Contacts of the strand formed by residues 37 - 51 (chain Q) in PDB entry 5GAG
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 37 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33Q VAL* 3.2 8.4 - - - +
34Q GLU* 2.9 38.1 + - + +
36Q SER* 1.3 87.6 - - - +
38Q LYS* 1.3 60.9 + - - +
39Q ARG* 3.8 43.7 - - + +
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Residues in contact with LYS 38 (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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17D GLU 5.7 5.0 + - - -
18D ASP* 6.0 5.6 - - - +
31Q TRP* 3.6 44.4 - - + -
32Q VAL 3.6 6.1 - - - +
33Q VAL* 3.8 24.0 - - + -
36Q SER 4.2 0.8 + - - -
37Q LYS* 1.3 73.3 - - - +
39Q ARG* 1.3 75.8 + - - +
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Residues in contact with ARG 39 (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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31Q TRP* 3.5 10.6 - - - -
32Q VAL* 2.9 34.0 + - - +
34Q GLU* 3.2 40.6 - - + +
37Q LYS* 3.8 46.1 + - + +
38Q LYS* 1.3 89.6 + - - +
40Q LEU* 1.3 63.1 + - - +
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Residues in contact with LEU 40 (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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29Q LYS* 4.2 22.9 - - + -
30Q VAL 3.6 5.6 - - - +
31Q TRP* 3.5 59.1 - - + +
32Q VAL* 4.6 0.4 - - - -
34Q GLU* 4.5 3.1 - - - +
39Q ARG* 1.3 78.5 - - - +
41Q GLN* 1.3 61.0 + - - +
42Q ALA 4.3 0.4 + - - -
82Q ASP* 3.6 27.4 - - + +
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Residues in contact with GLN 41 (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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105L ARG* 3.4 26.9 + - - +
122L VAL* 3.6 20.5 + - - +
123L LEU* 4.0 21.3 + - - +
28Q VAL 3.6 1.9 - - - +
29Q LYS* 4.3 2.0 - - - -
30Q VAL* 2.9 36.2 + - - +
32Q VAL* 4.0 20.4 - - + +
34Q GLU* 4.0 8.8 - - - +
40Q LEU* 1.3 75.6 - - - +
42Q ALA* 1.3 68.5 + - - +
43Q PHE* 3.6 5.3 + - + +
72Q ARG* 4.5 8.1 - - - +
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Residues in contact with ALA 42 (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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27Q GLU* 3.2 32.1 - - - +
28Q VAL 3.6 4.9 - - - -
29Q LYS* 4.0 15.7 - - + +
40Q LEU 4.3 0.2 - - - -
41Q GLN* 1.3 77.6 - - - +
43Q PHE* 1.3 59.1 + - - +
44Q GLU* 3.9 3.5 + - + +
63Q LYS* 4.5 5.0 + - - -
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Residues in contact with PHE 43 (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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123L LEU* 4.1 21.3 - - + -
26Q VAL 4.1 1.4 - - - +
27Q GLU 3.9 0.2 - - - -
28Q VAL* 2.9 39.2 + - - +
30Q VAL* 5.3 2.0 - - + -
41Q GLN* 3.6 7.0 + - + +
42Q ALA* 1.3 70.5 - - - +
44Q GLU* 1.3 60.9 + - - +
45Q GLY 4.3 0.2 + - - -
61Q VAL* 4.3 24.4 - - + +
63Q LYS* 3.3 45.1 - - + +
70Q VAL* 3.6 32.8 - - + -
72Q ARG* 3.7 34.3 - - + +
74Q PHE* 3.6 28.5 - + + -
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Residues in contact with GLU 44 (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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25Q THR* 3.7 15.4 - - + +
26Q VAL 3.2 15.9 - - - +
27Q GLU* 3.7 31.9 - - + +
42Q ALA 3.9 3.3 + - - +
43Q PHE* 1.3 76.6 - - - +
45Q GLY* 1.3 59.2 + - - +
61Q VAL* 4.7 1.1 - - - -
63Q LYS* 3.1 28.0 - - - +
87Q LYS* 3.3 24.9 - - - +
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Residues in contact with GLY 45 (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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25Q THR* 4.3 3.8 - - - -
26Q VAL* 2.8 29.7 + - - +
44Q GLU* 1.3 76.9 - - - +
46Q VAL* 1.3 65.6 + - - -
47Q VAL 4.0 0.2 + - - -
61Q VAL* 3.4 17.0 - - - +
62Q ARG 3.4 11.9 - - - -
63Q LYS* 3.9 6.7 - - - -
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Residues in contact with VAL 46 (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* 3.5 31.2 - - - +
24Q ASP 3.5 7.4 - - - +
25Q THR* 3.5 19.5 - - + +
45Q GLY* 1.3 76.3 - - - -
47Q VAL* 1.3 67.1 + - - +
48Q ILE* 3.4 10.2 + - + +
61Q VAL* 4.0 1.1 - - - -
62Q ARG* 2.9 32.6 + - + +
97Q LEU* 5.2 1.8 - - + -
100Q LEU* 5.6 4.3 - - + -
110Q ILE* 3.9 20.4 - - + -
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Residues in contact with VAL 47 (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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20Q PHE* 4.5 8.7 - - + -
21Q ARG 4.0 17.9 - - - +
22Q PRO* 3.5 4.1 - - + +
23Q GLY* 3.0 24.3 + - - -
24Q ASP 2.8 13.8 + - - +
26Q VAL* 3.7 26.2 - - + -
46Q VAL* 1.3 70.2 - - - +
48Q ILE* 1.3 60.6 + - - +
49Q ALA 3.6 23.1 - - - +
50Q ILE* 4.0 13.5 - - + -
59Q PHE* 4.1 9.4 - - + -
60Q THR 3.6 4.5 - - - +
61Q VAL* 3.7 22.7 - - + +
97Q LEU* 3.5 2.5 - - - +
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Residues in contact with ILE 48 (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 PRO* 4.9 0.9 - - - -
46Q VAL* 3.8 11.9 - - + +
47Q VAL* 1.3 77.2 - - - +
49Q ALA* 1.3 62.4 + - + +
60Q THR* 2.9 36.9 + - + +
62Q ARG* 4.2 25.6 - - + -
71Q GLU* 4.2 11.0 - - - +
95Q ALA 3.7 3.0 - - - +
96Q LYS* 3.5 7.6 - - - -
97Q LEU* 3.0 48.5 + - + +
98Q TYR* 4.0 10.4 - - + -
100Q LEU* 4.5 13.0 - - + -
101Q ARG* 3.9 25.1 - - + +
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Residues in contact with ALA 49 (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 PRO* 5.5 0.2 - - - -
47Q VAL* 3.5 5.1 - - - +
48Q ILE* 1.3 82.1 - - - +
50Q ILE* 1.3 67.5 + - - +
59Q PHE* 3.2 8.9 - - - +
60Q THR* 3.0 45.7 + - - +
95Q ALA 4.6 1.3 - - - -
96Q LYS* 4.0 17.0 - - + -
98Q TYR* 4.1 15.3 - - + +
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Residues in contact with ILE 50 (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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2846A G 4.6 2.8 + - - -
2847A U 5.1 1.6 + - - -
20Q PHE* 3.4 46.2 - - + +
21Q ARG* 3.5 19.7 - - - -
22Q PRO* 4.0 9.4 - - + +
47Q VAL* 4.0 11.4 - - + -
49Q ALA* 1.3 81.7 - - - +
51Q ARG* 1.3 64.7 + - - +
52Q ASN* 3.2 30.5 - - - +
57Q SER* 6.4 0.2 - - - -
58Q ALA 3.9 7.2 - - - +
59Q PHE* 4.7 1.6 - - + -
95Q ALA 4.9 2.4 + - - -
96Q LYS* 3.3 25.0 + - - +
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Residues in contact with ARG 51 (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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2683A C 2.6 35.7 + - - -
2684A U 2.7 37.9 + - - -
2685A G 5.6 2.9 - - - -
2720A U 5.0 2.2 + - - -
2846A G 3.8 4.3 - - - +
50Q ILE* 1.3 75.9 - - - +
52Q ASN* 1.3 62.3 + - - +
53Q ARG* 3.6 45.7 - - + +
56Q HIS 3.6 19.6 + - - -
57Q SER* 3.3 6.1 - - - -
58Q ALA* 2.9 40.3 + - + +
96Q LYS* 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