Contacts of the helix formed by residues 28 - 37 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23X GLU 3.5 3.3 + - - -
24X VAL* 3.6 8.1 - - - -
25X PHE* 2.7 22.2 + - - +
27X LEU* 1.3 87.4 - - - +
29X ASP* 1.3 60.5 + - - -
31X PHE* 3.5 1.2 - - - +
32X LYS* 3.0 32.4 - - - +
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Residues in contact with ASP 29 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24X VAL 4.5 1.3 + - - -
25X PHE* 3.1 11.5 + - + +
28X GLY* 1.3 68.1 - - - -
30X ARG* 1.3 56.3 + - - +
31X PHE 2.5 18.0 + - - -
32X LYS* 2.9 7.5 + - - +
33X ASN* 2.9 25.8 + - + +
34X PHE 3.5 1.9 + - - -
271X TYR* 4.6 5.2 - - - -
272X THR* 5.4 3.2 - - - +
275X GLU* 3.5 26.5 - - - +
449X LYS* 5.7 0.9 - - + +
452X ILE* 4.1 26.2 - - + +
453X TYR* 3.6 32.6 + - - +
456X LYS* 4.1 17.9 + - - +
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Residues in contact with ARG 30 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167U ASP 5.8 1.8 + - - -
168U ASN* 5.7 4.0 + - - +
25X PHE 3.3 3.7 + - - +
26X ALA 3.1 18.8 - - - +
27X LEU* 3.1 21.2 - - - +
29X ASP* 1.3 73.0 - - - +
31X PHE* 1.3 68.8 + - - +
33X ASN* 5.3 0.7 - - - -
34X PHE* 2.9 62.4 - - + +
250X ARG* 5.7 0.6 - - - +
251X ASP* 2.6 44.6 + - - +
259X VAL* 4.1 10.1 - - + -
449X LYS* 3.0 39.8 - - + +
452X ILE* 5.8 3.0 - - - +
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Residues in contact with PHE 31 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27X LEU* 3.0 20.4 - - + +
28X GLY 3.5 1.3 - - - +
29X ASP 2.5 5.7 + - - -
30X ARG* 1.3 82.0 - - - +
32X LYS* 1.3 76.3 + - + +
34X PHE* 3.0 18.2 - + - +
35X ILE* 2.8 43.8 + - + +
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Residues in contact with LYS 32 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28X GLY* 3.0 30.4 + - - +
29X ASP* 2.9 10.8 + - - +
31X PHE* 1.3 97.8 - - + +
33X ASN* 1.3 51.7 + - - +
35X ILE* 2.9 8.7 - - - +
36X SER* 2.8 33.1 + - - -
271X TYR* 2.9 23.5 + - + +
275X GLU* 3.0 35.2 + - - +
456X LYS* 4.7 2.6 - - - +
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Residues in contact with ASN 33 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29X ASP* 2.9 20.5 + - + +
30X ARG* 5.3 0.4 - - - -
32X LYS* 1.3 70.3 - - - +
34X PHE* 1.3 58.7 + - - +
35X ILE 2.5 17.4 + - - -
36X SER* 2.5 19.4 + - - -
37X ASN* 2.7 27.4 + - - +
259X VAL* 5.3 6.2 - - - +
264X GLN* 5.1 3.8 + - - +
267X ARG* 4.9 1.4 + - - +
268X ILE* 3.9 24.9 - - - +
271X TYR* 3.5 34.7 - - + +
447X SER* 5.2 0.3 + - - -
452X ILE* 3.8 25.5 - - + +
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Residues in contact with PHE 34 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167U ASP 5.7 2.7 - - - -
29X ASP 3.5 1.6 + - - -
30X ARG* 2.9 59.0 - - + +
31X PHE* 3.0 32.3 - + - +
33X ASN* 1.3 81.6 + - - +
35X ILE* 1.3 53.2 + - + +
37X ASN* 3.6 6.3 - - - +
38X CYS* 2.7 30.8 - - - -
248X LYS* 5.8 5.8 - - + -
249X ALA* 2.8 31.7 - - + +
250X ARG* 3.3 17.7 - - - -
259X VAL* 4.0 22.4 - - + -
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Residues in contact with ILE 35 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31X PHE* 2.8 29.1 + - + +
32X LYS* 2.9 19.7 - - - +
33X ASN 2.5 8.0 + - - -
34X PHE* 1.3 79.5 - - + +
36X SER* 1.3 67.1 + - - +
37X ASN 3.4 0.7 - - - -
38X CYS* 3.1 23.0 + - + +
39X LYS* 3.3 48.5 + - + +
248X LYS* 5.7 5.8 - - - +
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Residues in contact with SER 36 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32X LYS 2.8 12.6 + - - -
33X ASN* 2.5 18.4 + - - -
35X ILE* 1.3 74.9 - - - +
37X ASN* 1.3 58.4 + - - -
38X CYS 2.7 7.4 + - - -
39X LYS* 5.6 0.7 - - - -
40X THR* 2.6 33.8 + - - -
45X VAL* 5.0 9.4 - - - +
48X LEU* 5.7 7.3 - - - +
49X ILE* 5.8 1.9 - - - +
267X ARG* 5.7 5.1 - - - +
271X TYR* 3.7 31.2 - - - +
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Residues in contact with ASN 37 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33X ASN* 2.7 43.2 + - - +
34X PHE* 3.6 6.8 - - - +
36X SER* 1.3 72.8 + - - +
38X CYS* 1.3 57.8 + - - +
40X THR 3.7 14.6 - - - +
41X GLU* 3.9 12.8 - - - +
249X ALA* 3.4 24.6 + - - +
259X VAL* 5.4 2.5 - - - +
261X GLY* 4.0 9.7 - - - -
262X TYR 3.6 28.2 + - - +
264X GLN* 4.9 12.9 + - - +
267X ARG* 4.6 17.3 - - + +
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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