Contacts of the strand formed by residues 31 - 41 (chain B) in PDB entry 1MUC
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 GLN 31 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B ASP* 4.0 31.6 + - + +
16B LEU 3.2 15.9 - - - +
17B PRO* 4.9 3.4 - - + -
18B THR* 4.1 0.7 - - - -
20B ARG* 3.1 16.3 + - - -
30B GLN* 1.3 86.3 + - - +
32B GLN* 1.3 64.9 + - - +
33B THR* 5.3 2.4 + - - +
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Residues in contact with GLN 32 (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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14B VAL 3.6 0.5 - - - +
15B ASP* 3.6 1.0 - - - -
16B LEU* 2.8 30.4 + - - -
18B THR* 3.7 20.0 - - + -
20B ARG* 3.7 11.2 + - - +
31B GLN* 1.3 76.0 - - - +
33B THR* 1.3 66.8 + - - +
34B LEU* 3.7 20.1 - - + +
52B THR* 3.5 15.7 - - - +
53B THR 3.6 14.8 + - - +
54B ILE* 4.6 7.7 - - - +
55B GLY 5.4 1.7 + - - -
303B LEU* 3.0 41.9 + - - +
334B LEU* 4.0 12.8 - - + -
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Residues in contact with THR 33 (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 ILE* 3.2 34.5 - - + -
14B VAL 3.2 4.0 - - - +
15B ASP* 2.8 21.5 + - - +
31B GLN* 5.3 2.4 + - - +
32B GLN* 1.3 81.4 + - - +
34B LEU* 1.3 62.7 + - - +
52B THR* 3.6 20.4 - - - +
53B THR* 4.4 4.3 + - - +
64B PRO* 3.8 27.9 - - + +
372B ARG* 3.8 9.2 + - - +
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Residues in contact with LEU 34 (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 ILE 3.6 0.2 - - - +
13B ILE* 3.4 6.2 - - - +
14B VAL* 2.8 39.4 + - + +
16B LEU* 3.8 29.6 - - + -
32B GLN* 3.7 29.4 - - + +
33B THR* 1.3 81.9 - - - +
35B VAL* 1.3 66.0 + - - +
36B VAL* 3.8 6.5 - - + -
50B GLU* 3.5 24.0 - - + +
51B ALA 4.4 0.2 - - - -
52B THR* 3.4 18.8 - - + +
303B LEU 5.3 0.2 - - - +
305B GLY* 4.6 12.8 - - - +
307B ILE* 6.4 0.2 - - + -
334B LEU* 5.1 2.9 - - + -
337B GLU* 4.8 2.0 - - - +
338B ILE* 4.7 14.8 - - + -
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Residues in contact with VAL 35 (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 ALA* 4.3 19.5 - - + -
12B ILE 3.3 9.0 - - - +
13B ILE* 4.3 7.4 - - + -
33B THR 5.8 0.2 - - - +
34B LEU* 1.3 76.9 - - - +
36B VAL* 1.3 60.7 + - - +
37B LEU* 3.7 13.6 - - + +
50B GLU* 3.3 5.7 - - - +
51B ALA* 2.9 48.0 + - + +
64B PRO* 3.8 38.6 - - + +
67B ILE* 3.9 22.9 - - + -
68B LYS* 5.0 2.7 - - + +
71B ILE* 4.8 0.4 - - + -
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Residues in contact with VAL 36 (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 ASP 3.5 3.1 - - - +
11B ALA* 3.5 1.0 - - - -
12B ILE* 2.8 45.2 + - + +
14B VAL* 4.0 19.5 - - + -
34B LEU* 4.6 12.3 - - + -
35B VAL* 1.3 72.6 - - - +
37B LEU* 1.3 71.6 + - - +
38B ARG* 4.3 11.7 - - + -
48B ILE* 5.2 0.2 - - + -
49B GLY 3.5 6.7 - - - +
50B GLU* 4.7 2.0 - - + +
307B ILE* 4.3 8.3 - - + -
338B ILE* 3.8 23.1 - - + -
362B LEU* 4.3 23.6 - - + -
367B LEU* 4.7 6.5 - - + -
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Residues in contact with LEU 37 (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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9B ILE* 4.3 15.5 - - + -
10B ASP 3.3 9.6 - - - +
11B ALA* 4.1 8.1 - - + -
35B VAL* 3.7 24.9 - - + +
36B VAL* 1.3 75.4 - - - +
38B ARG* 1.3 64.0 + - - +
39B VAL* 4.1 2.5 - - + -
47B GLY 4.4 0.2 - - - -
48B ILE* 3.1 8.7 - - - +
49B GLY* 2.8 40.6 + - - +
51B ALA* 4.2 8.3 - - + +
71B ILE* 3.4 29.6 - - + -
104B ALA 5.3 0.2 - - - +
107B GLY* 3.9 33.9 - - - +
108B ILE* 4.2 6.5 - - + +
111B ALA* 4.4 6.1 - - + -
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Residues in contact with ARG 38 (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 ARG* 3.7 1.6 - - - +
9B ILE* 3.5 2.1 - - - -
10B ASP* 2.9 45.1 + - + +
12B ILE* 3.6 29.0 - - + +
36B VAL* 4.3 3.4 - - + -
37B LEU* 1.3 77.2 - - - +
39B VAL* 1.3 63.8 + - - +
40B ARG* 3.9 1.1 + - - +
46B GLU* 3.0 37.6 + - - +
47B GLY 3.5 4.9 - - - -
48B ILE* 4.6 1.1 - - + +
362B LEU* 3.5 25.4 - - + +
364B GLU* 2.9 39.6 + - - -
367B LEU* 3.3 15.5 - - - +
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Residues in contact with VAL 39 (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 ILE* 4.0 26.5 - - + -
8B ARG 3.5 4.7 - - - +
9B ILE* 4.1 21.5 - - + -
37B LEU* 5.1 2.2 - - + -
38B ARG* 1.3 75.9 - - - +
40B ARG* 1.3 64.2 + - - +
41B CYS* 4.5 9.1 - - - -
45B VAL 4.0 0.3 - - - +
46B GLU* 3.1 6.9 - - - +
47B GLY* 2.8 42.2 + - - +
108B ILE* 4.9 6.7 - - + +
111B ALA* 3.5 28.3 - - + +
112B LEU* 4.1 22.4 - - + -
115B ALA* 5.8 0.7 - - + -
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Residues in contact with ARG 40 (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 ILE* 3.8 2.9 - - - -
7B GLU* 2.8 43.7 + - - +
8B ARG* 2.8 42.8 + - + +
38B ARG 3.9 1.0 + - - -
39B VAL* 1.3 75.3 - - - +
41B CYS* 1.3 70.3 + - - +
44B GLY* 5.7 6.1 - - - +
45B VAL 4.0 3.8 - - - +
46B GLU* 4.4 11.9 - - + +
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Residues in contact with CYS 41 (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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4B ALA 4.6 0.9 - - - +
5B LEU 3.2 8.3 - - - +
6B ILE* 4.8 1.1 - - - -
7B GLU* 4.1 7.7 - - - +
39B VAL* 4.5 12.8 - - - -
40B ARG* 1.3 84.9 + - - +
42B SER* 1.3 58.4 + - - +
43B ASP* 3.0 21.8 - - - +
44B GLY* 2.9 22.7 + - - -
45B VAL 2.9 18.3 + - - +
84B ALA* 3.5 27.1 - - + -
112B LEU* 5.6 0.9 - - - -
115B ALA* 4.2 13.2 - - - -
119B ARG* 3.8 13.7 - - - +
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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