ALA* 3.5 9.6 - - - +
98A GLY 3.2 0.2 - - - -
99A GLN* 1.3 74.3 - - - +
101A ALA* 1.3 64.8 + - - +
103A ALA* 3.3 5.4 + - + +
104A CYS* 3.1 34.9 + - - -
112A ILE* 4.9 1.1 - - + -
142A LEU* 4.6 6.3 - - + -
146A LEU* 4.2 16.2 - - + -
354A GLU* 3.7 26.5 - - + +
357A ILE* 3.7 15.5 - - + -
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Residues in contact with ALA 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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97A ALA 3.1 7.1 + - - +
98A GLY 3.3 2.7 + - - +
100A ILE* 1.3 76.7 - - - +
102A ARG* 1.3 59.1 + - - +
104A CYS* 3.3 2.6 + - - +
105A ALA* 3.0 28.4 + - - +
112A ILE* 4.7 1.8 - - - -
146A LEU* 3.6 15.5 - - + +
149A LEU* 3.6 29.6 - - + -
175A LEU* 3.7 9.1 - - + +
262A TYR* 3.4 27.7 - - - +
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Residues in contact with ARG 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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98A GLY 2.9 18.0 + - - +
99A GLN* 4.0 3.1 - - - +
101A ALA* 1.3 74.2 - - - +
103A ALA* 1.3 60.8 + - - +
105A ALA* 3.8 2.7 - - - +
106A ILE* 2.8 44.8 + - - +
173A ASN* 3.5 28.7 - - + -
174A PRO 2.8 37.2 + - - +
175A LEU* 3.8 14.6 + - + -
176A ASP* 4.8 4.0 + - - -
348B SER* 2.9 22.9 + - - -
350B THR* 2.6 27.0 + - - -
351B ILE* 3.7 2.0 - - - +
352B ARG* 3.8 17.6 - - - +
355B GLU* 2.8 45.1 + - - +
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Residues in contact with ALA 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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99A GLN 3.0 18.4 + - - +
100A ILE* 3.7 7.0 - - + +
102A ARG* 1.3 76.3 - - - +
104A CYS* 1.3 62.7 + - - +
106A ILE* 3.5 1.0 + - - +
107A PHE* 3.3 29.1 + - - +
354A GLU 5.0 2.7 - - - +
357A ILE* 3.8 25.6 - - + -
358A LEU* 3.6 33.7 - - + -
361A LEU* 4.3 0.5 - - - +
355B GLU* 5.1 0.6 + - - -
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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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77A VAL* 4.1 31.0 - - - -
100A ILE* 3.1 23.2 + - - +
101A ALA 3.8 2.2 - - - +
102A ARG 3.2 0.2 - - - -
103A ALA* 1.3 77.7 - - - +
105A ALA* 1.3 62.1 + - - +
107A PHE 3.3 1.2 + - - -
108A CYS 3.1 4.2 + - - -
109A VAL* 2.9 43.0 + - + +
112A ILE* 3.6 37.0 - - + -
259A TYR* 4.4 1.3 - - - -
262A TYR* 4.8 2.5 - - + -
357A ILE* 4.6 9.0 - - - -
361A LEU* 4.9 0.7 - - - -
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Residues in contact with ALA 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 ALA 3.0 17.2 + - - +
102A ARG* 3.8 4.3 - - - +
104A CYS* 1.3 72.1 - - - +
106A ILE* 1.3 68.1 + - - +
108A CYS 3.0 10.2 + - - -
175A LEU* 4.2 24.7 - - + +
177A SER* 3.8 20.9 - - - +
259A TYR* 3.6 17.0 - - + +
262A TYR* 4.9 1.7 - - + -
347B GLY* 3.1 20.0 - - - +
348B SER* 4.8 2.2 - - - -
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Residues in contact with ILE 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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102A ARG* 2.8 29.5 + - - +
103A ALA* 3.8 8.5 - - - +
105A ALA* 1.3 76.9 - - - +
107A PHE* 1.3 70.6 + - + +
108A CYS* 3.5 2.4 + - - -
358A LEU* 4.5 7.4 - - + -
365A GLN* 5.5 0.5 + - - -
343B CYS* 3.6 25.7 - - - -
346B GLN* 3.5 7.8 - - + -
347B GLY 2.9 23.8 + - - +
348B SER* 4.0 19.5 - - - +
351B ILE* 4.0 27.4 - - + -
355B GLU* 3.7 31.4 - - - +
359B ILE* 4.0 3.1 - - + -
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Residues in contact with PHE 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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75A LEU* 3.8 15.1 - - + +
103A ALA 3.3 23.4 + - - +
104A CYS 4.2 1.3 - - - +
105A ALA 3.1 1.0 - - - -
106A ILE* 1.3 79.6 - - + +
108A CYS* 1.3 70.1 + - - +
109A VAL* 3.3 4.3 + - + -
358A LEU* 3.9 17.9 - - + -
361A LEU* 3.6 37.7 - - + -
362A ALA* 3.6 38.4 - - + -
365A GLN* 3.7 35.3 + - + +
343B CYS* 4.0 8.1 - - - -
359B ILE* 3.8 35.7 - - + -
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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