Contacts of the strand formed by residues 75 - 82 (chain Q) in PDB entry 5DM6
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 75 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28Q TRP* 3.2 62.4 - - + +
29Q VAL 4.9 2.5 - - - +
31Q PRO* 4.4 8.2 - - - +
57Q ASN* 3.7 9.5 + - - -
58Q VAL* 2.9 43.2 + - - +
60Q GLY* 5.7 3.2 - - - -
61Q LYS* 6.1 3.4 - - - +
73Q ASN* 3.3 20.1 + - + +
74Q ASP* 1.3 76.1 - - - +
76Q LYS* 1.3 64.7 + - - +
1338X G 4.8 14.8 + - - -
1339X G 5.8 1.4 + - - -
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Residues in contact with LYS 76 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28Q TRP* 3.2 8.3 - - - -
29Q VAL* 2.9 44.2 + - + +
30Q SER 4.0 11.0 - - - +
31Q PRO* 3.3 23.8 + - + -
33Q ALA 3.0 25.0 + - - +
38Q ILE* 4.3 15.0 - - + -
55Q THR* 4.5 12.2 + - + +
56Q MET 3.4 14.1 - - - +
57Q ASN* 3.4 19.3 + - - +
58Q VAL 4.4 0.7 - - - +
75Q ARG* 1.3 78.5 - - - +
77Q LYS* 1.3 68.5 + - - +
1599X C 4.3 4.2 + - - -
1600X C 3.0 28.5 + - - -
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Residues in contact with LYS 77 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11Q VAL* 4.0 24.9 - - + +
26Q SER* 5.0 2.7 - - - -
27Q PHE 3.7 2.5 - - - +
28Q TRP* 3.5 33.4 - - + -
54Q SER 4.1 0.2 - - - +
55Q THR* 3.2 5.2 - - - -
56Q MET* 2.9 60.3 + - + +
58Q VAL* 4.6 0.2 - - - +
76Q LYS* 1.3 74.8 - - - +
78Q ALA* 1.3 65.3 + - - +
79Q ILE* 3.6 21.0 + - + +
1339X G 2.8 36.4 + - - -
1340X A 3.3 20.0 + - - +
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Residues in contact with ALA 78 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25Q TYR 3.9 0.5 - - - +
26Q SER* 3.3 4.5 - - - -
27Q PHE* 2.9 40.1 + - + +
29Q VAL* 3.5 25.4 - - + -
38Q ILE* 4.2 13.9 - - + -
42Q ILE* 5.5 2.7 - - + -
53Q ILE* 4.5 2.7 - - + -
54Q SER 3.5 4.3 - - - +
55Q THR* 3.8 18.2 - - + -
76Q LYS* 5.5 0.2 - - + -
77Q LYS* 1.3 74.8 - - - +
79Q ILE* 1.3 64.5 + - - +
80Q VAL* 4.2 0.8 + - - -
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Residues in contact with ILE 79 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19Q ALA* 6.1 0.2 - - + -
22Q ARG* 5.6 0.4 - - - +
24Q VAL* 3.6 25.6 - - + -
25Q TYR 3.5 4.5 - - - +
26Q SER* 3.9 16.2 - - - +
52Q GLY 4.1 0.2 - - - +
53Q ILE* 3.3 5.4 - - - +
54Q SER* 2.8 48.0 + - - +
56Q MET* 4.8 9.2 - - - -
77Q LYS* 3.6 33.0 - - + +
78Q ALA* 1.3 81.9 - - - +
80Q VAL* 1.3 63.1 + - - +
1340X A 5.9 1.6 - - - +
1341X A 3.9 32.8 - - + +
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Residues in contact with VAL 80 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23Q GLY 4.6 0.2 - - - +
24Q VAL* 3.3 8.3 - - - +
25Q TYR* 2.9 44.7 + - + +
27Q PHE* 3.8 16.4 - - + -
39Q LYS* 5.6 2.0 - - - -
42Q ILE* 3.7 37.7 - - + -
50Q VAL* 4.1 15.7 - - + -
52Q GLY 3.4 4.9 - - - +
53Q ILE* 3.5 32.1 - - + -
78Q ALA 4.9 1.1 - - - +
79Q ILE* 1.3 73.2 - - - +
81Q ARG* 1.3 60.0 + - - +
82Q LEU* 4.6 10.3 - - + +
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Residues in contact with ARG 81 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22Q ARG* 5.3 2.4 - - - +
23Q GLY 4.4 3.8 - - - +
24Q VAL* 4.0 23.7 - - + +
50Q VAL* 3.6 1.6 - - - +
51Q ILE* 3.1 34.4 + - + +
52Q GLY* 2.9 37.4 + - - +
80Q VAL* 1.3 77.1 - - - +
82Q LEU* 1.3 72.1 + - - +
1399X C 3.4 32.1 + - - +
1400X U 3.7 31.2 + - - -
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Residues in contact with LEU 82 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23Q GLY 3.3 23.4 + - - +
25Q TYR* 3.6 21.1 - - + -
42Q ILE* 5.6 3.6 - - + -
48Q VAL* 3.5 20.9 - - + -
49Q ARG 3.3 12.8 - - - +
50Q VAL* 3.6 28.3 - - + -
51Q ILE* 3.5 18.3 - - - +
80Q VAL* 4.6 9.4 - - + +
81Q ARG* 1.3 93.6 + - - +
83Q ALA* 1.3 64.8 + - - +
85Q GLY* 5.2 0.6 + - - -
86Q GLN* 3.4 26.7 - - + +
88Q ILE* 5.8 2.0 - - + -
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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