Contacts of the strand formed by residues 34 - 43 (chain C) in PDB entry 1MGQ
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 ARG 34 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29B LYS* 3.7 19.0 - - - +
30B LEU 5.5 0.2 + - - -
33B ASP* 2.8 29.1 + - - -
77B VAL* 4.1 24.2 - - - +
78B TYR* 4.2 1.5 - - - -
29C LYS* 3.3 5.8 + - - -
30C LEU* 2.9 54.0 + - + +
31C LYS 3.8 14.0 + - - +
32C GLY 3.0 5.2 + - - +
33C ASP* 1.3 81.4 - - - +
35C GLU* 1.3 68.4 + - - +
36C PHE* 4.2 9.0 - - + -
56C GLU* 3.0 25.6 + - - +
57C LEU 3.5 9.4 - - - +
58C GLU* 3.3 25.2 + - + +
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Residues in contact with GLU 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ILE* 3.4 7.8 - - + +
28C ILE 3.2 16.2 - - - +
29C LYS* 3.6 15.4 - - + +
30C LEU* 4.1 1.1 - - - -
33C ASP 5.3 0.9 - - - +
34C ARG* 1.3 77.7 - - - +
36C PHE* 1.3 77.1 + - - +
37C ARG* 3.0 24.1 + - - -
56C GLU* 3.5 3.5 - - - +
57C LEU* 2.7 53.0 + - + +
60C GLY* 6.5 0.2 - - - -
64D ARG* 2.7 45.8 + - - -
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Residues in contact with PHE 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B TYR* 3.5 46.4 - + - -
26C VAL 4.0 0.5 - - - +
27C ILE* 3.6 2.6 - - - -
28C ILE* 2.8 37.9 + - + +
30C LEU* 3.9 19.3 - - + -
34C ARG* 4.2 6.1 - - - -
35C GLU* 1.3 76.1 - - - +
37C ARG* 1.3 65.3 + - - +
51C LEU* 3.6 17.3 - - + -
54C ALA* 4.2 12.8 - - + -
55C GLU 3.3 17.7 - - - -
56C GLU* 3.5 26.2 - - + -
66C LEU* 3.9 18.4 - - + -
69C VAL* 4.3 8.5 - - + -
71C ILE* 3.7 22.9 - - + -
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Residues in contact with ARG 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C VAL 3.4 7.4 - - - +
27C ILE* 4.3 17.2 - - + +
35C GLU* 3.0 25.6 + - - +
36C PHE* 1.3 79.6 - - - +
38C GLY* 1.3 58.7 + - - +
51C LEU* 4.5 0.4 - - - -
53C ASP 4.1 1.0 - - - +
54C ALA* 3.1 3.3 - - - -
55C GLU* 2.8 43.7 + - + +
57C LEU* 3.0 39.8 - - + +
62C VAL* 5.4 1.6 - - - +
64D ARG* 3.3 15.2 - - - +
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Residues in contact with GLY 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C PRO* 4.2 4.4 - - - +
26C VAL* 2.9 33.7 + - - +
37C ARG* 1.3 75.5 - - - +
39C VAL* 1.3 66.6 + - - -
40C LEU 3.5 0.7 + - - -
51C LEU* 4.1 9.2 - - - +
52C ASN 3.8 9.0 - - - -
53C ASP 3.9 7.0 - - - -
54C ALA* 3.9 7.2 - - - -
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Residues in contact with VAL 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C ASN* 3.6 34.5 - - - +
24C SER* 3.5 5.6 - - - +
25C PRO* 4.6 14.4 - - + -
38C GLY* 1.3 70.9 - - - -
40C LEU* 1.3 64.7 + - - +
41C LYS* 3.4 18.0 + - + +
51C LEU* 3.1 4.2 - - - -
52C ASN* 2.8 44.5 + - + +
53C ASP* 5.3 7.2 - - + +
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Residues in contact with LEU 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C LEU* 3.3 45.3 - - + +
21C SER* 4.0 16.4 - - - +
22C LEU* 3.7 13.6 - - + -
23C ASN* 2.6 35.0 + - - +
24C SER 3.1 15.5 + - - +
26C VAL* 4.0 17.0 - - + -
28C ILE* 5.6 0.2 - - + -
38C GLY 3.5 3.4 + - - -
39C VAL* 1.3 71.1 - - - +
41C LYS* 1.3 58.2 + - - +
42C SER 3.7 22.4 - - - +
43C PHE* 4.4 3.6 - - + -
49C LEU* 4.0 20.4 - - + -
50C VAL 3.7 9.2 - - - +
51C LEU* 3.8 10.1 - - + -
79C ILE* 6.6 0.4 - - + -
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Residues in contact with LYS 41 (chain C).
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 6.3 0.7 - - - +
9B VAL* 4.6 10.3 - - + +
11B VAL* 3.8 14.9 - - - +
22C LEU* 3.8 11.5 - - - +
23C ASN* 2.9 27.8 + - - +
39C VAL* 3.4 28.8 - - + +
40C LEU* 1.3 77.1 - - - +
42C SER* 1.3 65.3 + - - +
50C VAL* 2.8 21.2 + - + +
51C LEU 4.2 0.4 - - - -
52C ASN* 3.5 43.0 - - + +
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Residues in contact with SER 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B VAL* 3.7 15.7 - - - -
10B ASN 2.9 24.9 + - - -
11B VAL* 3.3 9.7 + - - +
14B PRO* 3.1 24.8 - - - +
22C LEU* 4.1 3.6 - - - +
40C LEU* 3.7 2.9 - - - +
41C LYS* 1.3 83.4 - - - +
43C PHE* 1.3 67.3 + - - +
49C LEU* 3.2 7.5 - - - +
50C VAL* 2.9 29.2 + - - -
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Residues in contact with PHE 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B VAL* 3.0 20.0 + - + +
12B GLN* 3.4 24.4 - - + +
14B PRO* 3.6 5.6 - - - -
15C LEU* 3.5 25.1 - - + -
16C ASP* 5.6 0.2 - - - -
18C LEU* 3.5 28.7 - - + -
19C GLY* 3.4 39.5 - - - -
22C LEU* 4.1 20.4 - - + -
40C LEU* 4.4 4.3 - - + -
42C SER* 1.3 78.7 + - - +
44C ASP* 1.3 74.6 + - - +
47C MET* 5.3 0.4 - - - -
48C ASN 3.1 13.7 - - - +
49C LEU* 4.0 8.1 - - + -
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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