Contacts of the helix formed by residues 28 - 37 (chain Q) in PDB entry 2GLJ
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 GLY 28 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23Q GLU 3.4 4.9 + - - -
24Q VAL* 3.6 8.1 - - - -
25Q PHE* 2.7 20.9 + - - +
27Q LEU* 1.3 85.7 - - - +
29Q ASP* 1.3 59.9 + - - -
31Q PHE* 3.5 1.0 - - - +
32Q LYS* 3.0 32.5 - - - +
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Residues in contact with ASP 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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24Q VAL 4.4 1.3 + - - -
25Q PHE* 3.1 11.6 + - + +
28Q GLY* 1.3 68.7 - - - -
30Q ARG* 1.3 56.6 + - - +
31Q PHE 2.4 18.0 + - - -
32Q LYS* 2.9 6.9 + - - +
33Q ASN* 2.9 26.6 + - + +
34Q PHE 3.5 1.7 + - - -
271Q TYR* 4.6 4.8 - - - -
272Q THR* 5.4 3.0 - - - +
275Q GLU* 3.5 27.0 - - - +
449Q LYS 5.8 0.4 - - - +
452Q ILE* 4.1 25.3 - - + +
453Q TYR* 3.7 31.9 + - - +
456Q LYS* 4.0 19.9 + - - +
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Residues in contact with ARG 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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25Q PHE 3.3 4.0 + - - +
26Q ALA 3.1 18.4 - - - +
27Q LEU* 3.1 21.5 - - - +
29Q ASP* 1.3 73.0 - - - +
31Q PHE* 1.3 70.2 + - - +
33Q ASN* 5.3 0.4 - - - -
34Q PHE* 2.9 61.8 - - + +
250Q ARG* 4.5 1.0 - - - +
251Q ASP* 2.7 44.0 + - - +
259Q VAL* 4.1 10.5 - - + -
449Q LYS* 3.0 40.9 - - + +
452Q ILE* 5.8 3.4 - - + +
167T ASP 5.8 1.4 + - - -
168T ASN* 5.8 3.2 + - - +
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Residues in contact with PHE 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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27Q LEU* 3.0 21.5 - - + +
28Q GLY 3.5 0.9 - - - +
29Q ASP 2.4 5.3 + - - -
30Q ARG* 1.3 81.7 - - - +
32Q LYS* 1.3 75.5 + - + +
34Q PHE* 3.0 18.7 - + - +
35Q ILE* 2.8 44.7 + - + +
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Residues in contact with LYS 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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28Q GLY* 3.0 31.1 + - - +
29Q ASP* 2.9 10.8 + - - +
31Q PHE* 1.3 97.3 - - + +
33Q ASN* 1.3 51.5 + - - +
35Q ILE* 3.0 8.9 - - - +
36Q SER* 2.8 32.9 + - - -
271Q TYR* 2.8 24.0 + - + +
275Q GLU* 3.0 35.1 + - - +
456Q LYS* 4.7 3.6 - - - +
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Residues in contact with ASN 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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29Q ASP* 2.9 20.8 + - + +
30Q ARG* 5.3 0.6 - - - -
32Q LYS* 1.3 69.6 - - - +
34Q PHE* 1.3 58.0 + - - +
35Q ILE 2.5 18.2 + - - -
36Q SER* 2.6 18.3 + - - -
37Q ASN* 2.7 27.4 + - - +
259Q VAL* 5.2 6.6 - - - +
264Q GLN* 5.1 4.0 + - - +
267Q ARG* 4.9 2.0 + - - +
268Q ILE* 3.9 25.1 - - - +
271Q TYR* 3.5 34.7 - - + +
447Q SER* 5.1 0.2 + - - -
452Q ILE* 3.8 25.7 - - + +
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Residues in contact with PHE 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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29Q ASP 3.5 1.8 + - - -
30Q ARG* 2.9 61.2 - - + +
31Q PHE* 3.0 31.6 - + - +
33Q ASN* 1.3 81.5 + - - +
35Q ILE* 1.3 54.2 + - + +
37Q ASN* 3.6 5.1 - - - +
38Q CYS* 2.7 29.7 - - - -
248Q LYS* 5.8 5.2 - - + -
249Q ALA* 2.8 30.8 - - + +
250Q ARG* 3.3 17.7 - - - -
259Q VAL* 4.0 21.5 - - + -
167T ASP 5.8 2.0 - - - -
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Residues in contact with ILE 35 (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 PHE* 2.8 29.2 + - + +
32Q LYS* 3.0 20.0 - - - +
33Q ASN 2.5 4.4 + - - -
34Q PHE* 1.3 76.7 - - + +
36Q SER* 1.3 68.3 + - - +
37Q ASN 3.4 1.3 - - - -
38Q CYS* 3.1 22.2 + - + +
39Q LYS* 3.3 49.8 + - + +
248Q LYS* 5.7 6.3 - - - +
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Residues in contact with SER 36 (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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32Q LYS 2.8 13.3 + - - -
33Q ASN* 2.6 19.2 + - - -
35Q ILE* 1.3 75.2 - - - +
37Q ASN* 1.3 53.8 + - - -
38Q CYS 2.7 12.5 + - - -
39Q LYS* 4.5 0.8 - - - +
40Q THR* 2.6 31.8 + - - -
45Q VAL* 5.1 10.4 - - - +
48Q LEU* 5.7 7.5 - - - +
49Q ILE* 5.8 1.7 - - - +
267Q ARG* 5.7 4.4 - - - +
271Q TYR* 3.7 30.9 - - - +
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Residues in contact with ASN 37 (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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33Q ASN* 2.7 43.1 + - - +
34Q PHE* 3.6 6.9 - - - +
36Q SER* 1.3 72.5 - - - +
38Q CYS* 1.3 57.5 + - - +
40Q THR 3.7 14.8 - - - -
41Q GLU* 3.9 12.2 - - - +
249Q ALA* 3.4 23.6 + - - +
259Q VAL* 5.4 2.3 - - - +
261Q GLY* 4.0 9.9 - - - -
262Q TYR 3.6 27.3 + - - +
264Q GLN* 4.9 12.7 + - - +
267Q ARG* 4.6 18.1 - - + +
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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