Contacts of the strand formed by residues 25 - 34 (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 THR 25 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23Q GLY 3.5 2.8 + - - -
24Q ASP* 1.3 70.2 - - - +
26Q VAL* 1.3 62.7 + - - +
44Q GLU* 3.7 23.3 - - + +
45Q GLY* 3.6 15.3 - - - +
46Q VAL* 3.5 21.0 - - + +
86Q VAL* 3.9 0.9 - - - +
87Q LYS* 2.9 28.4 + - + -
88Q ARG* 3.2 41.7 + - + +
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Residues in contact with VAL 26 (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* 4.9 6.3 - - + -
24Q ASP* 3.5 22.7 - - + +
25Q THR* 1.3 80.5 - - - +
27Q GLU* 1.3 73.7 + - - +
28Q VAL* 3.7 16.8 - - + -
43Q PHE 4.1 1.2 - - - +
44Q GLU* 3.2 7.3 - - - +
45Q GLY 2.8 37.4 + - - +
47Q VAL* 3.7 21.1 - - + -
59Q PHE* 5.0 2.5 - - + -
61Q VAL* 4.6 3.5 - - + +
84Q ILE* 3.9 13.0 - - + -
85Q SER 3.4 12.1 - - - +
86Q VAL* 4.2 12.3 - - + -
87Q LYS* 4.6 0.2 - - - -
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Residues in contact with GLU 27 (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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26Q VAL* 1.3 76.8 - - - +
28Q VAL* 1.3 65.6 + - - +
29Q LYS* 4.1 19.3 + - + +
42Q ALA* 3.2 32.3 - - + +
43Q PHE 3.9 2.5 - - - +
44Q GLU* 3.7 23.4 - - + +
83Q SER 3.8 1.0 - - - +
84Q ILE* 3.6 1.2 - - - -
85Q SER* 2.9 44.5 + - - +
87Q LYS* 3.3 31.5 + - - +
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Residues in contact with VAL 28 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26Q VAL* 3.7 17.5 - - + -
27Q GLU* 1.3 79.3 - - - +
29Q LYS* 1.3 62.0 + - - +
30Q VAL* 3.6 22.4 + - + +
41Q GLN 3.6 1.9 - - - +
42Q ALA* 4.4 0.2 - - - -
43Q PHE* 2.9 43.3 + - - +
59Q PHE* 3.8 24.7 - - + -
61Q VAL* 4.9 2.5 - - + -
74Q PHE* 4.2 15.0 - - + -
81Q VAL* 3.7 28.9 - - + -
83Q SER 3.4 2.9 - - - +
84Q ILE* 4.1 6.7 - - + -
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Residues in contact with LYS 29 (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* 4.1 22.9 + - - -
28Q VAL* 1.3 71.7 - - - +
30Q VAL* 1.3 55.0 + - - +
40Q LEU* 4.2 23.3 - - + -
41Q GLN 3.6 4.9 - - - +
42Q ALA* 4.0 20.0 - - + +
81Q VAL* 3.7 1.0 - - - -
82Q ASP* 2.7 36.7 + - - +
83Q SER* 2.9 38.0 + - - +
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Residues in contact with VAL 30 (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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28Q VAL* 3.7 25.6 - - + +
29Q LYS* 1.3 76.2 - - - +
31Q TRP* 1.3 78.1 + - - +
32Q VAL* 3.3 17.0 + - + +
40Q LEU* 3.6 3.5 - - - -
41Q GLN* 2.9 37.1 + - + +
43Q PHE* 5.3 2.0 - - + -
72Q ARG* 4.4 16.4 - - - +
74Q PHE* 4.1 20.9 - - + -
80Q VAL* 3.6 20.4 - - + -
81Q VAL* 4.2 9.4 - - + -
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Residues in contact with TRP 31 (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 4.3 0.2 - - - -
30Q VAL* 1.3 83.2 - - - +
32Q VAL* 1.3 58.9 + - - +
38Q LYS* 3.6 52.0 - - + -
39Q ARG* 3.5 22.7 - - - -
40Q LEU* 3.5 24.2 - - + +
79Q PRO 3.8 13.0 - - - +
80Q VAL* 3.0 29.9 + - - +
82Q ASP* 3.2 36.3 + - + -
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Residues in contact with VAL 32 (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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71L ARG* 6.2 0.7 - - - +
105L ARG* 3.8 26.2 - - - +
123L LEU 5.4 1.8 - - - +
30Q VAL* 3.4 20.9 - - + +
31Q TRP* 1.3 81.4 - - - +
33Q VAL* 1.3 64.0 + - - +
34Q GLU* 3.6 32.1 - - + +
38Q LYS* 3.6 4.9 - - - +
39Q ARG 2.9 42.7 + - - +
41Q GLN* 4.0 20.4 - - + +
72Q ARG* 5.4 3.4 - - - +
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Residues in contact with VAL 33 (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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18D ASP 6.2 0.7 - - - +
105L ARG* 4.4 15.6 + - - +
32Q VAL* 1.3 75.4 - - - +
34Q GLU* 1.3 60.4 + - - +
35Q GLY 3.3 23.4 + - - +
36Q SER* 4.4 3.8 - - - +
37Q LYS 3.2 17.9 - - - +
38Q LYS* 3.8 23.3 - - + -
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Residues in contact with GLU 34 (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* 3.9 18.2 - - - +
108L ARG* 4.3 3.6 - - - +
32Q VAL* 3.6 26.8 + - + +
33Q VAL* 1.3 68.9 - - - +
35Q GLY* 1.3 58.8 + - - +
36Q SER 3.2 0.2 + - - -
37Q LYS* 2.9 40.2 + - + +
39Q ARG* 3.2 31.9 - - + +
40Q LEU 4.5 2.4 - - - +
41Q GLN* 4.0 16.3 - - - +
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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