Contacts of the helix formed by residues 6 - 17 (chain B) 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 LYS 6 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B VAL* 1.3 75.4 - - - +
7B LYS* 1.3 55.4 + - - +
8B THR* 4.0 12.1 - - - +
9B THR* 2.8 23.7 + - - +
10B GLN 2.7 32.2 + - - -
151B ASP* 4.7 15.0 + - - +
153B ASP* 5.7 0.2 - - - +
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Residues in contact with LYS 7 (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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5B VAL 3.3 3.2 + - - +
6B LYS* 1.3 69.4 - - - +
8B THR* 1.3 63.7 + - + +
10B GLN* 3.0 12.4 + - - +
11B LEU 2.9 19.2 + - - -
75B SER* 2.9 34.8 + - - +
78B SER* 2.8 29.7 + - - -
79B ASP* 3.8 20.4 - - - +
80B VAL 3.4 20.4 - - - +
81B PRO* 3.4 10.7 - - + +
82B ILE* 6.1 0.9 - - + -
107B GLY* 3.3 23.3 - - - +
109B ALA* 3.8 10.8 - - + -
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Residues in contact with THR 8 (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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6B LYS* 4.0 6.9 - - - +
7B LYS* 1.3 75.8 - - + +
9B THR* 1.3 66.1 + - - +
11B LEU* 3.3 2.4 + - - +
12B LYS* 2.8 25.3 + - - +
104B GLU* 6.2 0.2 - - + -
107B GLY 5.9 0.2 - - - +
108B VAL 4.0 4.7 - - - +
109B ALA* 3.6 34.1 - - - +
151B ASP* 2.9 27.4 + - + +
153B ASP* 3.4 16.7 - - - +
154B PHE* 3.6 31.0 - - + -
155B CYS* 4.1 0.2 - - - -
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Residues in contact with THR 9 (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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5B VAL* 4.5 9.6 - - + -
6B LYS* 2.8 29.8 + - - +
8B THR* 1.3 79.4 + - - +
10B GLN* 1.3 67.4 + - - +
12B LYS* 3.9 1.7 - - + +
13B GLN* 2.9 51.9 + - + +
153B ASP* 2.4 36.4 + - - +
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Residues in contact with GLN 10 (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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5B VAL* 3.2 42.1 + - + +
6B LYS 2.7 10.0 + - - +
7B LYS* 3.1 15.5 - - - +
9B THR* 1.3 75.9 - - - +
11B LEU* 1.3 60.4 + - - +
13B GLN* 3.5 12.0 + - - +
14B MET* 3.3 25.1 + - - +
41B LYS* 4.5 4.4 + - - +
79B ASP 3.3 21.5 + - - +
80B VAL* 3.8 11.7 - - - +
81B PRO* 3.6 25.9 - - + +
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Residues in contact with LEU 11 (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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7B LYS 2.9 8.8 + - - +
8B THR 3.7 2.9 - - - +
10B GLN* 1.3 75.7 - - - +
12B LYS* 1.3 65.6 + - - +
13B GLN 3.2 0.2 - - - -
14B MET* 3.1 6.5 + - + +
15B LEU* 3.0 29.6 + - + +
23B ILE* 5.4 4.0 - - + -
81B PRO* 3.6 24.0 - - + +
82B ILE 4.6 0.4 - - - +
83B LEU* 4.5 25.1 - - + +
109B ALA* 3.3 37.9 - - + +
110B GLY* 3.6 9.4 - - - +
155B CYS* 4.0 13.2 - - + -
234B MET* 4.2 21.8 - - + -
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Residues in contact with LYS 12 (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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8B THR 2.8 17.3 + - - +
9B THR* 3.9 5.6 - - - +
11B LEU* 1.3 70.8 - - - +
13B GLN* 1.3 57.8 + - + +
15B LEU* 3.1 5.5 + - + +
16B ASN* 2.9 47.5 + - - +
146B LYS* 4.0 4.6 - - - +
152B PRO 3.0 24.7 + - - -
153B ASP* 3.6 28.1 + - + +
154B PHE 3.9 4.0 + - - -
155B CYS* 3.4 21.4 - - - -
185B ASP* 2.9 31.0 + - - -
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Residues in contact with GLN 13 (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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5B VAL* 5.2 9.6 - - - +
9B THR* 2.9 42.1 + - + +
10B GLN* 3.5 12.6 + - - +
12B LYS* 1.3 77.9 - - - +
14B MET* 1.3 56.5 + - + +
16B ASN* 3.7 4.4 - - - +
17B SER* 3.0 29.6 + - - -
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Residues in contact with MET 14 (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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10B GLN* 3.3 15.9 + - - +
11B LEU* 3.1 10.2 + - - +
13B GLN* 1.3 75.4 - - + +
15B LEU* 1.3 63.7 + - - +
16B ASN 3.2 0.2 - - - -
17B SER* 2.7 23.8 + - - -
21B GLU* 3.5 39.0 - - + +
22B PHE 3.7 18.2 - - - +
23B ILE* 4.1 10.1 - - + -
41B LYS* 3.2 55.2 - - + +
42B GLY 4.4 0.4 - - - -
81B PRO* 4.5 8.7 - - - -
233B SER* 3.4 6.9 + - - +
234B MET* 3.7 14.7 - - + +
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Residues in contact with LEU 15 (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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11B LEU* 3.0 23.1 + - + +
12B LYS* 3.7 6.7 - - + +
14B MET* 1.3 76.5 - - - +
16B ASN* 1.3 62.3 + - - +
83B LEU* 5.4 1.1 - - + -
155B CYS* 3.8 35.7 - - + -
157B VAL* 3.9 19.1 - - + -
185B ASP* 4.5 8.3 - - + +
186B ALA* 4.0 15.5 - - + -
211B PRO* 3.0 21.2 - - + +
213B VAL* 3.7 22.4 - - + -
233B SER* 2.9 18.6 + - - +
234B MET* 3.7 30.1 - - + -
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Residues in contact with ASN 16 (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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12B LYS* 2.9 41.8 + - - +
13B GLN* 3.7 5.1 - - - +
15B LEU* 1.3 77.8 - - - +
17B SER* 1.3 65.3 + - - +
18B LYS* 3.7 1.2 + - - -
180B ARG* 5.7 0.9 + - - -
185B ASP 4.6 3.1 - - - +
211B PRO* 3.5 21.1 - - - +
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Residues in contact with SER 17 (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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13B GLN 3.0 14.4 + - - -
14B MET 2.7 21.6 + - - -
15B LEU 4.2 0.2 - - - +
16B ASN* 1.3 82.9 - - - +
18B LYS* 1.3 60.3 + - - +
19B ASP* 2.9 27.3 + - - +
21B GLU* 3.2 19.6 + - - +
233B SER* 3.3 17.3 + - - -
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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