Contacts of the helix formed by residues 92 - 107 (chain A) in PDB entry 1M1B
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 ASN 92 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A GLY* 1.3 74.6 - - - -
93A PHE* 1.3 85.7 + - + +
94A ASN* 2.9 22.0 + - - +
95A ASN* 3.1 18.0 + - - +
96A ALA* 2.9 20.4 + - - +
137A GLU* 6.4 2.0 - - - -
141A LYS* 3.9 8.7 - - - +
284B LEU* 6.3 0.2 - - - +
288B GLU* 5.3 4.4 + - - -
292B LEU* 5.2 13.2 - - + +
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Residues in contact with PHE 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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92A ASN* 1.3 95.5 - - - +
94A ASN* 1.3 64.8 + - + +
96A ALA* 3.2 9.5 - - - +
97A ARG* 2.7 50.3 + - - +
141A LYS* 3.9 21.9 - - + +
144A ALA* 3.8 19.7 - - + +
284B LEU* 4.2 4.0 - - + -
287B ALA* 3.9 13.5 - - + -
288B GLU* 3.8 33.0 - - + -
291B TYR* 3.5 46.7 - + + +
292B LEU* 4.0 22.9 - - + -
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Residues in contact with ASN 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ASN* 2.9 13.5 + - - +
93A PHE* 1.3 91.7 - - + +
95A ASN* 1.3 68.5 + - - +
97A ARG* 2.7 44.3 + - - +
98A ARG* 3.0 30.8 + - - +
284B LEU* 3.7 20.5 - - + +
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Residues in contact with ASN 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TRP* 5.4 11.9 + - + +
89A GLY 3.6 15.6 - - - +
90A TYR* 3.6 17.1 + - + +
91A GLY* 3.2 7.2 - - - -
92A ASN* 3.1 37.9 + - - +
94A ASN* 1.3 80.2 + - - +
96A ALA* 1.3 63.7 + - - +
98A ARG* 3.3 8.4 + - - +
99A LEU* 3.0 24.1 + - - +
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Residues in contact with ALA 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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89A GLY* 3.6 11.4 + - - +
92A ASN 2.9 13.1 + - - +
93A PHE* 3.2 11.7 - - - +
95A ASN* 1.3 77.6 - - - +
97A ARG* 1.3 61.8 + - - +
99A LEU* 3.3 9.1 + - - +
100A VAL* 3.1 24.4 + - - +
113A LEU* 4.3 6.7 - - + +
141A LYS* 3.7 20.2 - - + -
145A CYS* 3.6 22.8 - - - -
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Residues in contact with ARG 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PHE* 2.7 30.5 + - - +
94A ASN* 2.7 35.0 + - - +
96A ALA* 1.3 71.0 - - - +
98A ARG* 1.3 68.9 + - + +
100A VAL* 3.3 11.4 + - - +
101A ARG* 3.2 24.5 + - - +
144A ALA* 4.1 10.3 - - - +
145A CYS* 4.2 2.4 - - - -
148A SER* 3.2 32.4 + - - +
283B GLU* 3.2 39.5 + - - -
284B LEU* 3.7 15.8 - - - +
287B ALA* 3.8 15.3 - - - +
291B TYR* 5.1 6.0 - - - -
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Residues in contact with ARG 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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64A TRP* 3.9 28.3 - - + -
94A ASN* 3.0 23.0 + - - +
95A ASN* 3.7 8.3 - - - +
97A ARG* 1.3 79.0 - - + +
99A LEU* 1.3 63.7 + - - +
101A ARG* 3.1 17.7 + - + +
102A LYS* 3.1 40.6 + - - +
73B PHE* 3.3 35.6 - - - -
76B ASP* 4.6 6.7 + - - +
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Residues in contact with LEU 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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64A TRP* 3.6 34.5 - - + -
68A VAL* 3.6 17.9 - - + -
84A LEU* 4.8 2.9 - - + -
86A ALA* 3.8 18.4 - - + -
89A GLY* 4.8 6.7 - - - +
90A TYR* 3.3 36.8 - - + -
95A ASN 3.0 13.4 + - - +
96A ALA* 3.4 11.0 - - - +
98A ARG* 1.3 77.4 - - - +
100A VAL* 1.3 56.9 + - + +
102A LYS* 3.1 2.3 + - - +
103A LEU* 2.9 51.6 + - + +
111A ALA* 5.0 2.9 - - + -
113A LEU* 5.6 2.5 - - + -
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Residues in contact with VAL 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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96A ALA 3.1 14.7 + - - +
97A ARG* 3.5 11.2 - - - +
98A ARG 3.3 0.2 - - - -
99A LEU* 1.3 76.8 - - + +
101A ARG* 1.3 60.3 + - + +
103A LEU* 3.7 7.0 - - - +
104A GLU* 3.1 33.3 + - - +
111A ALA* 4.9 6.3 - - + -
113A LEU* 5.9 1.1 - - + -
145A CYS* 3.9 21.1 - - + +
148A SER* 5.0 2.7 - - - -
149A GLN* 4.0 31.2 - - + +
154A PHE* 4.0 12.2 - - + -
156A ILE* 3.8 24.7 - - + -
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Residues in contact with ARG 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 ARG 3.2 12.9 + - - +
98A ARG* 3.1 13.4 + - + +
100A VAL* 1.3 77.6 - - + +
102A LYS* 1.3 70.5 + - + +
104A GLU* 3.4 26.5 + - - +
105A ASP* 2.6 68.7 + - - +
148A SER* 4.6 14.6 - - - +
150A THR* 3.9 25.5 + - - +
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Residues in contact with LYS 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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64A TRP* 3.7 27.4 - - + -
68A VAL* 4.4 12.1 - - + -
98A ARG* 3.1 39.7 + - - +
99A LEU 3.1 7.0 + - - +
101A ARG* 1.3 82.0 - - - +
103A LEU* 1.3 64.0 + - - +
105A ASP* 3.5 6.9 + - - +
106A ARG* 3.2 44.2 + - - +
72B GLU* 3.1 27.7 + - - +
76B ASP* 2.5 36.5 + - - -
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Residues in contact with LEU 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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68A VAL* 4.6 13.0 - - + -
71A LEU* 5.4 2.9 - - + -
84A LEU* 3.8 25.4 - - + -
99A LEU* 2.9 40.5 + - + +
100A VAL* 3.7 5.8 - - - +
101A ARG 3.2 0.2 - - - -
102A LYS* 1.3 74.3 - - - +
104A GLU* 1.3 68.1 + - - +
106A ARG* 3.2 6.3 + - - -
108A VAL* 3.1 48.4 + - + +
110A GLY 4.5 3.4 - - - +
111A ALA* 3.5 33.4 - - + -
154A PHE* 3.7 16.6 - - + -
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Residues in contact with GLU 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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8A THR* 6.1 0.2 - - + -
100A VAL* 3.1 23.2 + - - +
101A ARG* 3.4 26.8 + - - +
103A LEU* 1.3 72.8 - - - +
105A ASP* 1.3 59.6 + - - +
107A GLY* 2.9 23.2 + - - -
108A VAL 4.3 7.0 - - - -
149A GLN* 3.3 17.6 - - - +
150A THR* 2.7 47.3 + - - +
151A ASP* 3.0 18.7 + - + +
154A PHE* 3.8 19.8 - - + +
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Residues in contact with ASP 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 ARG* 2.6 48.8 + - - +
102A LYS* 3.6 13.1 + - - +
104A GLU* 1.3 79.5 - - - +
106A ARG* 1.3 74.7 + - - +
107A GLY 3.4 0.7 + - - -
76B ASP* 5.5 2.1 - - - +
105B ASP* 3.7 43.6 - - + +
106B ARG* 5.8 2.5 - - - +
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Residues in contact with ARG 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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68A VAL* 4.2 17.9 - - + +
72A GLU* 3.7 38.7 + - + -
75A SER* 2.6 28.1 + - - -
76A ASP* 4.5 6.9 - - - +
102A LYS* 3.2 40.6 + - - +
103A LEU* 3.2 4.9 + - - +
104A GLU 3.2 0.2 + - - -
105A ASP* 1.3 86.6 + - - +
107A GLY* 1.3 52.5 + - - +
108A VAL* 3.4 12.1 - - + -
72B GLU* 3.0 38.6 + - - -
105B ASP* 5.5 4.5 - - - -
106B ARG* 3.6 34.5 - - - +
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Residues in contact with GLY 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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7A LYS* 3.3 33.1 - - - +
8A THR* 6.0 0.6 - - - +
75A SER* 3.4 9.1 + - - -
82A ILE* 6.1 0.2 - - - +
104A GLU 2.9 13.6 + - - -
105A ASP 3.2 2.0 + - - -
106A ARG* 1.3 78.5 - - - +
108A VAL* 1.3 63.3 + - - +
109A ALA 3.5 0.3 + - - -
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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