Contacts of the strand formed by residues 21 - 30 (chain M) in PDB entry 1MWA
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 21 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11M SER* 3.8 6.3 - - - -
12M ARG* 3.0 33.5 - - - +
13M HIS* 3.1 40.6 + - - +
14M PRO 4.2 5.4 - - - +
15M PRO* 4.8 2.6 - - + +
19M LYS* 3.1 7.8 + - - +
20M PRO* 1.3 76.5 - - - +
22M ILE* 1.3 91.6 + - - +
69M GLU* 3.0 14.9 - - - +
70M PHE* 2.5 32.7 + - + +
72M PRO* 4.3 4.7 - - + -
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Residues in contact with ILE 22 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237I GLY* 6.4 0.2 - - - -
11M SER 3.9 0.2 - - - -
12M ARG* 3.4 67.3 + - - +
13M HIS* 4.2 9.2 - - + +
20M PRO 5.0 2.0 - - - +
21M ASN* 1.3 104.7 - - - +
23M LEU* 1.3 71.6 + - - +
24M ASN* 3.8 6.6 + - - +
67M HIS* 4.1 26.5 - - + -
68M THR 4.0 8.3 - - - +
69M GLU* 3.6 17.0 - - + +
70M PHE* 3.0 4.7 - - - -
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Residues in contact with LEU 23 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9M VAL* 3.7 25.8 - - + -
10M TYR 3.8 10.5 - - - +
11M SER* 4.5 0.2 - - - +
22M ILE* 1.3 74.3 - - - +
24M ASN* 1.3 67.3 + - - +
39M MET* 3.1 31.2 - - + +
40M LEU 5.4 1.3 - - - +
67M HIS* 3.2 21.0 - - - +
68M THR* 3.1 19.1 + - - +
70M PHE* 3.0 31.4 - - + -
78M TYR* 3.6 35.7 - - + -
79M ALA 5.1 4.7 - - - +
95M TRP* 3.9 18.4 - - + +
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Residues in contact with ASN 24 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236I ALA 2.5 27.3 + - - +
237I GLY* 4.6 1.7 - - - -
8M GLN 4.2 0.9 - - - -
9M VAL* 3.1 11.8 - - - +
10M TYR* 2.9 56.6 + - + +
12M ARG* 4.2 11.5 - - - +
22M ILE* 3.9 11.1 + - - +
23M LEU* 1.3 79.3 + - - +
25M CYS* 1.3 59.1 + - - +
39M MET* 3.5 3.8 - - - +
65M LEU* 3.0 36.0 - - - +
66M ALA 3.4 2.5 - - - -
67M HIS* 3.7 12.2 - - - +
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Residues in contact with CYS 25 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7M ILE* 3.7 19.7 - - - -
8M GLN 3.5 3.8 - - - -
9M VAL* 4.1 1.1 - - - +
24M ASN* 1.3 76.0 - - - +
26M TYR* 1.3 57.7 + - - +
27M VAL* 3.9 12.9 + - - +
37M ILE* 5.9 0.4 - - - -
39M MET* 4.2 6.7 - - + -
64M ILE 4.1 0.3 - - - +
65M LEU* 3.2 3.9 - - - +
66M ALA* 2.8 49.5 + - + +
80M CYS* 2.0 53.6 - - + -
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Residues in contact with TYR 26 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232I GLU* 3.8 13.4 + - - -
233I THR 3.9 8.6 + - - -
234I ARG* 4.3 7.0 - - + -
235I PRO* 3.1 42.8 - - + +
241I PHE* 5.2 4.3 - - - -
6M GLN 3.2 4.5 - - - +
7M ILE* 3.5 0.7 - - - -
8M GLN* 3.0 36.3 + - + +
10M TYR* 3.5 22.2 - - + +
24M ASN 4.2 0.2 - - - -
25M CYS* 1.3 70.9 - - - +
27M VAL* 1.3 60.8 + - - +
28M THR* 3.4 32.1 + - + +
63M TYR* 3.9 27.0 - + - -
64M ILE 4.0 3.4 - - - -
65M LEU* 3.4 20.6 - - + -
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Residues in contact with VAL 27 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5M PRO* 3.3 30.7 - - + -
6M GLN 2.9 7.0 - - - +
7M ILE* 4.4 7.2 - - + -
25M CYS* 3.9 19.0 + - - +
26M TYR* 1.3 75.0 - - - +
28M THR* 1.3 73.0 + - - +
30M PHE* 3.8 15.2 - - + -
35M ILE* 5.3 5.4 - - + -
37M ILE* 4.5 9.6 - - + -
63M TYR* 3.4 1.7 - - - -
64M ILE* 3.1 36.7 + - + +
82M VAL* 4.1 26.9 - - + -
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Residues in contact with THR 28 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232I GLU* 3.5 21.5 + - - +
5M PRO* 3.1 1.4 - - - +
6M GLN* 2.6 54.6 + - - +
26M TYR* 3.4 36.9 + - + -
27M VAL* 1.3 87.1 - - - +
29M GLN* 1.3 73.5 + - - +
30M PHE* 3.2 4.7 - - - -
62M PHE 4.0 5.8 - - - -
63M TYR* 3.6 15.5 - - + -
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Residues in contact with GLN 29 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232I GLU* 3.0 18.5 - - - +
3M LYS* 3.1 33.9 - - + +
4M THR 3.5 5.4 - - - +
6M GLN* 3.3 29.7 - - + +
28M THR* 1.3 83.9 - - - +
30M PHE* 1.3 58.8 + - - +
59M ASP* 5.8 3.4 - - - +
61M SER* 3.6 22.5 + - - +
62M PHE 3.7 6.1 + - - -
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Residues in contact with PHE 30 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3M LYS* 3.0 16.4 - - - +
5M PRO* 3.4 22.4 - - + -
27M VAL* 3.8 37.5 - - + -
28M THR 4.1 3.6 - - - -
29M GLN* 1.3 77.9 - - - +
31M HIS* 1.3 81.4 + - - +
32M PRO 3.2 19.1 - - - -
33M PRO* 3.8 16.6 - - + -
35M ILE* 3.7 31.6 - - + -
54M MET* 5.0 1.6 - - + -
61M SER* 3.7 4.9 - - - -
62M PHE* 3.3 51.8 + - + -
63M TYR* 4.2 2.2 - - - -
64M ILE* 4.4 12.6 - - + -
84M HIS* 3.9 2.9 - + - +
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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